Journal Article
. 1995 Oct;270(5235).
doi: 10.1126/science.270.5235.467.

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

M Schena 1 D Shalon  R W Davis  P O Brown  
Affiliations
  • PMID: 7569999
  •     1694 citations

Abstract

A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes. Because of the small format and high density of the arrays, hybridization volumes of 2 microliters could be used that enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA. Differential expression measurements of 45 Arabidopsis genes were made by means of simultaneous, two-color fluorescence hybridization.

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Proc Natl Acad Sci U S A, 2001 Feb 07; 98(3). PMID: 11158560    Free PMC article.
Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue.
K Specht, T Richter, +3 authors, H Höfler.
Am J Pathol, 2001 Feb 13; 158(2). PMID: 11159180    Free PMC article.
Highly Cited.
Dynamic modeling of gene expression data.
N S Holter, A Maritan, +2 authors, J R Banavar.
Proc Natl Acad Sci U S A, 2001 Feb 15; 98(4). PMID: 11172013    Free PMC article.
Acid-induced gene expression in Helicobacter pylori: study in genomic scale by microarray.
S Ang, C Z Lee, +4 authors, J T Wang.
Infect Immun, 2001 Feb 17; 69(3). PMID: 11179343    Free PMC article.
Group A Streptococcus: allelic variation, population genetics, and host-pathogen interactions.
S D Reid, N P Hoe, L M Smoot, J M Musser.
J Clin Invest, 2001 Feb 22; 107(4). PMID: 11181637    Free PMC article.
Review.
Protein profiling comes of age.
I M Tomlinson, L J Holt.
Genome Biol, 2001 Feb 22; 2(2). PMID: 11182890    Free PMC article.
Review.
Microarray techniques in pathology: tool or toy?
A M Snijders, G A Meijer, +2 authors, P J van Diest.
Mol Pathol, 2001 Feb 24; 53(6). PMID: 11193046    Free PMC article.
Review.
The role of hexokinase in plant sugar signal transduction and growth and development.
W Xiao, J Sheen, J C Jang.
Plant Mol Biol, 2001 Feb 24; 44(4). PMID: 11197321
Apoptosis signals in atopy and asthma measured with cDNA arrays.
M H Brutsche, I C Brutsche, +9 authors, A Woodcock.
Clin Exp Immunol, 2001 Feb 24; 123(2). PMID: 11207646    Free PMC article.
Microarrays under the microscope.
S E Wildsmith, F J Elcock.
Mol Pathol, 2001 Feb 24; 54(1). PMID: 11212888    Free PMC article.
Review.
New tools in molecular pathology.
P Lichter.
J Mol Diagn, 2001 Mar 10; 2(4). PMID: 11232106    Free PMC article.
Review.
Microarray foray.
R J Coffey, D Threadgill.
Breast Cancer Res, 2001 Mar 16; 2(1). PMID: 11250685    Free PMC article.
Review.
Manufacturing DNA microarrays of high spot homogeneity and reduced background signal.
F Diehl, S Grahlmann, M Beier, J D Hoheisel.
Nucleic Acids Res, 2001 Mar 27; 29(7). PMID: 11266573    Free PMC article.
Molecular profiling of clinical tissues specimens: feasibility and applications.
M R Emmert-Buck, R L Strausberg, +30 authors, R H Waterston.
J Mol Diagn, 2001 Mar 29; 2(2). PMID: 11272889    Free PMC article.
Review.
DNA microarray analysis of cyanobacterial gene expression during acclimation to high light.
Y Hihara, A Kamei, +2 authors, M Ikeuchi.
Plant Cell, 2001 Apr 03; 13(4). PMID: 11283337    Free PMC article.
Highly Cited.
Microarray-based survey of repetitive genomic sequences in Vicia spp.
M Nouzová, P Neumann, +2 authors, J Macas.
Plant Mol Biol, 2001 Apr 06; 45(2). PMID: 11289513
Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarray.
S Li, D T Ross, +2 authors, M A Wasik.
Am J Pathol, 2001 Apr 06; 158(4). PMID: 11290540    Free PMC article.
An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression.
H Yue, P S Eastman, +8 authors, R Johnston.
Nucleic Acids Res, 2001 Apr 09; 29(8). PMID: 11292855    Free PMC article.
Development of a 950-gene DNA array for examining gene expression patterns in mouse testis.
J C Rockett, J Christopher Luft, +5 authors, D J Dix.
Genome Biol, 2001 Apr 18; 2(4). PMID: 11305942    Free PMC article.
Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus).
M Paulose-Murphy, N K Ha, +7 authors, S Zeichner.
J Virol, 2001 Apr 20; 75(10). PMID: 11312356    Free PMC article.
Highly Cited.
Development and validation of corynebacterium DNA microarrays.
A Loos, C Glanemann, +5 authors, A J Sinskey.
Appl Environ Microbiol, 2001 Apr 25; 67(5). PMID: 11319117    Free PMC article.
Statistical modeling of large microarray data sets to identify stimulus-response profiles.
L P Zhao, R Prentice, L Breeden.
Proc Natl Acad Sci U S A, 2001 May 10; 98(10). PMID: 11344303    Free PMC article.
Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast.
K Natarajan, M R Meyer, +4 authors, M J Marton.
Mol Cell Biol, 2001 Jun 08; 21(13). PMID: 11390663    Free PMC article.
Highly Cited.
Inventory of the superfamily of P-type ion pumps in Arabidopsis.
K B Axelsen, M G Palmgren.
Plant Physiol, 2001 Jun 13; 126(2). PMID: 11402198    Free PMC article.
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.
M L Bulyk, X Huang, Y Choo, G M Church.
Proc Natl Acad Sci U S A, 2001 Jun 19; 98(13). PMID: 11404456    Free PMC article.
Highly Cited.
Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method).
M He, M J Taussig.
Nucleic Acids Res, 2001 Jul 27; 29(15). PMID: 11470888    Free PMC article.
Antisense DNAs as multisite genomic modulators identified by DNA microarray.
Y S Cho, M K Kim, +3 authors, Y S Cho-Chung.
Proc Natl Acad Sci U S A, 2001 Aug 02; 98(17). PMID: 11481453    Free PMC article.
Image metrics in the statistical analysis of DNA microarray data.
C S Brown, P C Goodwin, P K Sorger.
Proc Natl Acad Sci U S A, 2001 Aug 02; 98(16). PMID: 11481466    Free PMC article.
Pathophysiological mechanisms of asthma. Application of cell and molecular biology techniques.
K F Chung, I M Adcock.
Mol Biotechnol, 2001 Aug 16; 18(3). PMID: 11503516
Review.
Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells.
C Uematsu, J Nishida, +4 authors, H Kambara.
Nucleic Acids Res, 2001 Aug 16; 29(16). PMID: 11504892    Free PMC article.
Mining mouse microarray data.
D A Wigle, J Rossant, I Jurisica.
Genome Biol, 2001 Aug 23; 2(7). PMID: 11516341    Free PMC article.
Review.
A critical evaluation of differential display as a tool to identify genes involved in legume nodulation: looking back and looking forward.
S Lievens, S Goormachtig, M Holsters.
Nucleic Acids Res, 2001 Aug 28; 29(17). PMID: 11522814    Free PMC article.
Plant gene expression response to Agrobacterium tumefaciens.
R F Ditt, E W Nester, L Comai.
Proc Natl Acad Sci U S A, 2001 Sep 06; 98(19). PMID: 11535836    Free PMC article.
cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.
K Birnbaum, P N Benfey, D E Shasha.
Genome Res, 2001 Sep 07; 11(9). PMID: 11544201    Free PMC article.
Molecular indexing of human genomic DNA.
D R Sibson, F E Gibbs.
Nucleic Acids Res, 2001 Sep 28; 29(19). PMID: 11574697    Free PMC article.
Molecular detection of antimicrobial resistance.
A C Fluit, M R Visser, F J Schmitz.
Clin Microbiol Rev, 2001 Oct 05; 14(4). PMID: 11585788    Free PMC article.
Review.
Ceramic capillaries for use in microarray fabrication.
R A George, J P Woolley, P T Spellman.
Genome Res, 2001 Oct 10; 11(10). PMID: 11591655    Free PMC article.
Genomic approaches to research in lung cancer.
E Gabrielson.
Respir Res, 2001 Oct 23; 1(1). PMID: 11667963    Free PMC article.
Review.
Progress in the application of DNA microarrays.
E K Lobenhofer, P R Bushel, C A Afshari, H K Hamadeh.
Environ Health Perspect, 2001 Oct 24; 109(9). PMID: 11673116    Free PMC article.
Review.
Using single nucleotide polymorphisms as a means to understanding the pathophysiology of asthma.
L J Palmer, W O Cookson.
Respir Res, 2001 Nov 01; 2(2). PMID: 11686872    Free PMC article.
Review.
Design of a retroviral-mediated ecdysone-inducible system and its application to the expression profiling of the PTEN tumor suppressor.
J Stolarov, K Chang, +4 authors, V Mittal.
Proc Natl Acad Sci U S A, 2001 Nov 01; 98(23). PMID: 11687610    Free PMC article.
Individual somatic H1 subtypes are dispensable for mouse development even in mice lacking the H1(0) replacement subtype.
Y Fan, A Sirotkin, +2 authors, A I Skoultchi.
Mol Cell Biol, 2001 Nov 02; 21(23). PMID: 11689686    Free PMC article.
BADGE, Beads Array for the Detection of Gene Expression, a high-throughput diagnostic bioassay.
L Yang, D K Tran, X Wang.
Genome Res, 2001 Nov 03; 11(11). PMID: 11691854    Free PMC article.
Robust and efficient synthetic method for forming DNA microarrays.
P L Dolan, Y Wu, +3 authors, G P Lopez.
Nucleic Acids Res, 2001 Nov 03; 29(21). PMID: 11691944    Free PMC article.
Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.
A Bhattacharjee, W G Richards, +16 authors, M Meyerson.
Proc Natl Acad Sci U S A, 2001 Nov 15; 98(24). PMID: 11707567    Free PMC article.
Highly Cited.
A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids.
X Gao, E LeProust, +6 authors, X Zhou.
Nucleic Acids Res, 2001 Nov 20; 29(22). PMID: 11713325    Free PMC article.
DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: evidence for anNew type of sulfur-reducing enzyme complex.
G J Schut, J Zhou, M W Adams.
J Bacteriol, 2001 Nov 22; 183(24). PMID: 11717259    Free PMC article.
A transcriptional roadmap to wood formation.
M Hertzberg, H Aspeborg, +10 authors, G Sandberg.
Proc Natl Acad Sci U S A, 2001 Nov 29; 98(25). PMID: 11724959    Free PMC article.
Highly Cited.
An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence.
Y L Chang, Q Tao, +3 authors, H B Zhang.
Genetics, 2001 Dec 01; 159(3). PMID: 11729165    Free PMC article.
Sources of nonlinearity in cDNA microarray expression measurements.
L Ramdas, K R Coombes, +5 authors, W Zhang.
Genome Biol, 2001 Dec 12; 2(11). PMID: 11737946    Free PMC article.
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash.
Nucleic Acids Res, 2001 Dec 26; 30(1). PMID: 11752295    Free PMC article.
Highly Cited.
Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways.
L Ma, J Li, +4 authors, X W Deng.
Plant Cell, 2001 Dec 26; 13(12). PMID: 11752374    Free PMC article.
Highly Cited.
New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis.
M A Pérez-Amador, P Lidder, +3 authors, P J Green.
Plant Cell, 2001 Dec 26; 13(12). PMID: 11752382    Free PMC article.
Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses.
Hidetoshi Urakawa, Peter A Noble, +2 authors, David A Stahl.
Appl Environ Microbiol, 2002 Jan 05; 68(1). PMID: 11772632    Free PMC article.
Gene expression analysis with universal n-mer arrays.
R Michael van Dam, Stephen R Quake.
Genome Res, 2002 Jan 10; 12(1). PMID: 11779839    Free PMC article.
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature.
Soumya Raychaudhuri, Jeffrey T Chang, Patrick D Sutphin, Russ B Altman.
Genome Res, 2002 Jan 10; 12(1). PMID: 11779846    Free PMC article.
The National Center for Toxicogenomics: using new technologies to inform mechanistic toxicology.
Raymond W Tennant.
Environ Health Perspect, 2002 Jan 10; 110(1). PMID: 11781174    Free PMC article.
A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae.
Brian J Akerley, Eric J Rubin, +3 authors, John J Mekalanos.
Proc Natl Acad Sci U S A, 2002 Jan 24; 99(2). PMID: 11805338    Free PMC article.
Highly Cited.
Attachment of benzaldehyde-modified oligodeoxynucleotide probes to semicarbazide-coated glass.
M A Podyminogin, E A Lukhtanov, M W Reed.
Nucleic Acids Res, 2002 Jan 29; 29(24). PMID: 11812841    Free PMC article.
Core biopsies can be used to distinguish differences in expression profiling by cDNA microarrays.
Christos Sotiriou, Chand Khanna, +2 authors, Edison T Liu.
J Mol Diagn, 2002 Feb 05; 4(1). PMID: 11826185    Free PMC article.
DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete.
Andrew T Revel, Adel M Talaat, Michael V Norgard.
Proc Natl Acad Sci U S A, 2002 Feb 07; 99(3). PMID: 11830671    Free PMC article.
Highly Cited.
Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling.
Stephen M Beverley, Natalia S Akopyants, +12 authors, Yujia Wang.
Philos Trans R Soc Lond B Biol Sci, 2002 Feb 13; 357(1417). PMID: 11839181    Free PMC article.
Evaluation of non-formalin tissue fixation for molecular profiling studies.
John W Gillespie, Carolyn J M Best, +21 authors, Michael R Emmert-Buck.
Am J Pathol, 2002 Feb 13; 160(2). PMID: 11839565    Free PMC article.
Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium.
David Finkelstein, Rob Ewing, +3 authors, Shauna Somerville.
Plant Mol Biol, 2002 Feb 28; 48(1-2). PMID: 11860205
Review.
DNA microarrays for functional plant genomics.
Asaph Aharoni, Oscar Vorst.
Plant Mol Biol, 2002 Feb 28; 48(1-2). PMID: 11860216
Comprehensive gene expression analysis by transcript profiling.
Jonathan Donson, Yiwen Fang, +5 authors, Wayne Volkmuth.
Plant Mol Biol, 2002 Feb 28; 48(1-2). PMID: 11860215
Review.
A novel medium throughput quantitative competitive PCR technology to simultaneously measure mRNA levels from multiple genes.
Junlong Zhang, Ian N M Day, Christopher D Byrne.
Nucleic Acids Res, 2002 Feb 28; 30(5). PMID: 11861925    Free PMC article.
High-density cell microarrays for parallel functional determinations.
C Wilson Xu.
Genome Res, 2002 Mar 05; 12(3). PMID: 11875037    Free PMC article.
Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions.
Nobuhide Doi, Hideaki Takashima, +8 authors, Hiroshi Yanagawa.
Genome Res, 2002 Mar 05; 12(3). PMID: 11875038    Free PMC article.
Molecular biologist's guide to proteomics.
Paul R Graves, Timothy A J Haystead.
Microbiol Mol Biol Rev, 2002 Mar 05; 66(1). PMID: 11875127    Free PMC article.
Review.
The role of n-3 polyunsaturated fatty acids in brain: modulation of rat brain gene expression by dietary n-3 fatty acids.
Klára Kitajka, László G Puskás, +4 authors, Tibor Farkas.
Proc Natl Acad Sci U S A, 2002 Mar 07; 99(5). PMID: 11880617    Free PMC article.
Differential screening technology in the service of ovarian biology.
Adriano B Tavares, Eli Y Adashi.
Rev Endocr Metab Disord, 2002 Mar 09; 3(1). PMID: 11883100
Review.
Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization.
John Fernandes, Volker Brendel, +6 authors, Virginia Walbot.
Plant Physiol, 2002 Mar 14; 128(3). PMID: 11891246    Free PMC article.
An assessment of Motorola CodeLink microarray performance for gene expression profiling applications.
Ramesh Ramakrishnan, David Dorris, +12 authors, Abhijit Mazumder.
Nucleic Acids Res, 2002 Mar 28; 30(7). PMID: 11917036    Free PMC article.
Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.
Charles W Whitfield, Mark R Band, +6 authors, Gene E Robinson.
Genome Res, 2002 Apr 05; 12(4). PMID: 11932240    Free PMC article.
Gene expression pattern in Caco-2 cells following rotavirus infection.
Mariela A Cuadras, Dino A Feigelstock, Sungwhan An, Harry B Greenberg.
J Virol, 2002 Apr 05; 76(9). PMID: 11932413    Free PMC article.
Importance of mast cells in the pathophysiology of asthma.
Seong H Cho, Andrea J Anderson, Chad K Oh.
Clin Rev Allergy Immunol, 2002 Apr 27; 22(2). PMID: 11975421
Review.
Genome-wide screening for trait conferring genes using DNA microarrays.
R T Gill, S Wildt, +2 authors, G Stephanopoulos.
Proc Natl Acad Sci U S A, 2002 May 09; 99(10). PMID: 11997466    Free PMC article.
Gammaherpesvirus lytic gene expression as characterized by DNA array.
Joo Wook Ahn, Kenneth L Powell, Paul Kellam, Dagmar G Alber.
J Virol, 2002 May 22; 76(12). PMID: 12021358    Free PMC article.
Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.
Aimée M Dudley, John Aach, Martin A Steffen, George M Church.
Proc Natl Acad Sci U S A, 2002 May 29; 99(11). PMID: 12032321    Free PMC article.
Symptomatic and asymptomatic benign prostatic hyperplasia: molecular differentiation by using microarrays.
Kulkarni Prakash, Gregorio Pirozzi, +5 authors, Robert H Getzenberg.
Proc Natl Acad Sci U S A, 2002 May 29; 99(11). PMID: 12032329    Free PMC article.
Comparative genomic hybridization analysis of sperm DNA apoptosis after exposure to heat shock.
Sylvia L Mann, William C Patton, Alan King, Philip J Chan.
J Assist Reprod Genet, 2002 May 31; 19(4). PMID: 12036087    Free PMC article.
A highly reproducible, linear, and automated sample preparation method for DNA microarrays.
David R Dorris, Ramesh Ramakrishnan, +6 authors, Abhijit Mazumder.
Genome Res, 2002 Jun 05; 12(6). PMID: 12045151    Free PMC article.
Microarray profile of differentially expressed genes in a monkey model of allergic asthma.
Jun Zou, Simon Young, +10 authors, Shelby Umland.
Genome Biol, 2002 Jun 07; 3(5). PMID: 12049661    Free PMC article.
Host-induced epidemic spread of the cholera bacterium.
D Scott Merrell, Susan M Butler, +6 authors, Andrew Camilli.
Nature, 2002 Jun 07; 417(6889). PMID: 12050664    Free PMC article.
Highly Cited.
Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803.
Ryan T Gill, Eva Katsoulakis, +3 authors, Gregory Stephanopoulos.
J Bacteriol, 2002 Jun 12; 184(13). PMID: 12057963    Free PMC article.
Approaches to the analysis of gene expression using mRNA: a technical overview.
John M S Bartlett.
Mol Biotechnol, 2002 Jun 13; 21(2). PMID: 12059114
Review.
Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals.
Peter H Tran, Daniel A Peiffer, +3 authors, Ken W Y Cho.
Nucleic Acids Res, 2002 Jun 13; 30(12). PMID: 12060692    Free PMC article.
Isolation of novel differentially expressed genes related to human glioma using cDNA microarray and characterizations of two novel full-length genes.
Zhen-Yu Qi, Yao Li, +6 authors, Yi Xie.
J Neurooncol, 2002 Jun 14; 56(3). PMID: 12061725
Gene expression profile of HIV-1 Tat expressing cells: a close interplay between proliferative and differentiation signals.
Cynthia de la Fuente, Francisco Santiago, +9 authors, Fatah Kashanchi.
BMC Biochem, 2002 Jun 19; 3. PMID: 12069692    Free PMC article.
Cluster analysis of gene expression dynamics.
Marco F Ramoni, Paola Sebastiani, Isaac S Kohane.
Proc Natl Acad Sci U S A, 2002 Jun 26; 99(14). PMID: 12082179    Free PMC article.
Highly Cited.
DNA microarrays in prostate cancer.
Shuk-Mei Ho, Kin-Mang Lau.
Curr Urol Rep, 2002 Jun 27; 3(1). PMID: 12084220
Review.
Prostate cancer genomics.
P E Li, P S Nelson.
Curr Urol Rep, 2002 Jun 27; 2(1). PMID: 12084298
Review.
Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization.
V Chizhikov, M Wagner, +3 authors, K Chumakov.
J Clin Microbiol, 2002 Jun 29; 40(7). PMID: 12089254    Free PMC article.
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays.
Jonathan A Bernstein, Arkady B Khodursky, +2 authors, Stanley N Cohen.
Proc Natl Acad Sci U S A, 2002 Jul 18; 99(15). PMID: 12119387    Free PMC article.
Highly Cited.
Effect of pentoxifylline on tumor suppressor and proto-oncogene apoptosis in sperm.
David T Maxwell, John D Jacobson, Alan King, Philip J Chan.
J Assist Reprod Genet, 2002 Aug 09; 19(6). PMID: 12166633    Free PMC article.
Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes.
Rodrigo A Gutierrez, Rob M Ewing, J Michael Cherry, Pamela J Green.
Proc Natl Acad Sci U S A, 2002 Aug 09; 99(17). PMID: 12167669    Free PMC article.
Microarray analysis of B-cell lymphoma cell lines with the t(14;18).
Ryan S Robetorye, Sandra D Bohling, +3 authors, Kojo S J Elenitoba-Johnson.
J Mol Diagn, 2002 Aug 10; 4(3). PMID: 12169673    Free PMC article.
Profiling of differentially expressed genes in human gastric carcinoma by cDNA expression array.
Lian-Xin Liu, Zhi-Hua Liu, +6 authors, Min Wu.
World J Gastroenterol, 2002 Aug 14; 8(4). PMID: 12174360    Free PMC article.
Integrin gene expression profiles of human hepatocellular carcinoma.
Lian-Xin Liu, Hong-Chi Jiang, +5 authors, Min Wu.
World J Gastroenterol, 2002 Aug 14; 8(4). PMID: 12174369    Free PMC article.
Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays.
Hongyue Dai, Michael Meyer, +2 authors, Roland Stoughton.
Nucleic Acids Res, 2002 Aug 15; 30(16). PMID: 12177314    Free PMC article.
DNA probes on beads arrayed in a capillary, 'Bead-array', exhibited high hybridization performance.
Yoshinobu Kohara, Hideyuki Noda, Kazunori Okano, Hideki Kambara.
Nucleic Acids Res, 2002 Aug 15; 30(16). PMID: 12177315    Free PMC article.
Application of physiological genomics to the study of hearing disorders.
Stefan Heller.
J Physiol, 2002 Aug 16; 543(Pt 1). PMID: 12181277    Free PMC article.
Review.
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
Jo Vandesompele, Katleen De Preter, +4 authors, Frank Speleman.
Genome Biol, 2002 Aug 20; 3(7). PMID: 12184808    Free PMC article.
Highly Cited.
Normalization and analysis of DNA microarray data by self-consistency and local regression.
Thomas B Kepler, Lynn Crosby, Kevin T Morgan.
Genome Biol, 2002 Aug 20; 3(7). PMID: 12184811    Free PMC article.
Oxidative stress responses--what have genome-scale studies taught us?
John G Scandalios.
Genome Biol, 2002 Aug 20; 3(7). PMID: 12184812    Free PMC article.
Review.
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.
Lao H Saal, Carl Troein, +3 authors, Carsten Peterson.
Genome Biol, 2002 Aug 21; 3(8). PMID: 12186655    Free PMC article.
Highly Cited.
A model for co-expression pattern analysis of genes implicated in angiogenesis and tumour cell invasion in cervical cancer.
P O Van Trappen, A Ryan, +8 authors, I J Jacobs.
Br J Cancer, 2002 Aug 22; 87(5). PMID: 12189553    Free PMC article.
Microarray results: how accurate are they?
Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran.
BMC Bioinformatics, 2002 Aug 27; 3. PMID: 12194703    Free PMC article.
Modulation of TCR-induced transcriptional profiles by ligation of CD28, ICOS, and CTLA-4 receptors.
James L Riley, Mao Mao, +6 authors, Peter S Linsley.
Proc Natl Acad Sci U S A, 2002 Aug 27; 99(18). PMID: 12195015    Free PMC article.
SAGE Genie: a suite with panoramic view of gene expression.
Peng Liang.
Proc Natl Acad Sci U S A, 2002 Aug 27; 99(18). PMID: 12195021    Free PMC article.
A new method for large scale isolation of kidney glomeruli from mice.
Minoru Takemoto, Noomi Asker, +4 authors, Christer Betsholtz.
Am J Pathol, 2002 Sep 06; 161(3). PMID: 12213707    Free PMC article.
Highly Cited.
Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometry.
Ljiljana Pasa-Tolić, Richard Harkewicz, +6 authors, Richard D Smith.
J Am Soc Mass Spectrom, 2002 Sep 10; 13(8). PMID: 12216736
Autoantibody profiling for the study and treatment of autoimmune disease.
Wolfgang Hueber, Paul J Utz, Lawrence Steinman, William H Robinson.
Arthritis Res, 2002 Sep 12; 4(5). PMID: 12223102    Free PMC article.
Review.
Have microarrays failed to deliver for developmental biology?
Rick Livesey.
Genome Biol, 2002 Sep 13; 3(9). PMID: 12225576    Free PMC article.
Gene-expression profile comparisons distinguish seven organs of maize.
Yangrae Cho, John Fernandes, Soo-Hwan Kim, Virginia Walbot.
Genome Biol, 2002 Sep 13; 3(9). PMID: 12225584    Free PMC article.
Significance and statistical errors in the analysis of DNA microarray data.
James P Brody, Brian A Williams, Barbara J Wold, Stephen R Quake.
Proc Natl Acad Sci U S A, 2002 Sep 18; 99(20). PMID: 12235357    Free PMC article.
Tripartite molecular beacons.
Razvan Nutiu, Yingfu Li.
Nucleic Acids Res, 2002 Sep 18; 30(18). PMID: 12235396    Free PMC article.
Epstein-barr virus-induced changes in B-lymphocyte gene expression.
Kara L Carter, Ellen Cahir-McFarland, Elliott Kieff.
J Virol, 2002 Sep 20; 76(20). PMID: 12239319    Free PMC article.
Yeast genomics: past, present, and future promise.
Michael Snyder, Anuj Kumar.
Funct Integr Genomics, 2002 Sep 24; 2(4-5). PMID: 12243128
Extracting functional information from microarrays: a challenge for functional genomics.
Michael Q Zhang.
Proc Natl Acad Sci U S A, 2002 Sep 25; 99(20). PMID: 12271149    Free PMC article.
Cross-species hybridisation of pig RNA to human nylon microarrays.
D E Moody, Z Zou, L McIntyre.
BMC Genomics, 2002 Oct 02; 3(1). PMID: 12354330    Free PMC article.
Large-scale gene-expression studies and the challenge of multiple sclerosis.
Sergio E Baranzini, Stephen L Hauser.
Genome Biol, 2002 Oct 10; 3(10). PMID: 12372148    Free PMC article.
Review.
Transcription profiling of the early gravitropic response in Arabidopsis using high-density oligonucleotide probe microarrays.
Nick Moseyko, Tong Zhu, +2 authors, Lewis J Feldman.
Plant Physiol, 2002 Oct 12; 130(2). PMID: 12376639    Free PMC article.
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.
Simon Kasif, Zhiping Weng, +2 authors, Charles DeLisi.
Nucleic Acids Res, 2002 Oct 18; 30(20). PMID: 12384608    Free PMC article.
A common reference for cDNA microarray hybridizations.
Ellen Sterrenburg, Rolf Turk, +2 authors, Johan T den Dunnen.
Nucleic Acids Res, 2002 Nov 01; 30(21). PMID: 12409475    Free PMC article.
Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens.
Atreya Dash, Ira P Maine, +3 authors, Mark A Rubin.
Am J Pathol, 2002 Nov 05; 161(5). PMID: 12414521    Free PMC article.
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.
Alvaro Mateos, Joaquín Dopazo, +3 authors, Gustavo Stolovitzky.
Genome Res, 2002 Nov 08; 12(11). PMID: 12421757    Free PMC article.
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography.
Emile F Nuwaysir, Wei Huang, +20 authors, Roland D Green.
Genome Res, 2002 Nov 08; 12(11). PMID: 12421762    Free PMC article.
Highly Cited.
Induction of the arginine decarboxylase ADC2 gene provides evidence for the involvement of polyamines in the wound response in Arabidopsis.
Miguel A Perez-Amador, Jose Leon, Pamela J Green, Juan Carbonell.
Plant Physiol, 2002 Nov 13; 130(3). PMID: 12428010    Free PMC article.
Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Ivana V Yang, Emily Chen, +10 authors, John Quackenbush.
Genome Biol, 2002 Nov 14; 3(11). PMID: 12429061    Free PMC article.
Highly Cited.
Integrating cytogenetics and gene expression profiling in the molecular analysis of multiple myeloma.
John D Shaughnessy, Bart Barlogie.
Int J Hematol, 2002 Nov 15; 76 Suppl 2. PMID: 12430902
Functional genomics and psychiatric illness.
Wendy Hasenkamp, Scott E Hemby.
Prog Brain Res, 2002 Nov 16; 138. PMID: 12432779    Free PMC article.
Review.
A genomic-scale view of the cAMP response element-enhancer decoy: a tumor target-based genetic tool.
Yee Sook Cho, Meyoung-Kon Kim, +4 authors, Yoon S Cho-Chung.
Proc Natl Acad Sci U S A, 2002 Nov 20; 99(24). PMID: 12438686    Free PMC article.
Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.
Hongjuan Zhao, Trevor Hastie, +2 authors, Stefanie S Jeffrey.
BMC Genomics, 2002 Nov 26; 3(1). PMID: 12445333    Free PMC article.
Identification of Listeria species by microarray-based assay.
Dmitriy Volokhov, Avraham Rasooly, Konstantin Chumakov, Vladimir Chizhikov.
J Clin Microbiol, 2002 Nov 28; 40(12). PMID: 12454178    Free PMC article.
Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress.
Alan G Hinnebusch, Krishnamurthy Natarajan.
Eukaryot Cell, 2002 Nov 29; 1(1). PMID: 12455968    Free PMC article.
Highly Cited. Review.
Domain-oriented functional analysis based on expression profiling.
Wei Ding, Luquan Wang, +3 authors, Marco Hernandez.
BMC Genomics, 2002 Nov 29; 3(1). PMID: 12456268    Free PMC article.
Validated genomic approach to study differentially expressed genes in complex tissues.
Elisa Wurmbach, Javier González-Maeso, +4 authors, Stuart C Sealfon.
Neurochem Res, 2002 Dec 05; 27(10). PMID: 12462402
Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders.
Julie Pongrac, Frank A Middleton, +2 authors, Károly Mirnics.
Neurochem Res, 2002 Dec 05; 27(10). PMID: 12462404
Review.
Transcriptional analysis in the brain: trophin-induced hippocampal synaptic plasticity.
Janet Alder, Smita Thakker-Varia, Ira B Black.
Neurochem Res, 2002 Dec 05; 27(10). PMID: 12462406
Expression profiling to understand actions of NMDA/glutamate receptor antagonists in rat brain.
Petri Törönen, Marcus Storvik, +5 authors, Garry Wong.
Neurochem Res, 2002 Dec 05; 27(10). PMID: 12462419
Network genomics--a novel approach for the analysis of biological systems in the post-genomic era.
Christian V Forst.
Mol Biol Rep, 2002 Dec 05; 29(3). PMID: 12463419
Review.
POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer.
Tapan K Bera, Drazen B Zimonjic, +4 authors, Ira Pastan.
Proc Natl Acad Sci U S A, 2002 Dec 12; 99(26). PMID: 12475935    Free PMC article.
Microarray analysis of host cell gene transcription in response to varicella-zoster virus infection of human T cells and fibroblasts in vitro and SCIDhu skin xenografts in vivo.
Jeremy O Jones, Ann M Arvin.
J Virol, 2002 Dec 28; 77(2). PMID: 12502844    Free PMC article.
Cyclooxygenase (COX)-2 and granulosa cell apoptosis in vitro.
Angela S Caffrey, William C Patton, +3 authors, Philip J Chan.
J Assist Reprod Genet, 2002 Dec 31; 19(12). PMID: 12503890    Free PMC article.
Gene expression profiles at different stages of human esophageal squamous cell carcinoma.
Jin Zhou, Li-Qun Zhao, +5 authors, Zhi-Hua Liu.
World J Gastroenterol, 2003 Jan 01; 9(1). PMID: 12508342    Free PMC article.
Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action.
Moriyah Zik, Vivian F Irish.
Plant Cell, 2003 Jan 02; 15(1). PMID: 12509532    Free PMC article.
The Stanford Microarray Database: data access and quality assessment tools.
Jeremy Gollub, Catherine A Ball, +11 authors, Gavin Sherlock.
Nucleic Acids Res, 2003 Jan 10; 31(1). PMID: 12519956    Free PMC article.
Application of DNA microarrays in pharmacogenomics and toxicogenomics.
Khew-Voon Chin, A N Tony Kong.
Pharm Res, 2003 Jan 14; 19(12). PMID: 12523654
Review.
Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies.
Alexei L Drobyshev, Christine Machka, +4 authors, Johannes Beckers.
Nucleic Acids Res, 2003 Jan 16; 31(2). PMID: 12527790    Free PMC article.
Elucidation of the Vibrio anguillarum genetic response to the potential fish probiont Pseudomonas fluorescens AH2, using RNA-arbitrarily primed PCR.
Kim Holmstrøm, Lone Gram.
J Bacteriol, 2003 Jan 21; 185(3). PMID: 12533458    Free PMC article.
A strategy for oligonucleotide microarray probe reduction.
Alena A Antipova, Pablo Tamayo, Todd R Golub.
Genome Biol, 2003 Jan 23; 3(12). PMID: 12537562    Free PMC article.
Heart-specific genes revealed by expressed sequence tag (EST) sampling.
Karine Mégy, Stéphane Audic, Jean-Michel Claverie.
Genome Biol, 2003 Jan 23; 3(12). PMID: 12537563    Free PMC article.
Systematic determination of patterns of gene expression during Drosophila embryogenesis.
Pavel Tomancak, Amy Beaton, +8 authors, Gerald M Rubin.
Genome Biol, 2003 Jan 23; 3(12). PMID: 12537577    Free PMC article.
Highly Cited.
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays.
Hong-Ying Wang, Renae L Malek, +6 authors, Norman H Lee.
Genome Biol, 2003 Jan 24; 4(1). PMID: 12540297    Free PMC article.
Information overload: assigning genetic functionality in the age of genomics and large-scale screening.
D Scott Merrell, Andrew Camilli.
Trends Microbiol, 2003 Feb 05; 10(12). PMID: 12564993    Free PMC article.
Review.
Monitoring gene expression in mixed microbial communities by using DNA microarrays.
Philip Dennis, Elizabeth A Edwards, Steven N Liss, Roberta Fulthorpe.
Appl Environ Microbiol, 2003 Feb 07; 69(2). PMID: 12570994    Free PMC article.
Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment.
Gaspar Taroncher-Oldenburg, Erin M Griner, Chris A Francis, Bess B Ward.
Appl Environ Microbiol, 2003 Feb 07; 69(2). PMID: 12571043    Free PMC article.
Directly labeled mRNA produces highly precise and unbiased differential gene expression data.
Vineet Gupta, Alex Cherkassky, +5 authors, James DiMeo.
Nucleic Acids Res, 2003 Feb 13; 31(4). PMID: 12582258    Free PMC article.
Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes.
Martin J Hessner, Xujing Wang, +5 authors, Soumitra Ghosh.
Nucleic Acids Res, 2003 Feb 13; 31(4). PMID: 12582259    Free PMC article.
Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays.
M Juanita Martinez, Anthony D Aragon, +5 authors, Margaret Werner-Washburne.
Nucleic Acids Res, 2003 Feb 13; 31(4). PMID: 12582263    Free PMC article.
Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots.
Christian Dubos, Christophe Plomion.
Plant Mol Biol, 2003 Feb 27; 51(2). PMID: 12602883
Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
Heenam Kim, Erik C Snesrud, +3 authors, John Quackenbush.
Genome Res, 2003 Mar 06; 13(3). PMID: 12618363    Free PMC article.
A classification-based machine learning approach for the analysis of genome-wide expression data.
James Lyons-Weiler, Satish Patel, Soumyaroop Bhattacharya.
Genome Res, 2003 Mar 06; 13(3). PMID: 12618382    Free PMC article.
Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis.
Haiqiong Montalta-He, Heinrich Reichert.
Genome Biol, 2003 Mar 07; 4(2). PMID: 12620112    Free PMC article.
Review.
Data extraction from composite oligonucleotide microarrays.
Ilya Shmulevich, Jaakko Astola, +2 authors, Wei Zhang.
Nucleic Acids Res, 2003 Mar 26; 31(7). PMID: 12655024    Free PMC article.
Regulation of host cell transcriptional physiology by the avian pneumovirus provides key insights into host-pathogen interactions.
Shirin Munir, Vivek Kapur.
J Virol, 2003 Mar 29; 77(8). PMID: 12663796    Free PMC article.
Gene expression profiles of hepatoma cell line HLE.
Lian-Xin Liu, Zhi-Hua Liu, +5 authors, Min Wu.
World J Gastroenterol, 2003 Apr 08; 9(4). PMID: 12679910    Free PMC article.
Detection of hepatitis B virus DNA in sera from patients with chronic hepatitis B virus infection by DNA microarray method.
Kazunori Kawaguchi, Shuichi Kaneko, +3 authors, Kenichi Kobayashi.
J Clin Microbiol, 2003 Apr 12; 41(4). PMID: 12682163    Free PMC article.
Predicting gene ontology biological process from temporal gene expression patterns.
Astrid Lagreid, Torgeir R Hvidsten, +2 authors, Arne K Sandvik.
Genome Res, 2003 Apr 16; 13(5). PMID: 12695321    Free PMC article.
Microarrays: new tools for transplantation research.
Mei-Sze Chua, Minnie M Sarwal.
Pediatr Nephrol, 2003 Apr 18; 18(4). PMID: 12700956
Review.
Paradoxical effects of a stress signal on pro- and anti-apoptotic machinery in HTLV-1 Tax expressing cells.
Cynthia de la Fuente, Lai Wang, +11 authors, Fatah Kashanchi.
Mol Cell Biochem, 2003 Apr 24; 245(1-2). PMID: 12708749
A new strategy to amplify degraded RNA from small tissue samples for microarray studies.
Charlie C Xiang, Mei Chen, +4 authors, Michael J Brownstein.
Nucleic Acids Res, 2003 Apr 25; 31(9). PMID: 12711698    Free PMC article.
Gene profiling for defining targets for new therapeutics in autoimmune diseases.
Lars Rogge.
Arthritis Res Ther, 2003 Apr 30; 5(2). PMID: 12718743    Free PMC article.
Review.
In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling.
Mark G Carter, Toshio Hamatani, +8 authors, Minoru S H Ko.
Genome Res, 2003 May 03; 13(5). PMID: 12727912    Free PMC article.
Global gene expression profiling in the study of multiple myeloma.
John D Shaughnessy.
Int J Hematol, 2003 May 07; 77(3). PMID: 12731663
Review.
GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers.
B Anders T Svensson, Arja J Kreeft, +2 authors, Judith M Boer.
Genome Biol, 2003 May 08; 4(5). PMID: 12734015    Free PMC article.
Immunological assays for chemokine detection in in-vitro culture of CNS cells.
Supriya D. Mahajan, Stanley A. Schwartz, Madhavan P.N. Nair.
Biol Proced Online, 2003 May 08; 5. PMID: 12734551    Free PMC article.
Microarray analysis: a novel research tool for cardiovascular scientists and physicians.
C Napoli, L O Lerman, +3 authors, F de Nigris.
Heart, 2003 May 16; 89(6). PMID: 12748210    Free PMC article.
Review.
Genome informatics: current status and future prospects.
Raimond L Winslow, Mark S Boguski.
Circ Res, 2003 May 17; 92(9). PMID: 12750305    Free PMC article.
Review.
Involvement of multiple signaling pathways in follicular lymphoma transformation: p38-mitogen-activated protein kinase as a target for therapy.
Kojo S J Elenitoba-Johnson, Stephen D Jenson, +12 authors, Megan S Lim.
Proc Natl Acad Sci U S A, 2003 May 21; 100(12). PMID: 12756297    Free PMC article.
Methodologies for the characterization of microbes in industrial environments: a review.
Johanna Maukonen, Jaana Mättö, +3 authors, Maria Saarela.
J Ind Microbiol Biotechnol, 2003 May 24; 30(6). PMID: 12764674
Review.
Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility.
Martin J Hessner, Xujing Wang, +6 authors, Soumitra Ghosh.
Nucleic Acids Res, 2003 May 29; 31(11). PMID: 12771224    Free PMC article.
Detection and identification of Mycobacterium species isolates by DNA microarray.
Masao Fukushima, Kenichi Kakinuma, +3 authors, Ryuji Kawaguchi.
J Clin Microbiol, 2003 Jun 07; 41(6). PMID: 12791887    Free PMC article.
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach.
Jean-Marie Rouillard, Michael Zuker, Erdogan Gulari.
Nucleic Acids Res, 2003 Jun 12; 31(12). PMID: 12799432    Free PMC article.
Highly Cited.
Optimization of high-density cDNA-microarray protocols by 'design of experiments'.
Gunnar Wrobel, Joerg Schlingemann, +3 authors, Meinhard Hahn.
Nucleic Acids Res, 2003 Jun 12; 31(12). PMID: 12799456    Free PMC article.
Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios.
David R Dorris, Allen Nguyen, +7 authors, Abhijit Mazumder.
BMC Biotechnol, 2003 Jun 13; 3. PMID: 12801425    Free PMC article.
The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy.
Bradley L Postier, Hong-Liang Wang, +10 authors, Robert L Burnap.
BMC Genomics, 2003 Jun 14; 4(1). PMID: 12803655    Free PMC article.
Synergistic effects of epoxy- and amine-silanes on microarray DNA immobilization and hybridization.
Sung-Kay Chiu, Mandy Hsu, +6 authors, Chi-Meng Tzeng.
Biochem J, 2003 Jun 18; 374(Pt 3). PMID: 12809552    Free PMC article.
Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides.
Gerrit J Schut, Scott D Brehm, Susmita Datta, Michael W W Adams.
J Bacteriol, 2003 Jun 19; 185(13). PMID: 12813088    Free PMC article.
Reproducibility of gene expression across generations of Affymetrix microarrays.
Ashish Nimgaonkar, Despina Sanoudou, +4 authors, Isaac S Kohane.
BMC Bioinformatics, 2003 Jun 26; 4. PMID: 12823866    Free PMC article.
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nicholas M Luscombe, Thomas E Royce, +5 authors, Mark Gerstein.
Nucleic Acids Res, 2003 Jun 26; 31(13). PMID: 12824348    Free PMC article.
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling.
Niels Tolstrup, Peter S Nielsen, +3 authors, Sakari Kauppinen.
Nucleic Acids Res, 2003 Jun 26; 31(13). PMID: 12824412    Free PMC article.
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).
Olga G Troyanskaya, Kara Dolinski, +2 authors, David Botstein.
Proc Natl Acad Sci U S A, 2003 Jun 27; 100(14). PMID: 12826619    Free PMC article.
Highly Cited.
Gene expression profiling of plant responses to abiotic stress.
Samuel P Hazen, Yajun Wu, Joel A Kreps.
Funct Integr Genomics, 2003 Jun 27; 3(3). PMID: 12827524
Review.
Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins.
Jens R Sydor, Steffen Nock.
Proteome Sci, 2003 Jul 02; 1(1). PMID: 12831399    Free PMC article.
Subsystem identification through dimensionality reduction of large-scale gene expression data.
Philip M Kim, Bruce Tidor.
Genome Res, 2003 Jul 04; 13(7). PMID: 12840046    Free PMC article.
Expression of NGF family and their receptors in gastric carcinoma: a cDNA microarray study.
Jian-Jun Du, Ke-Feng Dou, +8 authors, Ze-Guang Han.
World J Gastroenterol, 2003 Jul 11; 9(7). PMID: 12854135    Free PMC article.
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.
Rachel Lyne, Gavin Burns, +6 authors, Jürg Bähler.
BMC Genomics, 2003 Jul 12; 4(1). PMID: 12854975    Free PMC article.
Highly Cited.
Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE).
Zhijian J Chen, Laurent Gaté, +2 authors, Kenneth D Tew.
BMC Genomics, 2003 Jul 16; 4(1). PMID: 12859795    Free PMC article.
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Eugene Kolker, Samuel Purvine, +16 authors, Arnold L Smith.
J Bacteriol, 2003 Jul 18; 185(15). PMID: 12867470    Free PMC article.
The frequency gene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa.
Minou Nowrousian, Giles E Duffield, Jennifer J Loros, Jay C Dunlap.
Genetics, 2003 Jul 23; 164(3). PMID: 12871904    Free PMC article.
Molecular profiling of hepatocellular carcinomas (HCC) using a large-scale real-time RT-PCR approach: determination of a molecular diagnostic index.
Valérie Paradis, Ivan Bièche, +7 authors, Pierre Bedossa.
Am J Pathol, 2003 Jul 24; 163(2). PMID: 12875992    Free PMC article.
A rapid method for manual or automated purification of fluorescently labeled nucleic acids for sequencing, genotyping, and microarrays.
Amy L Springer, Lisa R Booth, +6 authors, Sergey Stolyar.
J Biomol Tech, 2003 Aug 07; 14(1). PMID: 12901608    Free PMC article.
Impact of surface chemistry and blocking strategies on DNA microarrays.
Scott Taylor, Stephanie Smith, Brad Windle, Anthony Guiseppi-Elie.
Nucleic Acids Res, 2003 Aug 09; 31(16). PMID: 12907739    Free PMC article.
Dendrimeric coating of glass slides for sensitive DNA microarrays analysis.
Véronique Le Berre, Emmanuelle Trévisiol, +5 authors, Jean François.
Nucleic Acids Res, 2003 Aug 09; 31(16). PMID: 12907740    Free PMC article.
Gene expression analysis using single molecule detection.
Kerstin Korn, Paola Gardellin, +17 authors, Rudolf Rigler.
Nucleic Acids Res, 2003 Aug 09; 31(16). PMID: 12907741    Free PMC article.
Transcriptional gene expression profiles of HGF/SF-met signaling pathway in colorectal carcinoma.
Xue-Nong Li, Yan-Qing Ding, Guo-Bing Liu.
World J Gastroenterol, 2003 Aug 15; 9(8). PMID: 12918110    Free PMC article.
New approaches to investigating heterogeneity in complex traits.
R Bomprezzi, P E Kovanen, R Martin.
J Med Genet, 2003 Aug 16; 40(8). PMID: 12920061    Free PMC article.
Review.
Screening for mammalian neural genes via fluorescence-activated cell sorter purification of neural precursors from Sox1-gfp knock-in mice.
Jerome Aubert, Marios P Stavridis, +8 authors, Austin Smith.
Proc Natl Acad Sci U S A, 2003 Aug 19; 100 Suppl 1. PMID: 12923295    Free PMC article.
EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human.
Christopher K Tuggle, Jon A Green, +18 authors, William Beavis.
Mamm Genome, 2003 Aug 20; 14(8). PMID: 12925889
Optimizing spotting solutions for increased reproducibility of cDNA microarrays.
David S Rickman, Christopher J Herbert, Lawrence P Aggerbeck.
Nucleic Acids Res, 2003 Sep 05; 31(18). PMID: 12954785    Free PMC article.
Microfabricated fountain pens for high-density DNA arrays.
Matthew O Reese, R Michael van Dam, Axel Scherer, Stephen R Quake.
Genome Res, 2003 Sep 17; 13(10). PMID: 12975313    Free PMC article.
Microarray and differential display identify genes involved in jasmonate-dependent anther development.
Ajin Mandaokar, V Dinesh Kumar, Matt Amway, John Browse.
Plant Mol Biol, 2003 Sep 19; 52(4). PMID: 13677466
A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach.
Andrew J Flavell, Viacheslav N Bolshakov, +4 authors, Peter Isaac.
Nucleic Acids Res, 2003 Sep 23; 31(19). PMID: 14500843    Free PMC article.
PNA microarrays for hybridisation of unlabelled DNA samples.
Ole Brandt, Julia Feldner, +5 authors, Anette Jacob.
Nucleic Acids Res, 2003 Sep 23; 31(19). PMID: 14500847    Free PMC article.
Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection.
Stephen C M Tsoi, Jacqueline M Cale, +3 authors, Susan Douglas.
Mar Biotechnol (NY), 2003 Sep 26; 5(6). PMID: 14508654
wCLUTO: a Web-enabled clustering toolkit.
Matthew D Rasmussen, Mukund S Deshpande, +3 authors, Ernest F Retzel.
Plant Physiol, 2003 Oct 14; 133(2). PMID: 14555780    Free PMC article.
Gene expression profiling during all-trans retinoic acid-induced cell differentiation of acute promyelocytic leukemia cells.
Lijun Yang, Hongshan Zhao, +6 authors, Jin-Xiong She.
J Mol Diagn, 2003 Oct 24; 5(4). PMID: 14573779    Free PMC article.
DANCER: a program for digital anatomical reconstruction of gene expression data.
Matti Kankainen, Garry Wong.
Nucleic Acids Res, 2003 Oct 25; 31(21). PMID: 14576332    Free PMC article.
Sizing of single fluorescently stained DNA fragments by scanning microscopy.
Stephan Laib, Michael Rankl, Thomas Ruckstuhl, Stefan Seeger.
Nucleic Acids Res, 2003 Nov 07; 31(22). PMID: 14602931    Free PMC article.
Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations.
Andrej-Nikolai Spiess, Nadine Mueller, Richard Ivell.
BMC Genomics, 2003 Nov 11; 4(1). PMID: 14606961    Free PMC article.
From peas to "chips" - the new millennium of molecular biology: a primer for the surgeon.
Iain Brown, Steven D Heys, Andrew C Schofield.
World J Surg Oncol, 2003 Nov 14; 1(1). PMID: 14613556    Free PMC article.
Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration.
Chiara Romualdi, Silvia Trevisan, +2 authors, Gerolamo Lanfranchi.
Nucleic Acids Res, 2003 Nov 25; 31(23). PMID: 14627839    Free PMC article.
Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling.
Michael Baum, Simone Bielau, +31 authors, Peer Friedrich Stähler.
Nucleic Acids Res, 2003 Nov 25; 31(23). PMID: 14627841    Free PMC article.
Expression profiling in ovarian clear cell carcinoma: identification of hepatocyte nuclear factor-1 beta as a molecular marker and a possible molecular target for therapy of ovarian clear cell carcinoma.
Akira Tsuchiya, Michiie Sakamoto, +6 authors, Setsuo Hirohashi.
Am J Pathol, 2003 Nov 25; 163(6). PMID: 14633622    Free PMC article.
Validation of cDNA microarray gene expression data obtained from linearly amplified RNA.
S D Jenson, R S Robetorye, +4 authors, K S J Elenitoba-Johnson.
Mol Pathol, 2003 Dec 03; 56(6). PMID: 14645691    Free PMC article.
Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale.
Caterina Holz, Bianka Prinz, +5 authors, Christine Lang.
J Struct Funct Genomics, 2003 Dec 03; 4(2-3). PMID: 14649293
Gene expression in the normal adult human kidney assessed by complementary DNA microarray.
John P T Higgins, Lingli Wang, +7 authors, Matt van de Rijn.
Mol Biol Cell, 2003 Dec 06; 15(2). PMID: 14657249    Free PMC article.
Multiclass classification of microarray data with repeated measurements: application to cancer.
Ka Yee Yeung, Roger E Bumgarner.
Genome Biol, 2003 Dec 09; 4(12). PMID: 14659020    Free PMC article.
Study of dosage compensation in Drosophila.
Pei-Wen Chiang, David M Kurnit.
Genetics, 2003 Dec 12; 165(3). PMID: 14668373    Free PMC article.
Network component analysis: reconstruction of regulatory signals in biological systems.
James C Liao, Riccardo Boscolo, +3 authors, Vwani P Roychowdhury.
Proc Natl Acad Sci U S A, 2003 Dec 16; 100(26). PMID: 14673099    Free PMC article.
Highly Cited.
High throughput gene expression profiling: a molecular approach to integrative physiology.
Mingyu Liang, Allen W Cowley, Andrew S Greene.
J Physiol, 2003 Dec 18; 554(Pt 1). PMID: 14678487    Free PMC article.
Review.
Gene expression profiling in ecotoxicology.
Terry W Snell, Sara E Brogdon, Michael B Morgan.
Ecotoxicology, 2003 Dec 19; 12(6). PMID: 14680327
Review.
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service.
David J Craigon, Nick James, +3 authors, Sean May.
Nucleic Acids Res, 2003 Dec 19; 32(Database issue). PMID: 14681484    Free PMC article.
Highly Cited.
Protein and Chemical Microarrays-Powerful Tools for Proteomics.
Qingchai Xu, Kit S. Lam.
J Biomed Biotechnol, 2003 Dec 23; 2003(5). PMID: 14688413    Free PMC article.
Expression profiling of favorable and unfavorable neuroblastomas.
Eiso Hiyama, Keiko Hiyama, +3 authors, Takashi Yokoyama.
Pediatr Surg Int, 2003 Dec 24; 20(1). PMID: 14691637
Identification of calcium- and nitric oxide-regulated genes by differential analysis of library expression (DAzLE).
Huiwu Li, Xiujing Gu, Valina L Dawson, Ted M Dawson.
Proc Natl Acad Sci U S A, 2004 Jan 01; 101(2). PMID: 14701905    Free PMC article.
Microarray-based gene expression profiling in pancreatic ductal carcinoma: status quo and perspectives.
Robert Grützmann, Hans Detlev Saeger, +4 authors, Christian Pilarsky.
Int J Colorectal Dis, 2004 Jan 28; 19(5). PMID: 14745573
Review.
Gene expression in the cyanobacterium Anabaena sp. PCC7120 under desiccation.
H Katoh, R K Asthana, M Ohmori.
Microb Ecol, 2004 Jan 30; 47(2). PMID: 14749909
Profiling ethylene-regulated gene expression in Arabidopsis thaliana by microarray analysis.
Guang Yan Zhong, Guang Van Zhong, Jacqueline K Burns.
Plant Mol Biol, 2004 Feb 06; 53(1-2). PMID: 14756311
Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray.
Inhan Lee, Alan A Dombkowski, Brian D Athey.
Nucleic Acids Res, 2004 Feb 06; 32(2). PMID: 14757833    Free PMC article.
Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.
Karen E Thum, Michael J Shin, +2 authors, Gloria M Coruzzi.
Genome Biol, 2004 Feb 05; 5(2). PMID: 14759260    Free PMC article.
Identification and analysis of plasticity-induced late-response genes.
Suk Jin Hong, Huiwu Li, +2 authors, Ted M Dawson.
Proc Natl Acad Sci U S A, 2004 Feb 10; 101(7). PMID: 14766980    Free PMC article.
Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant.
Nathalie Leonhardt, June M Kwak, +3 authors, Julian I Schroeder.
Plant Cell, 2004 Feb 20; 16(3). PMID: 14973164    Free PMC article.
Highly Cited.
Expression profiling of human breast cancers and gene regulation by progesterone receptors.
Britta M Jacobsen, Jennifer K Richer, Carol A Sartorius, Kathryn B Horwitz.
J Mammary Gland Biol Neoplasia, 2004 Feb 20; 8(3). PMID: 14973372
Review.
Interrogating mouse mammary cancer models: insights from gene expression profiling.
Antonio A Fargiano, Kartiki V Desai, Jeffrey E Green.
J Mammary Gland Biol Neoplasia, 2004 Feb 20; 8(3). PMID: 14973376
Review.
The Zap1 transcriptional activator also acts as a repressor by binding downstream of the TATA box in ZRT2.
Amanda J Bird, Elizabeth Blankman, +2 authors, Dennis R Winge.
EMBO J, 2004 Feb 21; 23(5). PMID: 14976557    Free PMC article.
NGEP, a gene encoding a membrane protein detected only in prostate cancer and normal prostate.
Tapan K Bera, Sudipto Das, +6 authors, Ira Pastan.
Proc Natl Acad Sci U S A, 2004 Feb 26; 101(9). PMID: 14981236    Free PMC article.
Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.
Christopher W Wong, Thomas J Albert, +6 authors, Lance D Miller.
Genome Res, 2004 Mar 03; 14(3). PMID: 14993206    Free PMC article.
Identifying transcriptional targets.
Nicola V Taverner, James C Smith, Fiona C Wardle.
Genome Biol, 2004 Mar 10; 5(3). PMID: 15005803    Free PMC article.
Review.
Transcriptome analysis of O3-exposed Arabidopsis reveals that multiple signal pathways act mutually antagonistically to induce gene expression.
Masanori Tamaoki, Nobuyoshi Nakajima, +3 authors, Hikaru Saji.
Plant Mol Biol, 2004 Mar 11; 53(4). PMID: 15010611
Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays.
Martin J Hessner, Vineet K Singh, +3 authors, Thomas C Zahrt.
BMC Genomics, 2004 Mar 17; 5(1). PMID: 15018646    Free PMC article.
Database development in toxicogenomics: issues and efforts.
William B Mattes, Syril D Pettit, +2 authors, Michael D Waters.
Environ Health Perspect, 2004 Mar 23; 112(4). PMID: 15033600    Free PMC article.
Review.
Whole-genome DNA array analysis of the response of Borrelia burgdorferi to a bactericidal monoclonal antibody.
Julie M Anderton, Rafal Tokarz, +5 authors, Jorge L Benach.
Infect Immun, 2004 Mar 25; 72(4). PMID: 15039324    Free PMC article.
Gene discovery in genetically labeled single dopaminergic neurons of the retina.
Stefano Gustincich, Massimo Contini, +9 authors, Elio Raviola.
Proc Natl Acad Sci U S A, 2004 Mar 30; 101(14). PMID: 15047890    Free PMC article.
Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry.
Tae Seok Seo, Xiaopeng Bai, +3 authors, Jingyue Ju.
Proc Natl Acad Sci U S A, 2004 Apr 06; 101(15). PMID: 15064393    Free PMC article.
The temporal expression profile of Mycobacterium tuberculosis infection in mice.
Adel M Talaat, Rick Lyons, Susan T Howard, Stephen Albert Johnston.
Proc Natl Acad Sci U S A, 2004 Apr 09; 101(13). PMID: 15070764    Free PMC article.
Highly Cited.
Decoding randomly ordered DNA arrays.
Kevin L Gunderson, Semyon Kruglyak, +17 authors, Mark S Chee.
Genome Res, 2004 Apr 14; 14(5). PMID: 15078854    Free PMC article.
Molecular analysis of metastasis in a polyomavirus middle T mouse model: the role of osteopontin.
Katayoun Alavi Jessen, Stephenie Y Liu, +8 authors, Jeffrey P Gregg.
Breast Cancer Res, 2004 Apr 16; 6(3). PMID: 15084239    Free PMC article.
Transcriptomic analysis in the leech Theromyzon tessulatum: involvement of cystatin B in innate immunity.
Christophe Lefebvre, Claude Cocquerelle, +4 authors, Michel Salzet.
Biochem J, 2004 Apr 20; 380(Pt 3). PMID: 15089746    Free PMC article.
Where, when and how much: regulation of myelin proteolipid protein gene expression.
P A Wight, A Dobretsova.
Cell Mol Life Sci, 2004 Apr 20; 61(7-8). PMID: 15095005
Review.
Attachment of oligonucleotide probes to poly carbodiimide-coated glass for microarray applications.
Naoki Kimura, Ryuichi Oda, Yoshiaki Inaki, Osamu Suzuki.
Nucleic Acids Res, 2004 Apr 27; 32(7). PMID: 15107483    Free PMC article.
Differential gene expression in human hepatocellular carcinoma Hep3B cells induced by apoptosis-related gene BNIPL-2.
Li Xie, Wen-Xin Qin, +4 authors, Jian-Ren Gu.
World J Gastroenterol, 2004 Apr 28; 10(9). PMID: 15112343    Free PMC article.
Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study.
Wuxiong Cao, Charles Epstein, +16 authors, Asher Zilberstein.
BMC Genomics, 2004 Apr 29; 5(1). PMID: 15113399    Free PMC article.
Gene expression profiling: from microarrays to medicine.
Ashani T Weeraratna, James E Nagel, Valeria de Mello-Coelho, Dennis D Taub.
J Clin Immunol, 2004 Apr 29; 24(3). PMID: 15114052    Free PMC article.
Review.
Hybrid clustering for microarray image analysis combining intensity and shape features.
Jörg Rahnenführer, Daniel Bozinov.
BMC Bioinformatics, 2004 May 01; 5. PMID: 15117421    Free PMC article.
An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays.
F Fixe, V Chu, D M F Prazeres, J P Conde.
Nucleic Acids Res, 2004 May 19; 32(9). PMID: 15148343    Free PMC article.
Quantitative analysis of highly parallel transfection in cell microarrays.
Sandrine Baghdoyan, Yoann Roupioz, +5 authors, Xavier Gidrol.
Nucleic Acids Res, 2004 May 25; 32(9). PMID: 15155824    Free PMC article.
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.
Brigham H Mecham, Gregory T Klus, +7 authors, Zoltan Szallasi.
Nucleic Acids Res, 2004 May 27; 32(9). PMID: 15161944    Free PMC article.
Gene expression profiles of hepatocytes treated with La(NO3)3 of rare earth in rats.
Hui Zhao, Wei-Dong Hao, +2 authors, You-Yong Lu.
World J Gastroenterol, 2004 May 27; 10(11). PMID: 15162537    Free PMC article.
Methods for transcriptional profiling in plants. Be fruitful and replicate.
Blake C Meyers, David W Galbraith, Timothy Nelson, Vikas Agrawal.
Plant Physiol, 2004 Jun 03; 135(2). PMID: 15173570    Free PMC article.
Review.
Transcriptome analysis of the ArgR regulon in Pseudomonas aeruginosa.
Chung-Dar Lu, Zhe Yang, Wei Li.
J Bacteriol, 2004 Jun 04; 186(12). PMID: 15175299    Free PMC article.
Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803.
Chao-Jung Tu, Jeffrey Shrager, +2 authors, Arthur R Grossman.
J Bacteriol, 2004 Jun 04; 186(12). PMID: 15175303    Free PMC article.
Experimental strategy to identify genes susceptible to oxidative stress in nigral dopaminergic neurons.
Myung S Yoo, Hibiki Kawamata, +2 authors, Jin H Son.
Neurochem Res, 2004 Jun 05; 29(6). PMID: 15176479
Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells.
Shirin Munir, Sushmita Singh, Kuljeet Kaur, Vivek Kapur.
Biol Proced Online, 2004 Jun 08; 6. PMID: 15181476    Free PMC article.
Miniaturized fluorescent RNA dot blot method for rapid quantitation of gene expression.
Fekadu Yadetie, Arne K Sandvik, +2 authors, Astrid Laegreid.
BMC Biotechnol, 2004 Jun 12; 4. PMID: 15191615    Free PMC article.
Improving signal intensities for genes with low-expression on oligonucleotide microarrays.
Latha Ramdas, David E Cogdell, +5 authors, Wei Zhang.
BMC Genomics, 2004 Jun 16; 5(1). PMID: 15196312    Free PMC article.
POBO, transcription factor binding site verification with bootstrapping.
Matti Kankainen, Liisa Holm.
Nucleic Acids Res, 2004 Jun 25; 32(Web Server issue). PMID: 15215385    Free PMC article.
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments.
Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa, Sorin Draghici.
Nucleic Acids Res, 2004 Jun 25; 32(Web Server issue). PMID: 15215428    Free PMC article.
Visualization and analysis of microarray and gene ontology data with treemaps.
Eric H Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman.
BMC Bioinformatics, 2004 Jun 30; 5. PMID: 15222902    Free PMC article.
Detection and quantification of gene expression in environmental bacteriology.
Freddie H Sharkey, Ibrahim M Banat, Roger Marchant.
Appl Environ Microbiol, 2004 Jul 09; 70(7). PMID: 15240248    Free PMC article.
Review.
Structural and functional analysis of rice genome.
Akhilesh K Tyagi, Jitendra P Khurana, +9 authors, Sulabha Sharma.
J Genet, 2004 Jul 09; 83(1). PMID: 15240912
Review.
Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression.
Cheng-Chung Chou, Chun-Houh Chen, Te-Tsui Lee, Konan Peck.
Nucleic Acids Res, 2004 Jul 10; 32(12). PMID: 15243142    Free PMC article.
A method for cross-species gene expression analysis with high-density oligonucleotide arrays.
Wan Ji, Wenli Zhou, +3 authors, Sara Davis.
Nucleic Acids Res, 2004 Jul 13; 32(11). PMID: 15247326    Free PMC article.
Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry.
Austin P So, Robin F B Turner, Charles A Haynes.
Nucleic Acids Res, 2004 Jul 13; 32(12). PMID: 15247329    Free PMC article.
Global analysis of gene expression by differential display: a mathematical model.
Shitao Yang, Peng Liang.
Mol Biotechnol, 2004 Jul 13; 27(3). PMID: 15247493
Lineage-specific gene duplication and loss in human and great ape evolution.
Andrew Fortna, Young Kim, +13 authors, James M Sikela.
PLoS Biol, 2004 Jul 15; 2(7). PMID: 15252450    Free PMC article.
Highly Cited.
Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays.
Hassan M Fathallah-Shaykh, Bin He, Li-Juan Zhao, Aamir Badruddin.
Nucleic Acids Res, 2004 Jul 22; 32(13). PMID: 15266007    Free PMC article.
Construction and selection of subtracted cDNA library of mouse hepatocarcinoma cell lines with different lymphatic metastasis potential.
Li Hou, Jan-Wu Tang, +3 authors, Lei Sun.
World J Gastroenterol, 2004 Jul 31; 10(16). PMID: 15285011    Free PMC article.
Statistical modeling for selecting housekeeper genes.
Aniko Szabo, Charles M Perou, +4 authors, Philip S Bernard.
Genome Biol, 2004 Aug 04; 5(8). PMID: 15287981    Free PMC article.
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.
Blake C Meyers, Shivakundan Singh Tej, +5 authors, Shannon Decola.
Genome Res, 2004 Aug 04; 14(8). PMID: 15289482    Free PMC article.
Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis.
Sabine Lezar, A A Myburg, +2 authors, B D Wingfield.
Theor Appl Genet, 2004 Aug 04; 109(7). PMID: 15290050
Melanoma genomics.
Mohammed Kashani-Sabet.
Curr Oncol Rep, 2004 Aug 05; 6(5). PMID: 15291985
Review.
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
Qing Zhou, Wing H Wong.
Proc Natl Acad Sci U S A, 2004 Aug 07; 101(33). PMID: 15297614    Free PMC article.
Genes for systemic vascular complications are differentially expressed in the livers of type 2 diabetic patients.
T Takamura, M Sakurai, +3 authors, S Kaneko.
Diabetologia, 2004 Aug 10; 47(4). PMID: 15298340
Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus.
Matias Kirst, Alexander A Myburg, +3 authors, Ronald Sederoff.
Plant Physiol, 2004 Aug 10; 135(4). PMID: 15299141    Free PMC article.
Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray.
Lefu Lan, Wei Chen, +11 authors, Yongbiao Xue.
Plant Mol Biol, 2004 Aug 19; 54(4). PMID: 15316284
RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples.
Charles E Rogler, Tatyana Tchaikovskaya, +5 authors, Leslie E Rogler.
Nucleic Acids Res, 2004 Aug 27; 32(15). PMID: 15329382    Free PMC article.
XHM: a system for detection of potential cross hybridizations in DNA microarrays.
Kristian Flikka, Fekadu Yadetie, Astrid Laegreid, Inge Jonassen.
BMC Bioinformatics, 2004 Aug 31; 5. PMID: 15333145    Free PMC article.
Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data.
Carsten O Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska.
BMC Bioinformatics, 2004 Sep 02; 5. PMID: 15339346    Free PMC article.
Genome image programs: visualization and interpretation of Escherichia coli microarray experiments.
Daniel P Zimmer, Oleg Paliy, +2 authors, Sydney Kustu.
Genetics, 2004 Sep 03; 167(4). PMID: 15342544    Free PMC article.
Microarray analysis of microRNA expression in the developing mammalian brain.
Eric A Miska, Ezequiel Alvarez-Saavedra, +5 authors, H Robert Horvitz.
Genome Biol, 2004 Sep 04; 5(9). PMID: 15345052    Free PMC article.
Highly Cited.
Biodiversity of vibrios.
Fabiano L Thompson, Tetsuya Iida, Jean Swings.
Microbiol Mol Biol Rev, 2004 Sep 09; 68(3). PMID: 15353563    Free PMC article.
Highly Cited. Review.
Whole-genome expression profiling through fragment display and combinatorial gene identification.
Ats Metsis, Ulf Andersson, +6 authors, Sten Linnarsson.
Nucleic Acids Res, 2004 Sep 10; 32(16). PMID: 15356287    Free PMC article.
High density peptide microarrays. In situ synthesis and applications.
Xiaolian Gao, Jean Philippe Pellois, +3 authors, Xiaochuan Zhou.
Mol Divers, 2004 Sep 24; 8(3). PMID: 15384411
A new compact disc format of high density array synthesis applied to peptide nucleic acids and in situ MALDI analysis.
Antonius J Dikmans, Michael Morr, +3 authors, Ronald Frank.
Mol Divers, 2004 Sep 24; 8(3). PMID: 15384413
Multiplexed sorting of libraries on libraries: a novel method for empirical protein design by affinity-driven phage enrichment on synthetic peptide arrays.
Claus Hultschig, Ronald Frank.
Mol Divers, 2004 Sep 24; 8(3). PMID: 15384416
Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays.
Paul M K Gordon, Christoph W Sensen.
Nucleic Acids Res, 2004 Oct 01; 32(17). PMID: 15456895    Free PMC article.
ArrayD: a general purpose software for microarray design.
Anu Sharma, Gyan Prakash Srivastava, Vineet K Sharma, Srinivasan Ramachandran.
BMC Bioinformatics, 2004 Oct 06; 5. PMID: 15461789    Free PMC article.
Muscle plasticity and high throughput gene expression studies.
Carlo Reggiani, Geertruuy Te Kronnie.
J Muscle Res Cell Motil, 2004 Oct 07; 25(3). PMID: 15467387
Review.
Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data.
Dietmar E Martin, Philippe Demougin, Michael N Hall, Michel Bellis.
BMC Bioinformatics, 2004 Oct 13; 5. PMID: 15476558    Free PMC article.
Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis.
Stephen J Robinson, Dustin J Cram, Christopher T Lewis, Isobel A P Parkin.
Plant Physiol, 2004 Oct 19; 136(2). PMID: 15489285    Free PMC article.
A gateway-compatible yeast one-hybrid system.
Bart Deplancke, Denis Dupuy, Marc Vidal, Albertha J M Walhout.
Genome Res, 2004 Oct 19; 14(10B). PMID: 15489331    Free PMC article.
High-coverage profiling analysis of genes expressed during rice seed development, using an improved amplified fragment length polymorphism technique.
Kiyoshi Suzuki, Atsushi Hattori, +3 authors, Shinichi Kitamura.
Funct Integr Genomics, 2004 Oct 19; 5(2). PMID: 15490295
RT-PCR analysis of RNA extracted from Bouin-fixed and paraffin-embedded lymphoid tissues.
Annunziata Gloghini, Barbara Canal, +4 authors, Antonino Carbone.
J Mol Diagn, 2004 Oct 28; 6(4). PMID: 15507667    Free PMC article.
Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays.
James Adjaye, Ralf Herwig, +8 authors, Hans Lehrach.
BMC Genomics, 2004 Oct 30; 5. PMID: 15511299    Free PMC article.
A novel, high-performance random array platform for quantitative gene expression profiling.
Kenneth Kuhn, Shawn C Baker, +7 authors, Mark S Chee.
Genome Res, 2004 Nov 03; 14(11). PMID: 15520296    Free PMC article.
DNA Macroarray profiling of Lactococcus lactis subsp. lactis IL1403 gene expression during environmental stresses.
Yi Xie, Lan-szu Chou, Adele Cutler, Bart Weimer.
Appl Environ Microbiol, 2004 Nov 06; 70(11). PMID: 15528540    Free PMC article.
Sample size for detecting differentially expressed genes in microarray experiments.
Caimiao Wei, Jiangning Li, Roger E Bumgarner.
BMC Genomics, 2004 Nov 10; 5. PMID: 15533245    Free PMC article.
Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens.
Steve N Bailey, David M Sabatini, Brent R Stockwell.
Proc Natl Acad Sci U S A, 2004 Nov 10; 101(46). PMID: 15534212    Free PMC article.
Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.
Kyeong Soo Jeong, Jaeyong Ahn, Arkady B Khodursky.
Genome Biol, 2004 Nov 13; 5(11). PMID: 15535862    Free PMC article.
A modified hybridization protocol for low-density diagnostic DNA microarrays.
Hai Huang, Wen Li Ma, +3 authors, Wen Ling Zheng.
Mol Biotechnol, 2004 Nov 16; 28(3). PMID: 15542919
Application of microarrays in high-throughput enzymatic profiling.
Mahesh Uttamchandani, Xuan Huang, +2 authors, Shao Q Yao.
Mol Biotechnol, 2004 Nov 16; 28(3). PMID: 15542923
Review.
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
Sonali Mukherjee, Michael F Berger, +5 authors, Martha L Bulyk.
Nat Genet, 2004 Nov 16; 36(12). PMID: 15543148    Free PMC article.
Highly Cited.
Overexpression of SPARC gene in human gastric carcinoma and its clinic-pathologic significance.
C-S Wang, K-H Lin, +2 authors, S Hsueh.
Br J Cancer, 2004 Nov 24; 91(11). PMID: 15558074    Free PMC article.
DNA microarray for rapid detection of mitochondrial DNA haplotypes of chum salmon.
Shogo Moriya, Shigehiko Urawa, +2 authors, Syuiti Abe.
Mar Biotechnol (NY), 2004 Dec 08; 6(5). PMID: 15583850
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information.
Yian A Chen, David J McKillen, +5 authors, Jonas S Almeida.
BMC Bioinformatics, 2004 Dec 09; 5. PMID: 15585062    Free PMC article.
Application of microarray technology in pulmonary diseases.
Argyris Tzouvelekis, George Patlakas, Demosthenes Bouros.
Respir Res, 2004 Dec 09; 5. PMID: 15585067    Free PMC article.
Review.
A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms.
Yong Woo, Jason Affourtit, +4 authors, Gary Churchill.
J Biomol Tech, 2004 Dec 09; 15(4). PMID: 15585824    Free PMC article.
Optimized LOWESS normalization parameter selection for DNA microarray data.
John A Berger, Sampsa Hautaniemi, +3 authors, Jaakko Astola.
BMC Bioinformatics, 2004 Dec 14; 5. PMID: 15588297    Free PMC article.
GECKO: a complete large-scale gene expression analysis platform.
Joachim Theilhaber, Anatoly Ulyanov, +6 authors, Steven Bushnell.
BMC Bioinformatics, 2004 Dec 14; 5. PMID: 15588317    Free PMC article.
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis.
Robert J Blick, Andrew T Revel, Eric J Hansen.
Bioinformatics, 2004 Dec 14; 19(13). PMID: 15593406    Free PMC article.
Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray.
Yoshihiro Narusaka, Mari Narusaka, +5 authors, Kazuo Shinozaki.
Plant Mol Biol, 2004 Dec 18; 55(3). PMID: 15604685
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.
Motohiko Tanino, Marie-Anne Debily, +19 authors, Kousaku Okubo.
Nucleic Acids Res, 2004 Dec 21; 33(Database issue). PMID: 15608263    Free PMC article.
Global analysis of gene expression in mammalian kidney.
Olga Soutourina, Lydie Cheval, Alain Doucet.
Pflugers Arch, 2004 Dec 22; 450(1). PMID: 15611884
Review.
DNA array-based gene profiling: from surgical specimen to the molecular portrait of cancer.
Simone Mocellin, Maurizio Provenzano, +3 authors, Mario Lise.
Ann Surg, 2004 Dec 29; 241(1). PMID: 15621987    Free PMC article.
Review.
An EST resource for cassava and other species of Euphorbiaceae.
James V Anderson, Michel Delseny, +10 authors, David P Horvath.
Plant Mol Biol, 2005 Jan 05; 56(4). PMID: 15630617
Gene Ontology: looking backwards and forwards.
Suzanna E Lewis.
Genome Biol, 2005 Jan 12; 6(1). PMID: 15642104    Free PMC article.
Microarrays, antiobesity and the liver.
Fernando Castro-Chávez.
Ann Hepatol, 2005 Jan 20; 3(4). PMID: 15657555    Free PMC article.
Review.
Interferon alpha 2a down-regulates VEGF expression through PI3 kinase and MAP kinase signaling pathways.
Wei-Zhong Wu, Hui-Chuan Sun, +5 authors, Kang-Da Liu.
J Cancer Res Clin Oncol, 2005 Jan 22; 131(3). PMID: 15662525
A robust two-way semi-linear model for normalization of cDNA microarray data.
Deli Wang, Jian Huang, +2 authors, Marcelo Bento Soares.
BMC Bioinformatics, 2005 Jan 25; 6. PMID: 15663789    Free PMC article.
Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid.
Matias Kirst, Christopher J Basten, +2 authors, Ronald R Sederoff.
Genetics, 2005 Feb 03; 169(4). PMID: 15687266    Free PMC article.
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset.
Sung E Choe, Michael Boutros, +2 authors, Marc S Halfon.
Genome Biol, 2005 Feb 08; 6(2). PMID: 15693945    Free PMC article.
Highly Cited.
Genomic analysis of early murine mammary gland development using novel probe-level algorithms.
Stephen R Master, Alexander J Stoddard, +3 authors, Lewis A Chodosh.
Genome Biol, 2005 Feb 08; 6(2). PMID: 15693949    Free PMC article.
Genome-wide analysis of the context-dependence of regulatory networks.
Balázs Papp, Stephen Oliver.
Genome Biol, 2005 Feb 08; 6(2). PMID: 15693953    Free PMC article.
Review.
A comparative analysis of transcript abundance using SAGE and Affymetrix arrays.
Adel F M Ibrahim, Peter E Hedley, +4 authors, Robbie Waugh.
Funct Integr Genomics, 2005 Feb 17; 5(3). PMID: 15714318
Microarray analysis of gene expression in germinating barley embryos (Hordeum vulgare L.).
Loraine Watson, Robert J Henry.
Funct Integr Genomics, 2005 Feb 17; 5(3). PMID: 15714320
Evolutionary significance of gene expression divergence.
I King Jordan, Leonardo Mariño-Ramírez, Eugene V Koonin.
Gene, 2005 Feb 18; 345(1). PMID: 15716085    Free PMC article.
Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome.
S Dinel, C Bolduc, +7 authors, J St-Amand.
Nucleic Acids Res, 2005 Feb 18; 33(3). PMID: 15716308    Free PMC article.
Blood-brain barrier genomics, proteomics, and new transporter discovery.
Eric V Shusta.
NeuroRx, 2005 Feb 18; 2(1). PMID: 15717066    Free PMC article.
Review.
Quantitative inference of dynamic regulatory pathways via microarray data.
Wen-Chieh Chang, Chang-Wei Li, Bor-Sen Chen.
BMC Bioinformatics, 2005 Mar 08; 6. PMID: 15748298    Free PMC article.
Secondary structure in the target as a confounding factor in synthetic oligomer microarray design.
Vladyslava G Ratushna, Jennifer W Weller, Cynthia J Gibas.
BMC Genomics, 2005 Mar 10; 6. PMID: 15755320    Free PMC article.
Transporter and ion channel gene expression after Caco-2 cell differentiation using 2 different microarray technologies.
Christopher P Landowski, Pascale Anderle, +2 authors, Gordon L Amidon.
AAPS J, 2005 Mar 12; 6(3). PMID: 15760106    Free PMC article.
A qualitative assessment of direct-labeled cDNA products prior to microarray analysis.
Sherry F Grissom, Edward K Lobenhofer, Charles J Tucker.
BMC Genomics, 2005 Mar 15; 6. PMID: 15762992    Free PMC article.
Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays.
Mong-Hsun Tsai, Hailing Yan, +6 authors, Eric Y Chuang.
Mol Biotechnol, 2005 Mar 16; 29(3). PMID: 15767699
A DNA microarray survey of gene expression in normal human tissues.
Radha Shyamsundar, Young H Kim, +7 authors, Jonathan R Pollack.
Genome Biol, 2005 Mar 19; 6(3). PMID: 15774023    Free PMC article.
Genetical genomics analysis of a yeast segregant population for transcription network inference.
Nan Bing, Ina Hoeschele.
Genetics, 2005 Mar 23; 170(2). PMID: 15781693    Free PMC article.
Gene expression profiling in neurological disorders: toward a systems-level understanding of the brain.
Sergio E Baranzini.
Neuromolecular Med, 2005 Mar 23; 6(1). PMID: 15781975
Review.
Profile of changes in gene expression in cultured hippocampal neurones evoked by the GABAB receptor agonist baclofen.
Mohamed T Ghorbel, Kevin G Becker, Jeremy M Henley.
Physiol Genomics, 2005 Mar 24; 22(1). PMID: 15784695    Free PMC article.
Analysis of host response to bacterial infection using error model based gene expression microarray experiments.
Dov J Stekel, Donatella Sarti, +7 authors, Francesco Falciani.
Nucleic Acids Res, 2005 Apr 01; 33(6). PMID: 15800204    Free PMC article.
Analysis of target genes induced by IL-13 cytotoxin in human glioblastoma cells.
Jing Han, Liming Yang, Raj K Puri.
J Neurooncol, 2005 Apr 02; 72(1). PMID: 15803373
Characterization of gene expression profiles of T cells during anti-tumor response.
Christian Stremmel, Renate Siebenhaar, +3 authors, Werner Hohenberger.
Int J Colorectal Dis, 2005 Apr 07; 20(6). PMID: 15812645
Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies.
J Forment, J Gadea, +50 authors, V Conejero.
Plant Mol Biol, 2005 Apr 15; 57(3). PMID: 15830128
MARS: microarray analysis, retrieval, and storage system.
Michael Maurer, Robert Molidor, +6 authors, Zlatko Trajanoski.
BMC Bioinformatics, 2005 Apr 20; 6. PMID: 15836795    Free PMC article.
Methods for genome-wide analysis of gene expression changes in polyploids.
Jianlin Wang, Jinsuk J Lee, +7 authors, Z Jeffrey Chen.
Methods Enzymol, 2005 May 04; 395. PMID: 15865985    Free PMC article.
In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication.
Matthew J Moorcroft, Wouter R A Meuleman, +3 authors, Edwin M Southern.
Nucleic Acids Res, 2005 May 05; 33(8). PMID: 15870385    Free PMC article.
Aberrant expression of RAB1A in human tongue cancer.
K Shimada, K Uzawa, +6 authors, H Tanzawa.
Br J Cancer, 2005 May 05; 92(10). PMID: 15870709    Free PMC article.
Three microarray platforms: an analysis of their concordance in profiling gene expression.
David Petersen, G V R Chandramouli, +12 authors, Ernest S Kawasaki.
BMC Genomics, 2005 May 07; 6. PMID: 15876355    Free PMC article.
An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays.
Mugdha Gadgil, Wei Lian, +2 authors, Wei-Shou Hu.
BMC Genomics, 2005 May 10; 6. PMID: 15877823    Free PMC article.
DNA microarrays--techniques and applications in microbial systems.
T Majtán, G Bukovská, J Timko.
Folia Microbiol (Praha), 2005 May 11; 49(6). PMID: 15881400
Review.
Bioluminescence regenerative cycle (BRC) system: theoretical considerations for nucleic acid quantification assays.
Arjang Hassibi, Christopher Contag, +4 authors, Nader Pourmand.
Biophys Chem, 2005 May 11; 116(3). PMID: 15882922    Free PMC article.
Monitoring microarray-based gene expression profile changes in hepatocellular carcinoma.
Hong-Ju Mao, Hong-Nian Li, +2 authors, Da-Fang Wan.
World J Gastroenterol, 2005 May 11; 11(18). PMID: 15884129    Free PMC article.
A study of inter-lab and inter-platform agreement of DNA microarray data.
Huixia Wang, Xuming He, +2 authors, Lei Liu.
BMC Genomics, 2005 May 13; 6. PMID: 15888200    Free PMC article.
Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data.
Jerilyn A Timlin, David M Haaland, +3 authors, Margaret Werner-Washburne.
BMC Genomics, 2005 May 13; 6. PMID: 15888208    Free PMC article.
Organ-specific expression of Arabidopsis genome during development.
Ligeng Ma, Ning Sun, +3 authors, Xing Wang Deng.
Plant Physiol, 2005 May 13; 138(1). PMID: 15888681    Free PMC article.
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
Sacha A F T van Hijum, Anne de Jong, +7 authors, Oscar P Kuipers.
BMC Genomics, 2005 May 24; 6. PMID: 15907200    Free PMC article.
Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.
Chris Cheadle, Jinshui Fan, +5 authors, Kevin G Becker.
BMC Genomics, 2005 May 24; 6. PMID: 15907206    Free PMC article.
An inexpensive gel electrophoresis-based polymerase chain reaction method for quantifying mRNA levels.
William D Bradford, Laty Cahoon, +2 authors, Todd T Eckdahl.
Cell Biol Educ, 2005 May 27; 4(2). PMID: 15917874    Free PMC article.
Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues.
T Mijalski, A Harder, +7 authors, J Beckers.
Proc Natl Acad Sci U S A, 2005 Jun 09; 102(24). PMID: 15939889    Free PMC article.
DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene.
Soon Jin Oh, Jimin Ju, +5 authors, Kwan Yong Choi.
Nucleic Acids Res, 2005 Jun 09; 33(10). PMID: 15939931    Free PMC article.
Metabolic engineering in the -omics era: elucidating and modulating regulatory networks.
Goutham N Vemuri, Aristos A Aristidou.
Microbiol Mol Biol Rev, 2005 Jun 10; 69(2). PMID: 15944454    Free PMC article.
Review.
Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips.
Fred van Ruissen, Jan M Ruijter, +4 authors, Frank Baas.
BMC Genomics, 2005 Jun 16; 6. PMID: 15955238    Free PMC article.
Microarray analysis of quorum-sensing-regulated genes in Porphyromonas gingivalis.
Lihui Yuan, Jeffrey D Hillman, Ann Progulske-Fox.
Infect Immun, 2005 Jun 24; 73(7). PMID: 15972504    Free PMC article.
T-profiler: scoring the activity of predefined groups of genes using gene expression data.
André Boorsma, Barrett C Foat, +2 authors, Harmen J Bussemaker.
Nucleic Acids Res, 2005 Jun 28; 33(Web Server issue). PMID: 15980543    Free PMC article.
How to improve quality assurance in fluorometry: fluorescence-inherent sources of error and suited fluorescence standards.
U Resch-Genger, K Hoffmann, +5 authors, R Macdonald.
J Fluoresc, 2005 Jun 30; 15(3). PMID: 15986157
Enhanced microarray performance using low complexity representations of the transcriptome.
Gaëlle Rondeau, Michael McClelland, +5 authors, John Welsh.
Nucleic Acids Res, 2005 Jul 01; 33(11). PMID: 15987785    Free PMC article.
Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds.
Frédérique Pasquer, Edwige Isidore, Jürg Zarn, Beat Keller.
Plant Mol Biol, 2005 Jul 01; 57(5). PMID: 15988564
Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling.
R Turk, E Sterrenburg, +3 authors, P A C 't Hoen.
BMC Genomics, 2005 Jul 14; 6. PMID: 16011810    Free PMC article.
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays.
Eric C Rouchka, Abdelnaby Khalyfa, Nigel G F Cooper.
BMC Bioinformatics, 2005 Jul 15; 6. PMID: 16014168    Free PMC article.
Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis.
Josephine N Harada, Kristen E Bower, +6 authors, Sumit K Chanda.
Genome Res, 2005 Jul 19; 15(8). PMID: 16024821    Free PMC article.
A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.
Zengjun Xu, Tucker A Patterson, +5 authors, William Slikker.
BMC Bioinformatics, 2005 Jul 20; 6 Suppl 2. PMID: 16026605    Free PMC article.
Analysis of epidermis- and mesophyll-specific transcript accumulation in powdery mildew-inoculated wheat leaves.
Rémy Bruggmann, Olaf Abderhalden, Philippe Reymond, Robert Dudler.
Plant Mol Biol, 2005 Jul 20; 58(2). PMID: 16027977
Multiple locus linkage analysis of genomewide expression in yeast.
John D Storey, Joshua M Akey, Leonid Kruglyak.
PLoS Biol, 2005 Jul 23; 3(8). PMID: 16035920    Free PMC article.
Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication.
Ryan D Egeland, Edwin M Southern.
Nucleic Acids Res, 2005 Aug 09; 33(14). PMID: 16085751    Free PMC article.
Data clustering in life sciences.
Ying Zhao, George Karypis.
Mol Biotechnol, 2005 Aug 25; 31(1). PMID: 16118415
Review.
Multiplexed quantification of bacterial 16S rRNA by solution hybridization with oligonucleotide probes and affinity capture.
Reetta M Satokari, Kari Kataja, Hans Söderlund.
Microb Ecol, 2005 Sep 01; 50(1). PMID: 16132427
CAM and cell fate targeting: molecular and energetic insights into cell growth and differentiation.
Carlo Ventura.
Evid Based Complement Alternat Med, 2005 Sep 02; 2(3). PMID: 16136206    Free PMC article.
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
Ligeng Ma, Chen Chen, +17 authors, Jian Wang.
Genome Res, 2005 Sep 06; 15(9). PMID: 16140994    Free PMC article.
The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.
Elzbieta Kierzek, Anna Ciesielska, +3 authors, Ryszard Kierzek.
Nucleic Acids Res, 2005 Sep 13; 33(16). PMID: 16155181    Free PMC article.
Comparison of transcript profiling on Arabidopsis microarray platform technologies.
Jeffrey D Pylatuik, Pierre R Fobert.
Plant Mol Biol, 2005 Sep 15; 58(5). PMID: 16158238
Lanthanide complex-based fluorescence label for time-resolved fluorescence bioassay.
Jingli Yuan, Guilan Wang.
J Fluoresc, 2005 Sep 17; 15(4). PMID: 16167214
Review.
RESOURCERER: a database for annotating and linking microarray resources within and across species.
J Tsai, R Sultana, +7 authors, J Quackenbush.
Genome Biol, 2005 Sep 22; 2(11). PMID: 16173164    Free PMC article.
A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays.
Kang Ning, Kwok Pui Choi, Hon Wai Leong, Louxin Zhang.
Nucleic Acids Res, 2005 Sep 30; 33(17). PMID: 16192568    Free PMC article.
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, +8 authors, Jill P Mesirov.
Proc Natl Acad Sci U S A, 2005 Oct 04; 102(43). PMID: 16199517    Free PMC article.
Highly Cited.
Expressible molecular colonies.
Timur R Samatov, Helena V Chetverina, Alexander B Chetverin.
Nucleic Acids Res, 2005 Oct 06; 33(17). PMID: 16204448    Free PMC article.
Isolation of mRNA from specific tissues of Drosophila by mRNA tagging.
Zhiyong Yang, Howard J Edenberg, Ronald L Davis.
Nucleic Acids Res, 2005 Oct 06; 33(17). PMID: 16204451    Free PMC article.
Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.).
Lefu Lan, Meina Li, +5 authors, Yongbiao Xue.
Plant Mol Biol, 2005 Oct 12; 59(1). PMID: 16217609
NF-kappaB and ERK-signaling pathways contribute to the gene expression induced by cag PAI-positive-Helicobacter pylori infection.
Wataru Shibata, Yoshihiro Hirata, +10 authors, Masao Omata.
World J Gastroenterol, 2005 Nov 08; 11(39). PMID: 16273640    Free PMC article.
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.
Eliot R Spindel, Mark A Pauley, +5 authors, Robert B Norgren.
BMC Genomics, 2005 Nov 18; 6. PMID: 16288651    Free PMC article.
A stepwise framework for the normalization of array CGH data.
Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward, Calum MacAulay.
BMC Bioinformatics, 2005 Nov 22; 6. PMID: 16297240    Free PMC article.
Transcription program of red sea bream iridovirus as revealed by DNA microarrays.
Dang Thi Lua, Motoshige Yasuike, Ikuo Hirono, Takashi Aoki.
J Virol, 2005 Nov 25; 79(24). PMID: 16306587    Free PMC article.
DNA microarrays: recent developments and applications to the study of pituitary tissues.
Xiang Qian, Bernd W Scheithauer, Kalman Kovacs, Ricardo V Lloyd.
Endocrine, 2005 Nov 29; 28(1). PMID: 16311410
Review.
Gene expression profile analysis in astaxanthin-induced Haematococcus pluvialis using a cDNA microarray.
Hyunsuk Eom, Choul-Gyun Lee, EonSeon Jin.
Planta, 2005 Dec 02; 223(6). PMID: 16320067
Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).
Roger A Hoskins, Mark Stapleton, +4 authors, Susan E Celniker.
Nucleic Acids Res, 2005 Dec 06; 33(21). PMID: 16326860    Free PMC article.
Conserved and variable functions of the sigmaE stress response in related genomes.
Virgil A Rhodius, Won Chul Suh, +2 authors, Carol A Gross.
PLoS Biol, 2005 Dec 13; 4(1). PMID: 16336047    Free PMC article.
Highly Cited.
Teaching systems biology: an active-learning approach.
Anuj Kumar.
Cell Biol Educ, 2005 Dec 13; 4(4). PMID: 16341259    Free PMC article.
Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control.
Giacomo Finocchiaro, Francesco Mancuso, Heiko Muller.
BMC Bioinformatics, 2005 Dec 15; 6 Suppl 4. PMID: 16351740    Free PMC article.
Changes in gene expression in maize kernel in response to water and salt stress.
Violeta Andjelkovic, Richard Thompson.
Plant Cell Rep, 2005 Dec 20; 25(1). PMID: 16362303
Design optimization methods for genomic DNA tiling arrays.
Paul Bertone, Valery Trifonov, +6 authors, Mark Gerstein.
Genome Res, 2005 Dec 21; 16(2). PMID: 16365382    Free PMC article.
Transcript analysis of early nodulation events in Medicago truncatula.
Dasharath Prasad Lohar, Natalya Sharopova, +5 authors, Kathryn A VandenBosch.
Plant Physiol, 2005 Dec 27; 140(1). PMID: 16377745    Free PMC article.
Development of cell therapy using autologous bone marrow cells for liver cirrhosis.
Isao Sakaida, Shuji Terai, Hiroshi Nishina, Kiwamu Okita.
Med Mol Morphol, 2005 Dec 27; 38(4). PMID: 16378227
Review.
Reliability and reproducibility issues in DNA microarray measurements.
Sorin Draghici, Purvesh Khatri, Aron C Eklund, Zoltan Szallasi.
Trends Genet, 2005 Dec 29; 22(2). PMID: 16380191    Free PMC article.
Highly Cited. Review.
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis.
Nils E Magnusson, Alessandra K Cardozo, +3 authors, Jens L Jensen.
BMC Bioinformatics, 2005 Dec 31; 6. PMID: 16384535    Free PMC article.
Recent applications of DNA microarray technology to toxicology and ecotoxicology.
Teresa Lettieri.
Environ Health Perspect, 2006 Jan 06; 114(1). PMID: 16393650    Free PMC article.
Review.
Detection of foot and mouth disease and porcine reproductive and respiratory syndrome viral genes using microarray chip.
Y-C Liu, G S Huang, +2 authors, K-P Hsiung.
Vet Res Commun, 2006 Jan 10; 30(2). PMID: 16400604
Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.
Zihua Hu, Gail R Willsky.
BMC Bioinformatics, 2006 Jan 13; 7. PMID: 16403228    Free PMC article.
A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.
Joost B Vos, Nicole A Datson, +7 authors, Pieter S Hiemstra.
BMC Genomics, 2006 Jan 20; 7. PMID: 16420688    Free PMC article.
Modulation of gene expression in MHCC97 cells by interferon alpha.
Wei-Zhong Wu, Hui-Chuan Sun, +3 authors, Zhao-You Tang.
World J Gastroenterol, 2006 Jan 21; 11(42). PMID: 16425353    Free PMC article.
Lithographic techniques and surface chemistries for the fabrication of PEG-passivated protein microarrays.
Balaji Kannan, Kenneth Castelino, Fanqing Frank Chen, Arun Majumdar.
Biosens Bioelectron, 2006 Feb 07; 21(10). PMID: 16457998    Free PMC article.
An ankyrin repeat-containing protein, characterized as a ubiquitin ligase, is closely associated with membrane-enclosed organelles and required for pollen germination and pollen tube growth in lily.
Jian Huang, Feng Chen, +8 authors, Yiqin Li.
Plant Physiol, 2006 Feb 08; 140(4). PMID: 16461387    Free PMC article.
Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray.
Siok Hwee Tan, Antonio Reverter, +3 authors, Sigrid A Lehnert.
Funct Integr Genomics, 2006 Feb 14; 6(3). PMID: 16470362
Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling.
Vigdis Nygaard, Eivind Hovig.
Nucleic Acids Res, 2006 Feb 14; 34(3). PMID: 16473852    Free PMC article.
Review.
On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes.
Lukas M Wick, Jean Marie Rouillard, +3 authors, Syed A Hashsham.
Nucleic Acids Res, 2006 Feb 16; 34(3). PMID: 16478712    Free PMC article.
GO-Diff: mining functional differentiation between EST-based transcriptomes.
Zuozhou Chen, Weilin Wang, +2 authors, Liangbiao Chen.
BMC Bioinformatics, 2006 Feb 17; 7. PMID: 16480524    Free PMC article.
Central nervous system drug development: an integrative biomarker approach toward individualized medicine.
B Gomez-Mancilla, E Marrer, +5 authors, M E Schmidt.
NeuroRx, 2006 Feb 21; 2(4). PMID: 16489375    Free PMC article.
Review.
Transcriptomic response to differentiation induction.
G W Patton, R Stephens, +5 authors, G Tudor.
BMC Bioinformatics, 2006 Mar 01; 7. PMID: 16503971    Free PMC article.
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation.
Donglin Liu, Joel H Graber.
BMC Bioinformatics, 2006 Mar 01; 7. PMID: 16503995    Free PMC article.
Determination of strongly overlapping signaling activity from microarray data.
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F Ochs.
BMC Bioinformatics, 2006 Mar 02; 7. PMID: 16507110    Free PMC article.
A multivariate prediction model for microarray cross-hybridization.
Yian A Chen, Cheng-Chung Chou, +5 authors, Jonas S Almeida.
BMC Bioinformatics, 2006 Mar 03; 7. PMID: 16509965    Free PMC article.
SimArray: a user-friendly and user-configurable microarray design tool.
Richard P Auburn, Roslin R Russell, +3 authors, Steven Russell.
BMC Bioinformatics, 2006 Mar 03; 7. PMID: 16509966    Free PMC article.
Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method.
Henrik Bengtsson, Ola Hössjer.
BMC Bioinformatics, 2006 Mar 03; 7. PMID: 16509971    Free PMC article.
A flexible representation of omic knowledge for thorough analysis of microarray data.
Yoshikazu Hasegawa, Motoaki Seki, +13 authors, Tetsuro Toyoda.
Plant Methods, 2006 Mar 03; 2. PMID: 16509996    Free PMC article.
Use of single-point genome signature tags as a universal tagging method for microbial genome surveys.
Daniel van der Lelie, Celine Lesaulnier, +3 authors, John Dunn.
Appl Environ Microbiol, 2006 Mar 07; 72(3). PMID: 16517658    Free PMC article.
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures.
Kevin A Greer, Matthew R McReynolds, Heddwen L Brooks, James B Hoying.
BMC Bioinformatics, 2006 Mar 18; 7. PMID: 16542461    Free PMC article.
The contributions of normal variation and genetic background to mammalian gene expression.
Colin Pritchard, David Coil, +2 authors, Peter S Nelson.
Genome Biol, 2006 Apr 06; 7(3). PMID: 16584536    Free PMC article.
A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray.
Danielle L Leiske, Anis Karimpour-Fard, +2 authors, Ryan T Gill.
BMC Genomics, 2006 Apr 06; 7. PMID: 16595014    Free PMC article.
Analysis of tag-position bias in MPSS technology.
Junfeng Chen, Magnus Rattray.
BMC Genomics, 2006 Apr 11; 7. PMID: 16603069    Free PMC article.
Novel susceptibility genes in inflammatory bowel disease.
Colin Noble, Elaine Nimmo, +2 authors, Jack Satsangi.
World J Gastroenterol, 2006 Apr 13; 12(13). PMID: 16610046    Free PMC article.
Review.
An antibody-based microarray assay for small RNA detection.
Zonglin Hu, Aixia Zhang, +2 authors, Stephen H Leppla.
Nucleic Acids Res, 2006 Apr 15; 34(7). PMID: 16614443    Free PMC article.
In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.
Sheng-Ying Pao, Win-Li Lin, Ming-Jing Hwang.
BMC Genomics, 2006 Apr 22; 7. PMID: 16626500    Free PMC article.
RCL2, a new fixative, preserves morphology and nucleic acid integrity in paraffin-embedded breast carcinoma and microdissected breast tumor cells.
Christophe Delfour, Pascal Roger, +7 authors, Nathalie Boulle.
J Mol Diagn, 2006 Apr 29; 8(2). PMID: 16645201    Free PMC article.
Genomic platforms for cancer research: potential diagnostic and prognostic applications in clinical oncology.
Pedro Jares, Elías Campo.
Clin Transl Oncol, 2006 May 02; 8(3). PMID: 16648115
Review.
Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray.
Xingming Lian, Shiping Wang, +7 authors, Qifa Zhang.
Plant Mol Biol, 2006 May 02; 60(5). PMID: 16649102
High-throughput three-dimensional gel electrophoresis for versatile utilities: a stacked slice-gel system for separation and reactions (4SR).
Md Salimullah, Masaki Mori, Koichi Nishigaki.
Genomics Proteomics Bioinformatics, 2006 May 13; 4(1). PMID: 16689699    Free PMC article.
Involvement of c-myc-regulated genes in hepatocellular carcinoma related to genotype-C hepatitis B virus.
Norio Iizuka, Ryouichi Tsunedomi, +8 authors, Masaaki Oka.
J Cancer Res Clin Oncol, 2006 May 17; 132(7). PMID: 16703398
Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes.
Valerie W Hu, Bryan C Frank, +2 authors, John Quackenbush.
BMC Genomics, 2006 May 20; 7. PMID: 16709250    Free PMC article.
Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors.
Igor Ponomarev, Rajani Maiya, +11 authors, R Adron Harris.
J Neurosci, 2006 May 26; 26(21). PMID: 16723524    Free PMC article.
Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach.
Yi-Shin Pan, Yun-Shien Lee, +2 authors, Sen-Yung Hsieh.
BMC Genomics, 2006 Jun 02; 7. PMID: 16737534    Free PMC article.
Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes?
Naftali Kaminski, Ivan O Rosas.
Proc Am Thorac Soc, 2006 Jun 02; 3(4). PMID: 16738198    Free PMC article.
Review.
The ABRF MARG microarray survey 2005: taking the pulse of the microarray field.
Kevin L Knudtson, Herbert Auer, +8 authors, Agnes Viale.
J Biomol Tech, 2006 Jun 03; 17(2). PMID: 16741246    Free PMC article.
Bioinformatic approach for understanding the heterogeneity of cholangiocytes.
Koji Fukushima, Yoshiyuki Ueno.
World J Gastroenterol, 2006 Jun 15; 12(22). PMID: 16773705    Free PMC article.
Review.
Design of a system for combined analysis of microarray-based gene expression and FlyBase-derived annotation in Drosophila.
Bormi Shin, Tian Zhao, Min Wu, Chaoyang Zeng.
AMIA Annu Symp Proc, 2006 Jun 17;. PMID: 16779400    Free PMC article.
Development and applications of microbial ecogenomic indicators for monitoring water quality: report of a workshop assessing the state of the science, research needs and future directions.
Richard Devereux, Parke Rublee, +2 authors, Jorge W Santo Domingo.
Environ Monit Assess, 2006 Jun 17; 116(1-3). PMID: 16779607
Genetic dissection of gene regulation in multiple mouse tissues.
Chris J Cotsapas, Rohan B H Williams, +4 authors, Peter F R Little.
Mamm Genome, 2006 Jun 20; 17(6). PMID: 16783630
Review.
Gene expression profiling analysis in nephrology: towards molecular definition of renal disease.
Yoshinari Yasuda, Clemens D Cohen, +2 authors, European Renal cDNA Bank (ERCB) Consortium.
Clin Exp Nephrol, 2006 Jun 23; 10(2). PMID: 16791393
Review.
cDNA array analysis for prediction of hepatic metastasis of colorectal carcinoma.
Osamu Takata, Yutaka J Kawamura, +5 authors, Toshihiko Tsukamoto.
Surg Today, 2006 Jun 24; 36(7). PMID: 16794795
Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray.
Bing Wang, Fuhua Li, +3 authors, Jianhai Xiang.
Mar Biotechnol (NY), 2006 Jun 24; 8(5). PMID: 16794954
Charging behavior of single-stranded DNA polyelectrolyte brushes.
Gang Shen, Napoleon Tercero, +3 authors, Rastislav Levicky.
J Am Chem Soc, 2006 Jun 29; 128(26). PMID: 16802807    Free PMC article.
Gene expression profiles during heat acclimation in Arabidopsis thaliana suspension-culture cells.
Chan Ju Lim, Kyung Ae Yang, +7 authors, Chae Oh Lim.
J Plant Res, 2006 Jun 30; 119(4). PMID: 16807682
Single cell gene expression profiling in Alzheimer's disease.
Stephen D Ginsberg, Shaoli Che, Scott E Counts, Elliott J Mufson.
NeuroRx, 2006 Jul 04; 3(3). PMID: 16815214    Free PMC article.
Review.
Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification.
Liyou Wu, Xueduan Liu, Christopher W Schadt, Jizhong Zhou.
Appl Environ Microbiol, 2006 Jul 06; 72(7). PMID: 16820490    Free PMC article.
Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films.
Dora Peelen, Voula Kodoyianni, +3 authors, Lloyd M Smith.
J Proteome Res, 2006 Jul 11; 5(7). PMID: 16823965    Free PMC article.
DNA microarray technologies for measuring protein-DNA interactions.
Martha L Bulyk.
Curr Opin Biotechnol, 2006 Jul 15; 17(4). PMID: 16839757    Free PMC article.
Review.
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis.
Johannes Rainer, Fatima Sanchez-Cabo, +2 authors, Zlatko Trajanoski.
Nucleic Acids Res, 2006 Jul 18; 34(Web Server issue). PMID: 16845058    Free PMC article.
Genome-wide approaches for identification of nuclear receptor target genes.
Luz E Tavera-Mendoza, Sylvie Mader, John H White.
Nucl Recept Signal, 2006 Jul 25; 4. PMID: 16862224    Free PMC article.
From functional genomics to functional immunomics: new challenges, old problems, big rewards.
Ulisses M Braga-Neto, Ernesto T A Marques.
PLoS Comput Biol, 2006 Jul 26; 2(7). PMID: 16863395    Free PMC article.
Review.
The end of the microarray Tower of Babel: will universal standards lead the way?
Ernest S Kawasaki.
J Biomol Tech, 2006 Jul 28; 17(3). PMID: 16870711    Free PMC article.
Review.
Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening.
Orly Alter, Gene H Golub.
Proc Natl Acad Sci U S A, 2006 Aug 01; 103(32). PMID: 16877539    Free PMC article.
Design of microarray experiments for genetical genomics studies.
Júlio S S Bueno Filho, Steven G Gilmour, Guilherme J M Rosa.
Genetics, 2006 Aug 05; 174(2). PMID: 16888340    Free PMC article.
Review.
Analysis of microarray experiments of gene expression profiling.
Adi L Tarca, Roberto Romero, Sorin Draghici.
Am J Obstet Gynecol, 2006 Aug 08; 195(2). PMID: 16890548    Free PMC article.
2005 Curt Stern Award address. Introductory speech for Patrick O. Brown.
Evan Eichler.
Am J Hum Genet, 2006 Aug 16; 79(3). PMID: 16909379    Free PMC article.
2005 Curt Stern Award address. Exploring along a crooked path.
Patrick O Brown.
Am J Hum Genet, 2006 Aug 16; 79(3). PMID: 16909380    Free PMC article.
Gene expression signatures and outcome prediction in mature B-cell malignancies.
Sandeep S Dave.
Curr Treat Options Oncol, 2006 Aug 19; 7(4). PMID: 16916486
Review.
The emergence and diffusion of DNA microarray technology.
Tim Lenoir, Eric Giannella.
J Biomed Discov Collab, 2006 Aug 24; 1. PMID: 16925816    Free PMC article.
Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs.
Yi Huang, Lida Zhang, +6 authors, Qifa Zhang.
Plant Mol Biol, 2006 Aug 31; 62(4-5). PMID: 16941221
Automatic layout and visualization of biclusters.
Gregory A Grothaus, Adeel Mufti, T M Murali.
Algorithms Mol Biol, 2006 Sep 06; 1. PMID: 16952321    Free PMC article.
Difference of gene expression profiles between Barrett's esophagus and cardia intestinal metaplasia by gene chip.
Ying Chang, Bin Liu.
J Huazhong Univ Sci Technolog Med Sci, 2006 Sep 12; 26(3). PMID: 16961278
Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions.
M T Horne, D J Fish, A S Benight.
Biophys J, 2006 Sep 12; 91(11). PMID: 16963510    Free PMC article.
Unraveling the dynamic transcriptome.
Siobhan M Brady, Terri A Long, Philip N Benfey.
Plant Cell, 2006 Sep 14; 18(9). PMID: 16968906    Free PMC article.
Review.
Gene expression profiling of human ovarian tumours.
S Biade, M Marinucci, +6 authors, S W Johnson.
Br J Cancer, 2006 Sep 14; 95(8). PMID: 16969345    Free PMC article.
AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.
Guohong Hu, Hui-Yun Wang, +8 authors, Honghua Li.
Nucleic Acids Res, 2006 Sep 20; 34(17). PMID: 16982644    Free PMC article.
Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.
N Yalamanchili, D E Zak, +3 authors, B N Kholodenko.
Syst Biol (Stevenage), 2006 Sep 22; 153(4). PMID: 16986625    Free PMC article.
State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling.
Mark Sevecka, Gavin MacBeath.
Nat Methods, 2006 Sep 23; 3(10). PMID: 16990815    Free PMC article.
Nanoliter high throughput quantitative PCR.
Tom Morrison, James Hurley, +9 authors, Colin J H Brenan.
Nucleic Acids Res, 2006 Sep 27; 34(18). PMID: 17000636    Free PMC article.
Genes involved in neuroendocrine tumor biology.
Eva Hofsli.
Pituitary, 2006 Sep 27; 9(3). PMID: 17001466
Review.
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen.
BMC Bioinformatics, 2006 Oct 03; 7. PMID: 17010188    Free PMC article.
Whole genome expression analysis for biologic rational pathway modeling: application in cancer prognosis and therapy prediction.
D Kemming, U Vogt, +11 authors, B Brandt.
Mol Diagn Ther, 2006 Oct 07; 10(5). PMID: 17022690
Review.
Effects of THBS3, SPARC and SPP1 expression on biological behavior and survival in patients with osteosarcoma.
Cristiane A Dalla-Torre, Maisa Yoshimoto, +7 authors, Jeremy A Squire.
BMC Cancer, 2006 Oct 07; 6. PMID: 17022822    Free PMC article.
A Fisheye Viewer for microarray-based gene expression data.
Min Wu, Cheng Thao, Xiangming Mu, Ethan V Munson.
BMC Bioinformatics, 2006 Oct 14; 7. PMID: 17038193    Free PMC article.
Solid-phase translation and RNA-protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA.
Manish Biyani, Yuzuru Husimi, Naoto Nemoto.
Nucleic Acids Res, 2006 Oct 26; 34(20). PMID: 17062621    Free PMC article.
Profile of Gene E. Robinson.
Nick Zagorski.
Proc Natl Acad Sci U S A, 2006 Oct 27; 103(44). PMID: 17065325    Free PMC article.
Incorporating genome-scale tools for studying energy homeostasis.
R Michael Raab.
Nutr Metab (Lond), 2006 Nov 04; 3. PMID: 17081308    Free PMC article.
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression.
Rodrigo Malig, Cristian Varela, Eduardo Agosin, Francisco Melo.
BMC Bioinformatics, 2006 Nov 07; 7. PMID: 17083742    Free PMC article.
Transcriptome analysis reveals a critical role of CHS7 and CHS8 genes for isoflavonoid synthesis in soybean seeds.
Sangeeta Dhaubhadel, Mark Gijzen, Pat Moy, Mana Farhangkhoee.
Plant Physiol, 2006 Nov 14; 143(1). PMID: 17098860    Free PMC article.
ProCAT: a data analysis approach for protein microarrays.
Xiaowei Zhu, Mark Gerstein, Michael Snyder.
Genome Biol, 2006 Nov 18; 7(11). PMID: 17109749    Free PMC article.
Gene expression profiling following constitutive activation of MEK1 and transformation of rat intestinal epithelial cells.
Koga Komatsu, F Gregory Buchanan, +5 authors, Raymond N Dubois.
Mol Cancer, 2006 Nov 23; 5. PMID: 17112382    Free PMC article.
CoXpress: differential co-expression in gene expression data.
Michael Watson.
BMC Bioinformatics, 2006 Nov 23; 7. PMID: 17116249    Free PMC article.
Expression profiling of drug response--from genes to pathways.
Ralf Herwig, Hans Lehrach.
Dialogues Clin Neurosci, 2006 Nov 23; 8(3). PMID: 17117610    Free PMC article.
Review.
Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions.
Tao Han, Cathy D Melvin, +5 authors, James C Fuscoe.
BMC Bioinformatics, 2006 Nov 23; 7 Suppl 2. PMID: 17118138    Free PMC article.
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists.
Lei Guo, Hong Fang, +8 authors, Yvonne P Dragan.
BMC Bioinformatics, 2006 Nov 23; 7 Suppl 2. PMID: 17118139    Free PMC article.
Protein microarray technology.
David A Hall, Jason Ptacek, Michael Snyder.
Mech Ageing Dev, 2006 Nov 28; 128(1). PMID: 17126887    Free PMC article.
Review.
Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer.
Kenji Kinoshita, Kentaro Fujimoto, +13 authors, Kenichi Matsubara.
Nucleic Acids Res, 2006 Dec 01; 35(1). PMID: 17135189    Free PMC article.
The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.
Owen Z Woody, Robert Nadon.
Source Code Biol Med, 2006 Dec 07; 1. PMID: 17147786    Free PMC article.
Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.
Malali Gowda, R C Venu, +10 authors, Guo-Liang Wang.
BMC Genomics, 2006 Dec 13; 7. PMID: 17156450    Free PMC article.
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
Haiyuan Yu, Katherine Nguyen, +4 authors, Mark Gerstein.
Nucleic Acids Res, 2006 Dec 13; 35(2). PMID: 17158151    Free PMC article.
Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli.
Eric Guisbert, Virgil A Rhodius, +2 authors, Carol A Gross.
J Bacteriol, 2006 Dec 13; 189(5). PMID: 17158661    Free PMC article.
Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species.
Hyeon-Se Lee, Jianlin Wang, +11 authors, Z Jeffrey Chen.
Plant Biotechnol J, 2006 Dec 15; 2(1). PMID: 17166142    Free PMC article.
Target discovery and validation in pancreatic cancer.
Robert M Beaty, Mads Gronborg, Jonathan R Pollack, Anirban Maitra.
Methods Mol Biol, 2006 Dec 19; 360. PMID: 17172725    Free PMC article.
Review.
DNA microarrays in herbal drug research.
Preeti Chavan, Kalpana Joshi, Bhushan Patwardhan.
Evid Based Complement Alternat Med, 2006 Dec 19; 3(4). PMID: 17173108    Free PMC article.
Probe selection and expression index computation of Affymetrix Exon Arrays.
Yi Xing, Karen Kapur, Wing Hung Wong.
PLoS One, 2006 Dec 22; 1. PMID: 17183719    Free PMC article.
Label-free detection of biomolecules on microarrays using surface-colloid interaction.
Ye Sun, K Bruce Jacobson, Val Golovlev.
Anal Biochem, 2006 Dec 23; 361(2). PMID: 17184721    Free PMC article.
Genetic stock identification of chum salmon in the Bering Sea and North Pacific Ocean using mitochondrial DNA microarray.
Shogo Moriya, Shunpei Sato, +4 authors, Syuiti Abe.
Mar Biotechnol (NY), 2006 Dec 23; 9(2). PMID: 17186428
Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses.
Kristine Kleivi, Guro E Lind, +8 authors, Ragnhild A Lothe.
Mol Cancer, 2007 Jan 05; 6. PMID: 17201907    Free PMC article.
Microarray-based analysis of ventilator-induced lung injury.
Mark M Wurfel.
Proc Am Thorac Soc, 2007 Jan 05; 4(1). PMID: 17202295    Free PMC article.
Review.
Global gene expression profiling of preimplantation embryos.
Toshio Hamatani, Minoru Sh Ko, +7 authors, Yasunori Yoshimura.
Hum Cell, 2007 Jan 06; 19(3). PMID: 17204093
Review.
Determination of the minimum number of microarray experiments for discovery of gene expression patterns.
Fang-Xiang Wu, W J Zhang, Anthony J Kusalik.
BMC Bioinformatics, 2007 Jan 16; 7 Suppl 4. PMID: 17217505    Free PMC article.
The impact of sample imbalance on identifying differentially expressed genes.
Kun Yang, Jianzhong Li, Hong Gao.
BMC Bioinformatics, 2007 Jan 16; 7 Suppl 4. PMID: 17217526    Free PMC article.
Enhancement of the synthesis of RpoN, Cra, and H-NS by polyamines at the level of translation in Escherichia coli cultured with glucose and glutamate.
Yusuke Terui, Kyohei Higashi, +6 authors, Kazuei Igarashi.
J Bacteriol, 2007 Jan 16; 189(6). PMID: 17220219    Free PMC article.
An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta.
John Wang, Stephanie Jemielity, +3 authors, Laurent Keller.
Genome Biol, 2007 Jan 17; 8(1). PMID: 17224046    Free PMC article.
Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile.
Paolo Fardin, Stefano Moretti, +3 authors, Luigi Varesio.
BMC Genomics, 2007 Jan 19; 8. PMID: 17229315    Free PMC article.
Component retention in principal component analysis with application to cDNA microarray data.
Richard Cangelosi, Alain Goriely.
Biol Direct, 2007 Jan 19; 2. PMID: 17229320    Free PMC article.
Identification of the differential expressive tumor associated genes in rectal cancers by cDNA microarray.
Xue-Qin Gao, Jin-Xiang Han, +3 authors, Hai-Yan Huang.
World J Gastroenterol, 2007 Jan 19; 13(3). PMID: 17230600    Free PMC article.
Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory.
Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J Ortoleva.
BMC Bioinformatics, 2007 Jan 25; 8. PMID: 17244365    Free PMC article.
Development and applications of a BRAF oligonucleotide microarray.
Il-Jin Kim, Hio Chung Kang, +3 authors, Jae-Gahb Park.
J Mol Diagn, 2007 Jan 26; 9(1). PMID: 17251336    Free PMC article.
Total syntheses, fragmentation studies, and antitumor/antiproliferative activities of FR901464 and its low picomolar analogue.
Brian J Albert, Ananthapadmanabhan Sivaramakrishnan, +2 authors, Kazunori Koide.
J Am Chem Soc, 2007 Feb 07; 129(9). PMID: 17279752    Free PMC article.
Analysis of the quality of contact-pin fabricated oligonucleotide microarrays.
Amy X Yang, Josef Mejido, +4 authors, Raj K Puri.
Mol Biotechnol, 2007 Feb 08; 34(3). PMID: 17284778
Expression of ectonucleotide pyrophosphate phosphodiesterase and peroxisome proliferator activated receptor gamma in morbidly obese patients.
Fred Brody, Sarah Hill, +4 authors, Sidney Fu.
Surg Endosc, 2007 Feb 09; 21(6). PMID: 17287921
Protein binding microarrays for the characterization of DNA-protein interactions.
Martha L Bulyk.
Adv Biochem Eng Biotechnol, 2007 Feb 13; 104. PMID: 17290819    Free PMC article.
Review.
Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose.
Orianne Cholet, Alain Hénaut, Serge Casaregola, Pascal Bonnarme.
Appl Environ Microbiol, 2007 Feb 20; 73(8). PMID: 17308183    Free PMC article.
From bytes to bedside: data integration and computational biology for translational cancer research.
Jomol P Mathew, Barry S Taylor, +6 authors, Bud Mishra.
PLoS Comput Biol, 2007 Feb 27; 3(2). PMID: 17319736    Free PMC article.
Review.
Analysis of time-series gene expression data: methods, challenges, and opportunities.
I P Androulakis, E Yang, R R Almon.
Annu Rev Biomed Eng, 2007 Mar 08; 9. PMID: 17341157    Free PMC article.
Unravelling microbial communities with DNA-microarrays: challenges and future directions.
Michael Wagner, Hauke Smidt, Alexander Loy, Jizhong Zhou.
Microb Ecol, 2007 Mar 09; 53(3). PMID: 17345135
Review.
Network-based prediction of protein function.
Roded Sharan, Igor Ulitsky, Ron Shamir.
Mol Syst Biol, 2007 Mar 14; 3. PMID: 17353930    Free PMC article.
Highly Cited. Review.
Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line.
Abdelnaby Khalyfa, Timothy Chlon, +2 authors, Nigel G F Cooper.
Mol Vis, 2007 Mar 16; 13. PMID: 17356516    Free PMC article.
Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat.
Rebecca Poole, Gary Barker, +2 authors, Keith J Edwards.
Funct Integr Genomics, 2007 Mar 17; 7(3). PMID: 17364174
Including probe-level uncertainty in model-based gene expression clustering.
Xuejun Liu, Kevin K Lin, Bogi Andersen, Magnus Rattray.
BMC Bioinformatics, 2007 Mar 23; 8. PMID: 17376221    Free PMC article.
Advances in swine transcriptomics.
Christopher K Tuggle, Yanfang Wang, Oliver Couture.
Int J Biol Sci, 2007 Mar 27; 3(3). PMID: 17384733    Free PMC article.
Review.
Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis.
Gulisa Turashvili, Jan Bouchal, +10 authors, Zdenek Kolar.
BMC Cancer, 2007 Mar 29; 7. PMID: 17389037    Free PMC article.
Highly Cited.
Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.
Nader Pourmand, Stefano Caramuta, +4 authors, Ronald W Davis.
Proc Natl Acad Sci U S A, 2007 Mar 29; 104(15). PMID: 17389407    Free PMC article.
Sex differences in lumbar spinal cord gene expression following experimental lumbar radiculopathy.
Michael L LaCroix-Fralish, Vivianne L Tawfik, Kevin F Spratt, Joyce A DeLeo.
J Mol Neurosci, 2007 Apr 03; 30(3). PMID: 17401154
Transcriptome analysis in response to heat shock and cadmium in the aquatic fungus Blastocladiella emersonii.
Raphaela C Georg, Suely L Gomes.
Eukaryot Cell, 2007 Apr 24; 6(6). PMID: 17449658    Free PMC article.
Discovery of tissue-specific exons using comprehensive human exon microarrays.
Tyson A Clark, Anthony C Schweitzer, +5 authors, John E Blume.
Genome Biol, 2007 Apr 26; 8(4). PMID: 17456239    Free PMC article.
Highly Cited.
Comparative analysis of human conjunctival and corneal epithelial gene expression with oligonucleotide microarrays.
Helen C Turner, Murat T Budak, M A Murat Akinci, J Mario Wolosin.
Invest Ophthalmol Vis Sci, 2007 Apr 27; 48(5). PMID: 17460260    Free PMC article.
Construction and analysis of tree models for chromosomal classification of diffuse large B-cell lymphomas.
Hui-Yong Jiang, Zhong-Xi Huang, +2 authors, Tong Zhao.
World J Gastroenterol, 2007 Apr 28; 13(11). PMID: 17461480    Free PMC article.
A search engine to identify pathway genes from expression data on multiple organisms.
Chunnuan Chen, Matthew T Weirauch, +2 authors, Joshua M Stuart.
BMC Syst Biol, 2007 May 05; 1. PMID: 17477880    Free PMC article.
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.
Jüri Reimand, Meelis Kull, +2 authors, Jaak Vilo.
Nucleic Acids Res, 2007 May 05; 35(Web Server issue). PMID: 17478515    Free PMC article.
Highly Cited.
High-throughput, high-sensitivity analysis of gene expression in Arabidopsis.
Richard Martin Kris, Stephen Felder, +6 authors, David W Galbraith.
Plant Physiol, 2007 May 15; 144(3). PMID: 17496109    Free PMC article.
Tilescope: online analysis pipeline for high-density tiling microarray data.
Zhengdong D Zhang, Joel Rozowsky, +3 authors, Mark Gerstein.
Genome Biol, 2007 May 16; 8(5). PMID: 17501994    Free PMC article.
Exon arrays provide accurate assessments of gene expression.
Karen Kapur, Yi Xing, Zhengqing Ouyang, Wing Hung Wong.
Genome Biol, 2007 May 17; 8(5). PMID: 17504534    Free PMC article.
Large-scale clustering of CAGE tag expression data.
Kazuro Shimokawa, Yuko Okamura-Oho, +4 authors, Yoshihide Hayashizaki.
BMC Bioinformatics, 2007 May 23; 8. PMID: 17517134    Free PMC article.
RNA quality in frozen breast cancer samples and the influence on gene expression analysis--a comparison of three evaluation methods using microcapillary electrophoresis traces.
Carina Strand, Johan Enell, Ingrid Hedenfalk, Mårten Fernö.
BMC Mol Biol, 2007 May 24; 8. PMID: 17519006    Free PMC article.
A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.
Carlos J Paredes, Ryan S Senger, +3 authors, Eleftherios T Papoutsakis.
Appl Environ Microbiol, 2007 May 29; 73(14). PMID: 17526797    Free PMC article.
A simple and rapid method for preserving RNA of aquatic invertebrates for ecotoxicogenomics.
Lars-Henrik Heckmann, Anthony Bouetard, +2 authors, Amanda Callaghan.
Ecotoxicology, 2007 May 29; 16(6). PMID: 17530397
Bottleneck genes and community structure in the cell cycle network of S. pombe.
Cécile Caretta-Cartozo, Paolo De Los Rios, Francesco Piazza, Pietro Liò.
PLoS Comput Biol, 2007 Jun 05; 3(6). PMID: 17542643    Free PMC article.
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease.
Yue Lu, Xin He, Sheng Zhong.
Nucleic Acids Res, 2007 Jun 05; 35(Web Server issue). PMID: 17545194    Free PMC article.
Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells.
Katia Margiotti, Latif A Wafa, +3 authors, Paul S Rennie.
Mol Cancer, 2007 Jun 08; 6. PMID: 17553164    Free PMC article.
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.
Fang Liu, Tor-Kristian Jenssen, +5 authors, Winston Patrick Kuo.
BMC Genomics, 2007 Jun 09; 8. PMID: 17555589    Free PMC article.
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen.
BMC Bioinformatics, 2007 Jun 15; 8. PMID: 17559637    Free PMC article.
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches.
Victor X Jin, Henriette O'Geen, +2 authors, Peggy J Farnham.
Genome Res, 2007 Jun 15; 17(6). PMID: 17567999    Free PMC article.
Orthogonal projections to latent structures as a strategy for microarray data normalization.
Max Bylesjö, Daniel Eriksson, +3 authors, Johan Trygg.
BMC Bioinformatics, 2007 Jun 20; 8. PMID: 17577396    Free PMC article.
iGentifier: indexing and large-scale profiling of unknown transcriptomes.
Achim Fischer, Alistair Lenhard, +11 authors, Leo Gaelweiler.
Nucleic Acids Res, 2007 Jun 27; 35(14). PMID: 17591615    Free PMC article.
A perspective on DNA microarrays in pathology research and practice.
Jonathan R Pollack.
Am J Pathol, 2007 Jun 30; 171(2). PMID: 17600117    Free PMC article.
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.
Miika Ahdesmäki, Harri Lähdesmäki, +2 authors, Olli Yli-Harja.
BMC Bioinformatics, 2007 Jul 04; 8. PMID: 17605777    Free PMC article.
Performance characteristics of 65-mer oligonucleotide microarrays.
Myoyong Lee, Charlie C Xiang, Jeffrey M Trent, Michael L Bittner.
Anal Biochem, 2007 Jul 10; 368(1). PMID: 17617369    Free PMC article.
Simcluster: clustering enumeration gene expression data on the simplex space.
Ricardo Z N Vêncio, Leonardo Varuzza, +2 authors, Ilya Shmulevich.
BMC Bioinformatics, 2007 Jul 13; 8. PMID: 17625017    Free PMC article.
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
Anthony R Borneman, Zhengdong D Zhang, +3 authors, Michael Snyder.
Funct Integr Genomics, 2007 Jul 20; 7(4). PMID: 17638031
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface.
Nikoleta Dupl'áková, David Renák, +3 authors, David Honys.
BMC Plant Biol, 2007 Jul 25; 7. PMID: 17645793    Free PMC article.
Difference in gene expression of macrophage between normal spleen and portal hypertensive spleen identified by cDNA microarray.
Feng Yan, Xiao-Min Wang.
World J Gastroenterol, 2007 Jul 31; 13(24). PMID: 17659678    Free PMC article.
Gene expression profile analyses of mice livers injured by Leigongteng.
Yong Chen, Xiao-Ming Zhang, +2 authors, Qi-Song Xia.
World J Gastroenterol, 2007 Jul 31; 13(26). PMID: 17659714    Free PMC article.
Effects of water-deficit stress on the transcriptomes of developing immature ear and tassel in maize.
Yunlong Zhuang, Guijie Ren, +5 authors, Juren Zhang.
Plant Cell Rep, 2007 Aug 02; 26(12). PMID: 17668218
Nanotechnologies applied to the analysis of the animal genome.
P Ajmone Marsan, S Tramontana, R Mazza.
Vet Res Commun, 2007 Oct 10; 31 Suppl 1. PMID: 17682864
Mapping the genome landscape using tiling array technology.
Junshi Yazaki, Brian D Gregory, Joseph R Ecker.
Curr Opin Plant Biol, 2007 Aug 21; 10(5). PMID: 17703988    Free PMC article.
Review.
Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine.
Seung Pil Pack, Nagendra Kumar Kamisetty, +6 authors, Keisuke Makino.
Nucleic Acids Res, 2007 Aug 24; 35(17). PMID: 17715142    Free PMC article.
Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought.
Nitin L Mantri, Rebecca Ford, Tristan E Coram, Edwin C K Pang.
BMC Genomics, 2007 Sep 04; 8. PMID: 17764573    Free PMC article.
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages.
Laurent Bianchetti, Yan Wu, +2 authors, Olivier Poch.
Nucleic Acids Res, 2007 Sep 22; 35(18). PMID: 17884916    Free PMC article.
Saccharomyces cerevisiae: a versatile eukaryotic system in virology.
Rui P Galao, Nicoletta Scheller, +3 authors, Juana Díez.
Microb Cell Fact, 2007 Oct 12; 6. PMID: 17927824    Free PMC article.
Harnessing naturally randomized transcription to infer regulatory relationships among genes.
Lin S Chen, Frank Emmert-Streib, John D Storey.
Genome Biol, 2007 Oct 13; 8(10). PMID: 17931418    Free PMC article.
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.
Bernd Bodenmiller, Johan Malmstrom, +11 authors, Ruedi Aebersold.
Mol Syst Biol, 2007 Oct 18; 3. PMID: 17940529    Free PMC article.
Review.
A comprehensive genetic characterization of bacterial motility.
Hany S Girgis, Yirchung Liu, William S Ryu, Saeed Tavazoie.
PLoS Genet, 2007 Oct 19; 3(9). PMID: 17941710    Free PMC article.
Highly Cited.
How many genes are needed to make a pollen tube? Lessons from transcriptomics.
Jörg D Becker, José A Feijó.
Ann Bot, 2007 Oct 24; 100(6). PMID: 17951360    Free PMC article.
Growing functional modules from a seed protein via integration of protein interaction and gene expression data.
Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos.
BMC Bioinformatics, 2007 Oct 25; 8. PMID: 17956603    Free PMC article.
A universal framework for regulatory element discovery across all genomes and data types.
Olivier Elemento, Noam Slonim, Saeed Tavazoie.
Mol Cell, 2007 Oct 30; 28(2). PMID: 17964271    Free PMC article.
Highly Cited.
Functional genomics in radiation biology: a gateway to cellular systems-level studies.
Sally A Amundson.
Radiat Environ Biophys, 2007 Nov 02; 47(1). PMID: 17973116
Review.
Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender.
Xiangru Xu, Ming Zhan, +12 authors, Mark P Mattson.
Genome Biol, 2007 Nov 09; 8(11). PMID: 17988385    Free PMC article.
Novel translational strategies in colorectal cancer research.
Ignacio Gil-Bazo.
World J Gastroenterol, 2007 Nov 09; 13(44). PMID: 17990355    Free PMC article.
Review.
A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis.
Junfeng Chen, Vikas Agrawal, +5 authors, Blake C Meyers.
BMC Genomics, 2007 Nov 14; 8. PMID: 17997849    Free PMC article.
Investigation of DNA-protein sequence-specific interactions with a ds-DNA array.
Yunfei Bai, Qinyu Ge, +3 authors, Zuhong Lu.
Molecules, 2007 Nov 17; 10(2). PMID: 18007313    Free PMC article.
A tetrafluorophenyl activated ester self-assembled monolayer for the immobilization of amine-modified oligonucleotides.
Matthew R Lockett, Margaret F Phillips, +2 authors, Lloyd M Smith.
Langmuir, 2007 Dec 01; 24(1). PMID: 18047381    Free PMC article.
Differential gene expression profiles in acute hepatic failure model in mice infected with MHV-3 virus intervened by anti-hepatic failure compound.
Jiaquan Huang, Fei Xiao, +3 authors, Qin Ning.
J Huazhong Univ Sci Technolog Med Sci, 2007 Dec 07; 27(5). PMID: 18060630
Quantification of global transcription patterns in prokaryotes using spotted microarrays.
Ben Sidders, Mike Withers, +10 authors, Neil G Stoker.
Genome Biol, 2007 Dec 15; 8(12). PMID: 18078514    Free PMC article.
The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects.
Z Jeffrey Chen, Jianlin Wang, +15 authors, Thomas C Osborn.
Biol J Linn Soc Lond, 2007 Dec 15; 82(4). PMID: 18079994    Free PMC article.
Mosquito transcriptome changes and filarial worm resistance in Armigeres subalbatus.
Matthew T Aliota, Jeremy F Fuchs, +2 authors, Bruce M Christensen.
BMC Genomics, 2007 Dec 20; 8. PMID: 18088420    Free PMC article.
Expression profiling of microRNA using oligo DNA arrays.
Chang-Gong Liu, Riccardo Spizzo, George Adrian Calin, Carlo Maria Croce.
Methods, 2007 Dec 26; 44(1). PMID: 18158129    Free PMC article.
Review.
Evaluation of gene expression profiling in a mouse model of L-gulonolactone oxidase gene deficiency.
Jian Yan, Yan Jiao, +4 authors, Weikuan Gu.
Genet Mol Biol, 2008 Jan 03; 30(2). PMID: 18167513    Free PMC article.
Genome-wide microarray expression analysis of CD4+ T Cells from nonobese diabetic congenic mice identifies Cd55 (Daf1) and Acadl as candidate genes for type 1 diabetes.
Junichiro Irie, Brian Reck, +5 authors, William M Ridgway.
J Immunol, 2008 Jan 08; 180(2). PMID: 18178847    Free PMC article.
A highly sensitive and specific system for large-scale gene expression profiling.
Guohong Hu, Qifeng Yang, +4 authors, Honghua Li.
BMC Genomics, 2008 Jan 12; 9. PMID: 18186939    Free PMC article.
In silico approach to identify the expression of the undiscovered molecules from microarray public database: identification of odorant receptors expressed in non-olfactory tissues.
Atsuhiko Ichimura, Tadashi Kadowaki, +3 authors, Gozoh Tsujimoto.
Naunyn Schmiedebergs Arch Pharmacol, 2008 Jan 30; 377(2). PMID: 18228002
A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging.
Jeremy A Miller, Michael C Oldham, Daniel H Geschwind.
J Neurosci, 2008 Feb 08; 28(6). PMID: 18256261    Free PMC article.
Highly Cited.
Magnetic assembly of high-density DNA arrays for genomic analyses.
Kristopher D Barbee, Xiaohua Huang.
Anal Chem, 2008 Feb 12; 80(6). PMID: 18260655    Free PMC article.
'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups.
Akihiro Ohkubo, Rintaro Kasuya, +8 authors, Mitsuo Sekine.
Nucleic Acids Res, 2008 Feb 15; 36(6). PMID: 18272535    Free PMC article.
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas.
Kartik M Mani, Celine Lefebvre, +4 authors, Andrea Califano.
Mol Syst Biol, 2008 Feb 16; 4. PMID: 18277385    Free PMC article.
Highly Cited.
Covalent attachment of functional protein to polymer surfaces: a novel one-step dry process.
Christopher MacDonald, Richard Morrow, Anthony S Weiss, Marcela M M Bilek.
J R Soc Interface, 2008 Feb 21; 5(23). PMID: 18285286    Free PMC article.
Modeling transcriptome based on transcript-sampling data.
Jiang Zhu, Fuhong He, Jing Wang, Jun Yu.
PLoS One, 2008 Feb 21; 3(2). PMID: 18286206    Free PMC article.
A technique of mRNA extraction and labeling from circulating lymphocytes of children treated with growth hormone replacement therapy for microarray analysis.
M Camilot, F Teofoli, +4 authors, L Tatò.
J Endocrinol Invest, 2008 Feb 26; 31(1). PMID: 18296898
Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature.
Jeyakumar Natarajan, Jawahar Ganapathy.
Bioinformation, 2008 Feb 29; 2(5). PMID: 18305827    Free PMC article.
Finding distinct biclusters from background in gene expression matrices.
Zhengpeng Wu, Jiangni Ao, Xuegong Zhang.
Bioinformation, 2008 Feb 29; 2(5). PMID: 18305830    Free PMC article.
Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster.
Wensheng Zhang, Sige Zou, Jiuzhou Song.
BMC Bioinformatics, 2008 Mar 01; 9. PMID: 18307794    Free PMC article.
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays.
Shu-Hwa Chen, Chen-Zen Lo, +2 authors, Chung-Yen Lin.
BMC Bioinformatics, 2008 Mar 20; 9 Suppl 1. PMID: 18315861    Free PMC article.
Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments.
Hongya Zhao, Kwok-Leung Chan, Lee-Ming Cheng, Hong Yan.
BMC Bioinformatics, 2008 Mar 20; 9 Suppl 1. PMID: 18315862    Free PMC article.
Cells by design: a mini-review of targeting cell engineering using DNA microarrays.
Pratik Jaluria, Chia Chu, Michael Betenbaugh, Joseph Shiloach.
Mol Biotechnol, 2008 Mar 11; 39(2). PMID: 18327555
Review.
Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases.
Heiko Kuhn, Maxim D Frank-Kamenetskii.
Nucleic Acids Res, 2008 Mar 18; 36(7). PMID: 18344522    Free PMC article.
A dual-tag microarray platform for high-performance nucleic acid and protein analyses.
Olle Ericsson, Jonas Jarvius, +7 authors, Ulf Landegren.
Nucleic Acids Res, 2008 Mar 19; 36(8). PMID: 18346972    Free PMC article.
Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana.
Han-Hua Liu, Xin Tian, +2 authors, Cheng-Chao Zheng.
RNA, 2008 Mar 22; 14(5). PMID: 18356539    Free PMC article.
Highly Cited.
Integrating global gene expression analysis and genetics.
Charles R Farber, Aldons J Lusis.
Adv Genet, 2008 Mar 25; 60. PMID: 18358333    Free PMC article.
Review.
Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes.
Alison V Nairn, William S York, +3 authors, Kelley W Moremen.
J Biol Chem, 2008 Apr 16; 283(25). PMID: 18411279    Free PMC article.
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization.
Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu, Alan Wee-Chung Liew.
BMC Bioinformatics, 2008 Apr 25; 9. PMID: 18433478    Free PMC article.
Complex genetics of obesity in mouse models.
Daniel Pomp, Derrick Nehrenberg, Daria Estrada-Smith.
Annu Rev Nutr, 2008 Apr 26; 28. PMID: 18435591    Free PMC article.
Review.
M-BISON: microarray-based integration of data sources using networks.
Bernie J Daigle, Russ B Altman.
BMC Bioinformatics, 2008 Apr 29; 9. PMID: 18439292    Free PMC article.
Gene expression profiling of non-small cell lung cancer.
Sunil Singhal, Daniel Miller, Suresh Ramalingam, Shi-Yong Sun.
Lung Cancer, 2008 Apr 29; 60(3). PMID: 18440087    Free PMC article.
Review.
A copula method for modeling directional dependence of genes.
Jong-Min Kim, Yoon-Sung Jung, +3 authors, Insuk Sohn.
BMC Bioinformatics, 2008 May 02; 9. PMID: 18447957    Free PMC article.
Making a new technology work: the standardization and regulation of microarrays.
Susan Rogers, Alberto Cambrosio.
Yale J Biol Med, 2008 May 02; 80(4). PMID: 18449388    Free PMC article.
Review.
Clinical uses of microarrays in cancer research.
Carl Virtanen, James Woodgett.
Methods Mol Med, 2008 May 06; 141. PMID: 18453086    Free PMC article.
Review.
Bayesian hierarchical model for estimating gene expression intensity using multiple scanned microarrays.
Rashi Gupta, Elja Arjas, +2 authors, Petri Auvinen.
EURASIP J Bioinform Syst Biol, 2008 May 10;. PMID: 18464926    Free PMC article.
Predictive behavior within microbial genetic networks.
Ilias Tagkopoulos, Yir-Chung Liu, Saeed Tavazoie.
Science, 2008 May 10; 320(5881). PMID: 18467556    Free PMC article.
Highly Cited.
Wiring and volume transmission in rat amygdala. Implications for fear and anxiety.
Miguel Pérez de la Mora, Kirsten X Jacobsen, +2 authors, Kjell Fuxe.
Neurochem Res, 2008 May 14; 33(8). PMID: 18473172
Assessment of gene expression in many samples using vertical arrays.
Rosa Ana Risques, Gaelle Rondeau, +2 authors, John Welsh.
Nucleic Acids Res, 2008 May 14; 36(10). PMID: 18474526    Free PMC article.
Electromagnetic field change the expression of osteogenesis genes in murine bone marrow mesenchymal stem cells.
Dongming Zhao, Hua Wu, +2 authors, Chaoxiong Tao.
J Huazhong Univ Sci Technolog Med Sci, 2008 May 16; 28(2). PMID: 18480985
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches.
Daniel Aguilar, Lucy Skrabanek, +2 authors, Fabien Campagne.
Nucleic Acids Res, 2008 May 17; 36(11). PMID: 18483083    Free PMC article.
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method.
Mio Oshikawa, Yoshiko Sugai, +3 authors, Seishi Kato.
DNA Res, 2008 May 20; 15(3). PMID: 18487259    Free PMC article.
GEPAS, a web-based tool for microarray data analysis and interpretation.
Joaquín Tárraga, Ignacio Medina, +11 authors, Joaquín Dopazo.
Nucleic Acids Res, 2008 May 30; 36(Web Server issue). PMID: 18508806    Free PMC article.
Click chemistry, a powerful tool for pharmaceutical sciences.
Christopher D Hein, Xin-Ming Liu, Dong Wang.
Pharm Res, 2008 May 30; 25(10). PMID: 18509602    Free PMC article.
Review.
Exploiting orthologue diversity for systematic detection of gain-of-function phenotypes.
Maria Luisa Martelli, Claudio Isella, +3 authors, Enzo Medico.
BMC Genomics, 2008 May 31; 9. PMID: 18510758    Free PMC article.
Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice.
Jeremy D Edwards, Jaroslav Janda, +4 authors, David W Galbraith.
Plant Methods, 2008 May 31; 4. PMID: 18510771    Free PMC article.
Validation of oligoarrays for quantitative exploration of the transcriptome.
Vigdis Nygaard, Fang Liu, +9 authors, Heidi Lyng.
BMC Genomics, 2008 Jun 03; 9. PMID: 18513391    Free PMC article.
Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells.
Tatiana Subkhankulova, Michael J Gilchrist, Frederick J Livesey.
BMC Genomics, 2008 Jun 05; 9. PMID: 18522723    Free PMC article.
Label-free and dynamic detection of biomolecular interactions for high-throughput microarray applications.
Emre Ozkumur, James W Needham, +5 authors, M Selim Unlü.
Proc Natl Acad Sci U S A, 2008 Jun 05; 105(23). PMID: 18523019    Free PMC article.
Comparison of gene expression profiles of Fenneropenaeus chinensis challenged with WSSV and Vibrio.
Bing Wang, Fuhua Li, +6 authors, Jianhai Xiang.
Mar Biotechnol (NY), 2008 Jun 14; 10(6). PMID: 18551345
Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants.
Lingkang Huang, Alexandra N Heinloth, +2 authors, Pierre R Bushel.
BMC Genomics, 2008 Jun 19; 9. PMID: 18558008    Free PMC article.
The incredible shrinking world of DNA microarrays.
Sarah J Wheelan, Francisco Martínez Murillo, Jef D Boeke.
Mol Biosyst, 2008 Jun 20; 4(7). PMID: 18563246    Free PMC article.
Review.
In praise of arrays.
Lihua Ying, Minnie Sarwal.
Pediatr Nephrol, 2008 Jun 24; 24(9). PMID: 18568367    Free PMC article.
Review.
National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines for use of tumor markers in clinical practice: quality requirements.
Catharine M Sturgeon, Barry R Hoffman, +11 authors, National Academy of Clinical Biochemistry.
Clin Chem, 2008 Jul 09; 54(8). PMID: 18606634    Free PMC article.
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study.
Emi Arikawa, Yanyang Sun, +5 authors, Jingping Yang.
BMC Genomics, 2008 Jul 16; 9. PMID: 18620571    Free PMC article.
Small sample issues for microarray-based classification.
E R Dougherty.
Comp Funct Genomics, 2008 Jul 17; 2(1). PMID: 18628896    Free PMC article.
Microarray probe expression measures, data normalization and statistical validation.
Silvia Saviozzi, Raffaele A Calogero.
Comp Funct Genomics, 2008 Jul 17; 4(4). PMID: 18629084    Free PMC article.
The MGED ontology: a framework for describing functional genomics experiments.
Christian J Stoeckert, Helen Parkinson.
Comp Funct Genomics, 2008 Jul 17; 4(1). PMID: 18629093    Free PMC article.
Global analysis of cell type-specific gene expression.
David W Galbraith.
Comp Funct Genomics, 2008 Jul 17; 4(2). PMID: 18629131    Free PMC article.
Emerging use of gene expression microarrays in plant physiology.
Stan D Wullschleger, Stephen P Difazio.
Comp Funct Genomics, 2008 Jul 17; 4(2). PMID: 18629133    Free PMC article.
Navigating public microarray databases.
Christopher J Penkett, Jürg Bähler.
Comp Funct Genomics, 2008 Jul 17; 5(6-7). PMID: 18629145    Free PMC article.
Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. Taeda, P. Sylvestris or Picea abies.
Leonel van Zyl, Sara von Arnold, +7 authors, David H Clapham.
Comp Funct Genomics, 2008 Jul 17; 3(4). PMID: 18629264    Free PMC article.
Reproducibility assessment of independent component analysis of expression ratios from DNA microarrays.
David Philip Kreil, David J C MacKay.
Comp Funct Genomics, 2008 Jul 17; 4(3). PMID: 18629283    Free PMC article.
Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains.
Russell Howson, Won-Ki Huh, +7 authors, Erin K O'Shea.
Comp Funct Genomics, 2008 Jul 17; 6(1-2). PMID: 18629296    Free PMC article.
Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803.
Zhigang Zhang, Ninad D Pendse, +2 authors, Arkady Khodursky.
BMC Genomics, 2008 Jul 23; 9. PMID: 18644144    Free PMC article.
Consolidated strategy for the analysis of microarray spike-in data.
Matthew N McCall, Rafael A Irizarry.
Nucleic Acids Res, 2008 Aug 05; 36(17). PMID: 18676452    Free PMC article.
Combining transcriptional datasets using the generalized singular value decomposition.
Andreas W Schreiber, Neil J Shirley, Rachel A Burton, Geoffrey B Fincher.
BMC Bioinformatics, 2008 Aug 09; 9. PMID: 18687147    Free PMC article.
Methodologies for extracting functional pharmacogenomic experiments from international repository.
Yi-An Lin, Annie Chiang, +3 authors, Atul Janardhan Butte.
AMIA Annu Symp Proc, 2008 Aug 13;. PMID: 18693879    Free PMC article.
Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.
Sebastian Martini, Felix Eichinger, Viji Nair, Matthias Kretzler.
Rev Endocr Metab Disord, 2008 Aug 16; 9(4). PMID: 18704688    Free PMC article.
Review.
Characterizing intercellular signaling peptides in drug addiction.
Elena V Romanova, Nathan G Hatcher, Stanislav S Rubakhin, Jonathan V Sweedler.
Neuropharmacology, 2008 Aug 30; 56 Suppl 1. PMID: 18722391    Free PMC article.
Review.
Translational bioinformatics: coming of age.
Atul J Butte.
J Am Med Inform Assoc, 2008 Aug 30; 15(6). PMID: 18755990    Free PMC article.
Advances in chemical carcinogenesis: a historical review and prospective.
Lawrence A Loeb, Curtis C Harris.
Cancer Res, 2008 Sep 02; 68(17). PMID: 18757397    Free PMC article.
Review.
The proteogenomic path towards biomarker discovery.
Tara K Sigdel, Minnie M Sarwal.
Pediatr Transplant, 2008 Sep 04; 12(7). PMID: 18764911    Free PMC article.
Review.
Key issues in conducting a meta-analysis of gene expression microarray datasets.
Adaikalavan Ramasamy, Adrian Mondry, Chris C Holmes, Douglas G Altman.
PLoS Med, 2008 Sep 05; 5(9). PMID: 18767902    Free PMC article.
Highly Cited. Review.
An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association.
Charles R Farber, Atila van Nas, +10 authors, Aldons J Lusis.
J Bone Miner Res, 2008 Sep 05; 24(1). PMID: 18767929    Free PMC article.
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.
André Boorsma, Xiang-Jun Lu, +2 authors, Harmen J Bussemaker.
PLoS One, 2008 Sep 05; 3(9). PMID: 18769540    Free PMC article.
Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing.
Ana Rotter, Matjaz Hren, +2 authors, Kristina Gruden.
OMICS, 2008 Sep 06; 12(3). PMID: 18771401    Free PMC article.
Studying aminoglycoside modification by the acetyltransferase class of resistance-causing enzymes via microarray.
Olivia J Barrett, Alexei Pushechnikov, Meilan Wu, Matthew D Disney.
Carbohydr Res, 2008 Sep 09; 343(17). PMID: 18774127    Free PMC article.
A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data.
Olena Morozova, Vyacheslav Morozov, +2 authors, Marco A Marra.
PLoS One, 2008 Sep 13; 3(9). PMID: 18787709    Free PMC article.
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.
Leming Shi, Wendell D Jones, +46 authors, Weida Tong.
BMC Bioinformatics, 2008 Sep 20; 9 Suppl 9. PMID: 18793455    Free PMC article.
Highly Cited.
Very Important Pool (VIP) genes--an application for microarray-based molecular signatures.
Zhenqiang Su, Huixiao Hong, +3 authors, Weida Tong.
BMC Bioinformatics, 2008 Sep 20; 9 Suppl 9. PMID: 18793473    Free PMC article.
Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs.
Eric Christian Rouchka, Abhijit Waman Phatak, Amar Vir Singh.
Bioinformation, 2008 Sep 17; 2(9). PMID: 18795114    Free PMC article.
DNA-coated AFM cantilevers for the investigation of cell adhesion and the patterning of live cells.
Sonny C Hsiao, Ailey K Crow, +3 authors, Matthew B Francis.
Angew Chem Int Ed Engl, 2008 Sep 18; 47(44). PMID: 18798192    Free PMC article.
Identifying gene regulatory modules of heat shock response in yeast.
Wei-Sheng Wu, Wen-Hsiung Li.
BMC Genomics, 2008 Sep 25; 9. PMID: 18811975    Free PMC article.
Statistical challenges in preprocessing in microarray experiments in cancer.
Kouros Owzar, William T Barry, +2 authors, Stephen L George.
Clin Cancer Res, 2008 Oct 03; 14(19). PMID: 18829474    Free PMC article.
Review.
Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference.
Yunfeng Yang, Mengxia Zhu, Liyou Wu, Jizhong Zhou.
BMC Genomics, 2008 Oct 10; 9 Suppl 2. PMID: 18831796    Free PMC article.
Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning.
Cole Harris, Noushin Ghaffari.
BMC Genomics, 2008 Oct 10; 9 Suppl 2. PMID: 18831798    Free PMC article.
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription.
Rebecca L Poole, Gary L A Barker, +6 authors, Keith J Edwards.
BMC Genomics, 2008 Oct 14; 9. PMID: 18847483    Free PMC article.
Target identification for CNS diseases by transcriptional profiling.
C Anthony Altar, Marquis P Vawter, Stephen D Ginsberg.
Neuropsychopharmacology, 2008 Oct 17; 34(1). PMID: 18923405    Free PMC article.
Review.
Applications of emerging molecular technologies in glioblastoma multiforme.
Hari R Kumar, Xiaoling Zhong, +2 authors, Linda H Malkas.
Expert Rev Neurother, 2008 Oct 22; 8(10). PMID: 18928343    Free PMC article.
Review.
Design and analysis of mismatch probes for long oligonucleotide microarrays.
Ye Deng, Zhili He, Joy D Van Nostrand, Jizhong Zhou.
BMC Genomics, 2008 Oct 22; 9. PMID: 18928550    Free PMC article.
OligoArrayDb: pangenomic oligonucleotide microarray probe sets database.
Jean-Marie Rouillard, Erdogan Gulari.
Nucleic Acids Res, 2008 Oct 25; 37(Database issue). PMID: 18948290    Free PMC article.
Biological and functional analysis of statistically significant pathways deregulated in colon cancer by using gene expression profiles.
Angela Distaso, Luca Abatangelo, +5 authors, Nicola Ancona.
Int J Biol Sci, 2008 Oct 28; 4(6). PMID: 18953405    Free PMC article.
Gene expression profiling of breast cancer.
Ting Bao, Nancy E Davidson.
Adv Surg, 2008 Oct 29; 42. PMID: 18953822    Free PMC article.
Review.
An in silico method for detecting overlapping functional modules from composite biological networks.
Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos.
BMC Syst Biol, 2008 Nov 04; 2. PMID: 18976494    Free PMC article.
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.
Weijun Luo, Kurt D Hankenson, Peter J Woolf.
BMC Bioinformatics, 2008 Nov 05; 9. PMID: 18980677    Free PMC article.
A multiple-loop, double-cube microarray design applied to prostate cancer cell lines with variable sensitivity to histone deacetylase inhibitors.
Madeleine S Q Kortenhorst, Marianna Zahurak, +5 authors, Michael A Carducci.
Clin Cancer Res, 2008 Nov 05; 14(21). PMID: 18980983    Free PMC article.
Using cell engineering and omic tools for the improvement of cell culture processes.
Darrin Kuystermans, Britta Krampe, Halina Swiderek, Mohamed Al-Rubeai.
Cytotechnology, 2008 Nov 13; 53(1-3). PMID: 19003186    Free PMC article.
A comprehensive functional analysis of tissue specificity of human gene expression.
Zoltán Dezso, Yuri Nikolsky, +11 authors, Tatiana Nikolskaya.
BMC Biol, 2008 Nov 19; 6. PMID: 19014478    Free PMC article.
A single molecule array for digital targeted molecular analyses.
Jenny Göransson, Carolina Wählby, +3 authors, Mats Nilsson.
Nucleic Acids Res, 2008 Nov 27; 37(1). PMID: 19033366    Free PMC article.
Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.
Peter M Levine, Ping Gong, Rastislav Levicky, Kenneth L Shepard.
Biosens Bioelectron, 2008 Dec 05; 24(7). PMID: 19054661    Free PMC article.
Direct observation of conformation of a polymeric coating with implications in microarray applications.
Ayça Yalçin, Francesco Damin, +4 authors, M Selim Unlü.
Anal Chem, 2008 Dec 09; 81(2). PMID: 19061409    Free PMC article.
Multiplex protein assays based on real-time magnetic nanotag sensing.
Sebastian J Osterfeld, Heng Yu, +10 authors, Shan X Wang.
Proc Natl Acad Sci U S A, 2008 Dec 17; 105(52). PMID: 19074273    Free PMC article.
Integrated microfluidic bioprocessor for single-cell gene expression analysis.
Nicholas M Toriello, Erik S Douglas, +4 authors, Richard A Mathies.
Proc Natl Acad Sci U S A, 2008 Dec 17; 105(51). PMID: 19075237    Free PMC article.
Regulation by transcription factors in bacteria: beyond description.
Enrique Balleza, Lucia N López-Bojorquez, +5 authors, Julio Collado-Vides.
FEMS Microbiol Rev, 2008 Dec 17; 33(1). PMID: 19076632    Free PMC article.
Review.
Information systems for cancer research.
Michael F Ochs, John T Casagrande.
Cancer Invest, 2008 Dec 19; 26(10). PMID: 19093263    Free PMC article.
Clinical impact of high-throughput gene expression studies in lung cancer.
Jennifer Beane, Avrum Spira, Marc E Lenburg.
J Thorac Oncol, 2008 Dec 20; 4(1). PMID: 19096318    Free PMC article.
Review.
Global expression profiling in atopic eczema reveals reciprocal expression of inflammatory and lipid genes.
Annika M Sääf, Maria Tengvall-Linder, +5 authors, Maria Bradley.
PLoS One, 2008 Dec 25; 3(12). PMID: 19107207    Free PMC article.
Identification of genes that exhibit changes in expression on the 8p chromosomal arm by the Systematic Multiplex RT-PCR (SM RT-PCR) and DNA microarray hybridization methods.
Fumiichiro Yamamoto, Miyako Yamamoto.
Gene Expr, 2008 Dec 30; 14(4). PMID: 19110721    Free PMC article.
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies.
Henrik Hornshøj, Emøke Bendixen, +4 authors, Christian Bendixen.
BMC Genomics, 2009 Jan 21; 10. PMID: 19152685    Free PMC article.
Differential gene expression in vertebrate embryos.
Igor B Dawid.
J Biol Chem, 2009 Jan 23; 284(20). PMID: 19158075    Free PMC article.
Review.
Benchmarking regulatory network reconstruction with GRENDEL.
Brian C Haynes, Michael R Brent.
Bioinformatics, 2009 Feb 04; 25(6). PMID: 19188190    Free PMC article.
Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.
Steven P Wilder, Pamela J Kaisaki, +4 authors, Dominique Gauguier.
BMC Genomics, 2009 Feb 07; 10. PMID: 19196459    Free PMC article.
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Michael Dondrup, Stefan P Albaum, +14 authors, Alexander Goesmann.
BMC Bioinformatics, 2009 Feb 10; 10. PMID: 19200358    Free PMC article.
A statistical framework for integrating two microarray data sets in differential expression analysis.
Yinglei Lai, Sarah E Eckenrode, Jin-Xiong She.
BMC Bioinformatics, 2009 Feb 28; 10 Suppl 1. PMID: 19208123    Free PMC article.
Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation.
Hayato Yokoi, Yi-Lin Yan, +4 authors, John H Postlethwait.
Dev Biol, 2009 Feb 13; 329(1). PMID: 19210963    Free PMC article.
Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection.
Ming Hu, Zhaohui S Qin.
PLoS One, 2009 Feb 14; 4(2). PMID: 19214232    Free PMC article.
SigmaS controls multiple pathways associated with intracellular multiplication of Legionella pneumophila.
Galadriel Hovel-Miner, Sergey Pampou, +6 authors, Sergey Kalachikov.
J Bacteriol, 2009 Feb 17; 191(8). PMID: 19218380    Free PMC article.
Normalization method for transcriptional studies of heterogeneous samples--simultaneous array normalization and identification of equivalent expression.
Li-Xuan Qin, Jaya M Satagopan.
Stat Appl Genet Mol Biol, 2009 Feb 19; 8. PMID: 19222377    Free PMC article.
Inverse Langmuir method for oligonucleotide microarray analysis.
Geert C W M Mulders, Gerard T Barkema, Enrico Carlon.
BMC Bioinformatics, 2009 Feb 24; 10. PMID: 19232092    Free PMC article.
Global expression profiling in epileptogenesis: does it add to the confusion?
Yi Yuen Wang, Paul Smith, Michael Murphy, Mark Cook.
Brain Pathol, 2009 Feb 27; 20(1). PMID: 19243383    Free PMC article.
Review.
Fabrication of DNA microarrays with poly(L-glutamic acid) monolayers on gold substrates for SPR imaging measurements.
Yulin Chen, Anh Nguyen, Lifang Niu, Robert M Corn.
Langmuir, 2009 Mar 04; 25(9). PMID: 19253965    Free PMC article.
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.
Donna M Toleno, Gabriel Renaud, +4 authors, Joseph G Hacia.
BMC Bioinformatics, 2009 Mar 07; 10. PMID: 19265541    Free PMC article.
MicroRNA expression profiles in conventional and micropropagated strawberry (Fragaria x ananassa Duch.) plants.
He Li, Zhihong Zhang, +2 authors, Yue Ma.
Plant Cell Rep, 2009 Mar 12; 28(6). PMID: 19277667
Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals.
Shinichi Sunagawa, Michael K DeSalvo, +2 authors, Mónica Medina.
PLoS One, 2009 Mar 14; 4(3). PMID: 19283069    Free PMC article.
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks.
Wen-Hsien Lin, Wei-Chung Liu, Ming-Jing Hwang.
BMC Syst Biol, 2009 Mar 17; 3. PMID: 19284572    Free PMC article.
Chipping away at diagnostics for neurodegenerative diseases.
Clemens R Scherzer.
Neurobiol Dis, 2009 Mar 17; 35(2). PMID: 19285134    Free PMC article.
Review.
From bench to bedside: current and future applications of molecular profiling in renal cell carcinoma.
Androu Arsanious, Georg A Bjarnason, George M Yousef.
Mol Cancer, 2009 Mar 18; 8. PMID: 19291329    Free PMC article.
Review.
Relating perturbation magnitude to temporal gene expression in biological systems.
Stephen J Callister, J Jacob Parnell, Michael E Pfrender, Syed A Hashsham.
BMC Res Notes, 2009 Mar 21; 2. PMID: 19298657    Free PMC article.
Measuring the activity of BioBrick promoters using an in vivo reference standard.
Jason R Kelly, Adam J Rubin, +7 authors, Drew Endy.
J Biol Eng, 2009 Mar 21; 3. PMID: 19298678    Free PMC article.
Highly Cited.
Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data.
Mingzhou Joe Song, Chris K Lewis, +5 authors, Susan E Bergeson.
EURASIP J Bioinform Syst Biol, 2009 Mar 21;. PMID: 19300527    Free PMC article.
Acyl chloride-modified amorphous carbon substrates for the attachment of alcohol-, thiol-, and amine-containing molecules.
Matthew R Lockett, Justin C Carlisle, Dinh V Le, Lloyd M Smith.
Langmuir, 2009 Mar 26; 25(9). PMID: 19317418    Free PMC article.
Application and analysis of structure-switching aptamers for small molecule quantification.
Shengnan Xie, S Patrick Walton.
Anal Chim Acta, 2009 Mar 31; 638(2). PMID: 19327463    Free PMC article.
Characterisation and correction of signal fluctuations in successive acquisitions of microarray images.
Annie Glatigny, Hervé Delacroix, +3 authors, Marie-Hélène Mucchielli-Giorgi.
BMC Bioinformatics, 2009 Apr 01; 10. PMID: 19331668    Free PMC article.
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia.
Thomas Fröhlich, Georg J Arnold, +2 authors, Christian Laforsch.
BMC Genomics, 2009 Apr 23; 10. PMID: 19383153    Free PMC article.
The utility of the DNA microarray scanner to simplify the immunofluorescence evaluation of autoimmune bullous diseases.
Satori Iwamoto, Alex T Iwamoto, +5 authors, Vincent Falanga.
Am J Dermatopathol, 2009 Apr 23; 31(3). PMID: 19384060    Free PMC article.
Microarrays in glycoproteomics research.
Tingting Yue, Brian B Haab.
Clin Lab Med, 2009 Apr 25; 29(1). PMID: 19389548    Free PMC article.
Review.
DNA microarray-based gene expression profiling in porcine keratocytes and corneal endothelial cells and comparative analysis associated with xeno-related rejection.
Mee Kum Kim, Joo Youn Oh, +9 authors, Seung Yong Hwang.
J Korean Med Sci, 2009 Apr 29; 24(2). PMID: 19399257    Free PMC article.
Identification of differently expressed genes in chemical carcinogen-induced rat bladder cancers.
Guangfu Chen, Franky L Chan, Xu Zhang, Peter S F Chan.
J Huazhong Univ Sci Technolog Med Sci, 2009 Apr 29; 29(2). PMID: 19399409
Fluorescent probes for live-cell RNA detection.
Gang Bao, Won Jong Rhee, Andrew Tsourkas.
Annu Rev Biomed Eng, 2009 Apr 30; 11. PMID: 19400712    Free PMC article.
Review.
Gene-expression profiling in rheumatic disease: tools and therapeutic potential.
Jason W Bauer, Hatice Bilgic, Emily C Baechler.
Nat Rev Rheumatol, 2009 May 05; 5(5). PMID: 19412192
Review.
Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers.
Andrew H Beck, Robert B West, Matt van de Rijn.
Virchows Arch, 2009 May 05; 456(2). PMID: 19412622    Free PMC article.
Review.
Towards nonspecific detection of malignant cervical cells with fluorescent silica beads.
Swaminathan Iyer, Craig D Woodworth, +2 authors, Igor Sokolov.
Small, 2009 May 06; 5(20). PMID: 19415648    Free PMC article.
Identification of the B-Raf/Mek/Erk MAP kinase pathway as a target for all-trans retinoic acid during skin cancer promotion.
Satish B Cheepala, Weihong Yin, +8 authors, John L Clifford.
Mol Cancer, 2009 May 13; 8. PMID: 19432991    Free PMC article.
Intra-platform repeatability and inter-platform comparability of microRNA microarray technology.
Fumiaki Sato, Soken Tsuchiya, Kazuya Terasawa, Gozoh Tsujimoto.
PLoS One, 2009 May 14; 4(5). PMID: 19436744    Free PMC article.
Genome-scale transcriptional profiling in Staphylococcus aureus : bringing order out of chaos.
Vijayaraj Nagarajan, Mark S Smeltzer, Mohamed O Elasri.
FEMS Microbiol Lett, 2009 May 23; 295(2). PMID: 19459979    Free PMC article.
Gene expression profiling in the rhesus macaque: methodology, annotation and data interpretation.
Nigel C Noriega, Steven G Kohama, Henryk F Urbanski.
Methods, 2009 May 27; 49(1). PMID: 19467334    Free PMC article.
VisHiC--hierarchical functional enrichment analysis of microarray data.
Darya Krushevskaya, Hedi Peterson, +2 authors, Jaak Vilo.
Nucleic Acids Res, 2009 Jun 02; 37(Web Server issue). PMID: 19483095    Free PMC article.
Comparative genomic hybridization on spotted oligonucleotide microarrays.
Young H Kim, Jonathan R Pollack.
Methods Mol Biol, 2009 Jun 03; 556. PMID: 19488869    Free PMC article.
Gene expression-based prognostic and predictive markers for breast cancer: a primer for practicing pathologists.
Chungyeul Kim, Yusuke Taniyama, Soonmyung Paik.
Arch Pathol Lab Med, 2009 Jun 06; 133(6). PMID: 19492877    Free PMC article.
Review.
Improved procedures to mine data obtained from spotted cDNA arrays.
Andrei D Iacobas, Marcia Urban, Aldo Massimi, David C Spray.
J Biomol Tech, 2002 Mar 01; 13(1). PMID: 19498959    Free PMC article.
Influence of protein abundance on high-throughput protein-protein interaction detection.
Joseph Ivanic, Xueping Yu, Anders Wallqvist, Jaques Reifman.
PLoS One, 2009 Jun 09; 4(6). PMID: 19503833    Free PMC article.
Gene expression profiling in peanut using high density oligonucleotide microarrays.
Paxton Payton, Kameswara Rao Kottapalli, +5 authors, Maria Gallo.
BMC Genomics, 2009 Jun 16; 10. PMID: 19523230    Free PMC article.
Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine.
Christian Krätzer, Paul Carini, Raymond Hovey, Uwe Deppenmeier.
J Bacteriol, 2009 Jun 16; 191(16). PMID: 19525341    Free PMC article.
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome.
Shu-Ye Jiang, Alan Christoffels, Rengasamy Ramamoorthy, Srinivasan Ramachandran.
Plant Physiol, 2009 Jun 19; 150(4). PMID: 19535473    Free PMC article.
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays.
Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, Joachim L Schultze.
BMC Bioinformatics, 2009 Jun 23; 10. PMID: 19538710    Free PMC article.
New Technologies for Diagnosing Pediatric Tumors Expert Opinion on Medical Diagnostics.
Jun S Wei, Thomas C Badgett, Javed Khan.
Expert Opin Med Diagn, 2009 Jun 26; 2(11). PMID: 19554203    Free PMC article.
Translational bioinformatics applications in genome medicine.
Atul J Butte.
Genome Med, 2009 Jul 02; 1(6). PMID: 19566916    Free PMC article.
Development of a novel peptide microarray for large-scale epitope mapping of food allergens.
Jing Lin, Ludmilla Bardina, +7 authors, Hugh A Sampson.
J Allergy Clin Immunol, 2009 Jul 07; 124(2). PMID: 19577281    Free PMC article.
Genomic and Proteomic Biomarker Discovery in Neurological Disease.
Rilee H Robeson, Andrew M Siegel, Travis Dunckley.
Biomark Insights, 2008 Jan 01; 3. PMID: 19578496    Free PMC article.
NanoPen: dynamic, low-power, and light-actuated patterning of nanoparticles.
Arash Jamshidi, Steven L Neale, +6 authors, Ming C Wu.
Nano Lett, 2009 Jul 11; 9(8). PMID: 19588985    Free PMC article.
cDNA microarray analysis of esophageal cancer: discoveries and prospects.
Yutaka Shimada, Fumiaki Sato, +2 authors, Kazuhiro Tsukada.
Gen Thorac Cardiovasc Surg, 2009 Jul 15; 57(7). PMID: 19597924
Review.
RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice.
Tae-Ho Lee, Yeon-Ki Kim, +9 authors, Baek Hie Nahm.
Plant Physiol, 2009 Jul 17; 151(1). PMID: 19605550    Free PMC article.
Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling.
Nicola Palmieri, Christian Schlötterer.
PLoS One, 2009 Jul 29; 4(7). PMID: 19636379    Free PMC article.
A dynamic network of transcription in LPS-treated human subjects.
Junhee Seok, Wenzhong Xiao, +2 authors, Markus W Covert.
BMC Syst Biol, 2009 Jul 30; 3. PMID: 19638230    Free PMC article.
From gene expression profiles to biological validation in enteroviral heart disease.
Bobby Yanagawa, Bruce McManus, +3 authors, Decheng Yang.
Exp Clin Cardiol, 2003 Oct 01; 8(3). PMID: 19641703    Free PMC article.
Deconvoluting the 'omics' for organ transplantation.
Minnie M Sarwal.
Curr Opin Organ Transplant, 2009 Aug 01; 14(5). PMID: 19644370    Free PMC article.
Review.
Comparison of next generation sequencing technologies for transcriptome characterization.
P Kerr Wall, Jim Leebens-Mack, +13 authors, Claude W dePamphilis.
BMC Genomics, 2009 Aug 04; 10. PMID: 19646272    Free PMC article.
High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.
S Ocak, M L Sos, R K Thomas, P P Massion.
Eur Respir J, 2009 Aug 04; 34(2). PMID: 19648524    Free PMC article.
Review.
The molecular characterization and clinical management of multiple myeloma in the post-genome era.
Y Zhou, B Barlogie, J D Shaughnessy.
Leukemia, 2009 Aug 07; 23(11). PMID: 19657360    Free PMC article.
Review.
Biomarkers in bladder cancer: present status and perspectives.
Wun-Jae Kim, Soongang Park, Yong-June Kim.
Biomark Insights, 2007 Jan 01; 2. PMID: 19662195    Free PMC article.
Biomarker discovery in animal health and disease: the application of post-genomic technologies.
Rowan E Moore, Jennifer Kirwan, Mary K Doherty, Phillip D Whitfield.
Biomark Insights, 2007 Jan 01; 2. PMID: 19662203    Free PMC article.
Global brain gene expression analysis links glutamatergic and GABAergic alterations to suicide and major depression.
Adolfo Sequeira, Firoza Mamdani, +10 authors, Gustavo Turecki.
PLoS One, 2009 Aug 12; 4(8). PMID: 19668376    Free PMC article.
Highly Cited.
Employing two distinct photonic crystal resonances to improve fluorescence enhancement.
Patrick C Mathias, Hsin-Yu Wu, Brian T Cunningham.
Appl Phys Lett, 2009 Aug 12; 95(2). PMID: 19668706    Free PMC article.
Target profiling of small molecules by chemical proteomics.
Uwe Rix, Giulio Superti-Furga.
Nat Chem Biol, 2009 Aug 20; 5(9). PMID: 19690537
Highly Cited. Review.
Genome-wide analysis of histone H3 lysine9 modifications in human mesenchymal stem cell osteogenic differentiation.
Jiang Tan, Jun Lu, +6 authors, Baiqu Huang.
PLoS One, 2009 Aug 28; 4(8). PMID: 19710927    Free PMC article.
Salivary biomarkers for clinical applications.
Lei Zhang, Hua Xiao, David T Wong.
Mol Diagn Ther, 2009 Aug 29; 13(4). PMID: 19712004
Review.
Microarray-based cancer prediction using soft computing approach.
Xiaosheng Wang, Osamu Gotoh.
Cancer Inform, 2009 Sep 01; 7. PMID: 19718448    Free PMC article.
Real-time DNA microarray analysis.
Arjang Hassibi, Haris Vikalo, José Luis Riechmann, Babak Hassibi.
Nucleic Acids Res, 2009 Sep 03; 37(20). PMID: 19723688    Free PMC article.
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells.
Alissar Nehmé, Edward K Lobenhofer, W Daniel Stamer, Jeffrey L Edelman.
BMC Med Genomics, 2009 Sep 12; 2. PMID: 19744340    Free PMC article.
Disease signatures are robust across tissues and experiments.
Joel T Dudley, Robert Tibshirani, Tarangini Deshpande, Atul J Butte.
Mol Syst Biol, 2009 Sep 17; 5. PMID: 19756046    Free PMC article.
Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
Adam M Phillippy, Xiangyu Deng, Wei Zhang, Steven L Salzberg.
BMC Bioinformatics, 2009 Sep 18; 10. PMID: 19758451    Free PMC article.
Quadruple 9-mer-based protein binding microarray with DsRed fusion protein.
Min-Jeong Kim, Tae-Ho Lee, +5 authors, Yeon-Ki Kim.
BMC Mol Biol, 2009 Sep 19; 10. PMID: 19761621    Free PMC article.
Tissue array methods for high-throughput clinicopathologic research.
Hye Seung Lee, Woo Ho Kim.
Cancer Res Treat, 2006 Feb 01; 38(1). PMID: 19771251    Free PMC article.
A Two-Stage Approach for Semilinear In-Slide Models.
Jinhong You, Haibo Zhou.
J Multivar Anal, 2009 Oct 06; 99(8). PMID: 19802362    Free PMC article.
A man-made ATP-binding protein evolved independent of nature causes abnormal growth in bacterial cells.
Joshua M Stomel, James W Wilson, +2 authors, John C Chaput.
PLoS One, 2009 Oct 09; 4(10). PMID: 19812699    Free PMC article.
p63 and p73 transcriptionally regulate genes involved in DNA repair.
Yu-Li Lin, Shomit Sengupta, +3 authors, Elsa R Flores.
PLoS Genet, 2009 Oct 10; 5(10). PMID: 19816568    Free PMC article.
Basic concepts of microarrays and potential applications in clinical microbiology.
Melissa B Miller, Yi-Wei Tang.
Clin Microbiol Rev, 2009 Oct 14; 22(4). PMID: 19822891    Free PMC article.
Review.
Knowledge-based data analysis comes of age.
Michael F Ochs.
Brief Bioinform, 2009 Oct 27; 11(1). PMID: 19854753    Free PMC article.
Accurate molecular classification of cancer using simple rules.
Xiaosheng Wang, Osamu Gotoh.
BMC Med Genomics, 2009 Oct 31; 2. PMID: 19874631    Free PMC article.
Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi.
Hugo Lavoie, Hervé Hogues, Malcolm Whiteway.
Curr Opin Microbiol, 2009 Oct 31; 12(6). PMID: 19875326    Free PMC article.
Review.
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm.
Marek Mutwil, Björn Usadel, +3 authors, Staffan Persson.
Plant Physiol, 2009 Nov 06; 152(1). PMID: 19889879    Free PMC article.
Matrix factorization for recovery of biological processes from microarray data.
Andrew V Kossenkov, Michael F Ochs.
Methods Enzymol, 2009 Nov 10; 467. PMID: 19897089    Free PMC article.
Reverse engineering a signaling network using alternative inputs.
Hiromasa Tanaka, Tau-Mu Yi.
PLoS One, 2009 Nov 10; 4(10). PMID: 19898612    Free PMC article.
Murine spinal cord transcriptome analysis following reduction of prevalent myelin cDNA sequences.
Zhi Yan, Kanan B Lathia, Patric A Clapshaw.
Cell Mol Neurobiol, 2009 Nov 11; 29(8). PMID: 19902351
Systems biology from a yeast omics perspective.
Michael Snyder, Jennifer E G Gallagher.
FEBS Lett, 2009 Nov 12; 583(24). PMID: 19903479    Free PMC article.
Review.
Carbon tetrachloride affects inflammation-related biochemical networks in the mouse liver as identified by a customized cDNA microarray system.
Hidekuni Inadera, Shinjiro Tachibana, Aya Suzuki, Akiko Shimomura.
Environ Health Prev Med, 2009 Nov 17; 15(2). PMID: 19911120    Free PMC article.
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.
Yan W Asmann, Eric W Klee, +8 authors, Jean-Pierre A Kocher.
BMC Genomics, 2009 Nov 18; 10. PMID: 19917133    Free PMC article.
Developing a systems biology approach to study disease progression caused by Heterodera glycines in Glycine max.
Vincent P Klink, Christopher C Overall, Benjamin F Matthews.
Gene Regul Syst Bio, 2007 Jan 01; 1. PMID: 19936075    Free PMC article.
Drivers of biodiagnostic development.
David A Giljohann, Chad A Mirkin.
Nature, 2009 Nov 27; 462(7272). PMID: 19940916    Free PMC article.
Highly Cited. Review.
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods.
Priit Adler, Raivo Kolde, +4 authors, Jaak Vilo.
Genome Biol, 2009 Dec 08; 10(12). PMID: 19961599    Free PMC article.
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases.
Lucas B Edelman, Giuseppe Toia, +2 authors, Nathan D Price.
BMC Genomics, 2009 Dec 08; 10. PMID: 19961616    Free PMC article.
The effects of HIF-1alpha on gene expression profiles of NCI-H446 human small cell lung cancer cells.
Jun Wan, Jinben Ma, Ju Mei, Genfa Shan.
J Exp Clin Cancer Res, 2009 Dec 17; 28. PMID: 20003295    Free PMC article.
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.
Erdem Arslan, Ian J Laurenzi.
BMC Bioinformatics, 2009 Dec 17; 10. PMID: 20003312    Free PMC article.
Systems biology of embryogenesis.
Lucas B Edelman, Sriram Chandrasekaran, Nathan D Price.
Reprod Fertil Dev, 2009 Dec 17; 22(1). PMID: 20003850    Free PMC article.
In vitro stable isotope labeling for discovery of novel metabolites by liquid chromatography-mass spectrometry: Confirmation of gamma-tocopherol metabolism in human A549 cell.
Wen-Chu Yang, Fred E Regnier, Qing Jiang, Jiri Adamec.
J Chromatogr A, 2009 Dec 17; 1217(5). PMID: 20006340    Free PMC article.
DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets.
Sudhir Husale, Henrik H J Persson, Ozgur Sahin.
Nature, 2009 Dec 17; 462(7276). PMID: 20010806    Free PMC article.
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
Daniel Ramsköld, Eric T Wang, Christopher B Burge, Rickard Sandberg.
PLoS Comput Biol, 2009 Dec 17; 5(12). PMID: 20011106    Free PMC article.
Highly Cited.
Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study.
Elizabeth H Robison, Tony S Mondala, +3 authors, Sunil M Kurian.
BMC Genomics, 2009 Dec 19; 10. PMID: 20017944    Free PMC article.
Fabrication and characterization of DNA arrays prepared on carbon-on-metal substrates.
Matthew R Lockett, Lloyd M Smith.
Anal Chem, 2009 Dec 22; 81(15). PMID: 20020675    Free PMC article.
Genome-wide transcriptome analysis of 150 cell samples.
Daniel Irimia, Michael Mindrinos, +8 authors, Mehmet Toner.
Integr Biol (Camb), 2009 Dec 22; 1(1). PMID: 20023796    Free PMC article.
2D-PCR: a method of mapping DNA in tissue sections.
Michael Armani, Jaime Rodriguez-Canales, +5 authors, Elisabeth Smela.
Lab Chip, 2009 Dec 22; 9(24). PMID: 20024032    Free PMC article.
VitisNet: "Omics" integration through grapevine molecular networks.
Jérôme Grimplet, Grant R Cramer, +3 authors, Anne Y Fennell.
PLoS One, 2009 Dec 23; 4(12). PMID: 20027228    Free PMC article.
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.
Keyan Salari, Robert Tibshirani, Jonathan R Pollack.
Bioinformatics, 2009 Dec 25; 26(3). PMID: 20031972    Free PMC article.
Microarray probes and probe sets.
Hongfang Liu, Ionut Bebu, Xin Li.
Front Biosci (Elite Ed), 2009 Dec 29; 2. PMID: 20036881    Free PMC article.
Review.
Disease gene characterization through large-scale co-expression analysis.
Allen Day, Jun Dong, +4 authors, Stanley F Nelson.
PLoS One, 2010 Jan 05; 4(12). PMID: 20046828    Free PMC article.
A Survey of Statistical Models for Reverse Engineering Gene Regulatory Networks.
Yufei Huang, Isabel M Tienda-Luna, Yufeng Wang.
IEEE Signal Process Mag, 2010 Jan 05; 26(1). PMID: 20046885    Free PMC article.
Multiple testing and its applications to microarrays.
Yongchao Ge, Stuart C Sealfon, Terence P Speed.
Stat Methods Med Res, 2010 Jan 06; 18(6). PMID: 20048384    Free PMC article.
Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways.
Michael C Wu, Xihong Lin.
Stat Methods Med Res, 2010 Jan 06; 18(6). PMID: 20048386    Free PMC article.
Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks.
Simon Rosenfeld.
Gene Regul Syst Bio, 2010 Jan 08; 3. PMID: 20054406    Free PMC article.
On the detection and refinement of transcription factor binding sites using ChIP-Seq data.
Ming Hu, Jindan Yu, +2 authors, Zhaohui S Qin.
Nucleic Acids Res, 2010 Jan 09; 38(7). PMID: 20056654    Free PMC article.
A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes.
Anastasios Markitsis, Yinglei Lai.
Bioinformatics, 2010 Jan 19; 26(5). PMID: 20080506    Free PMC article.
Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.
Emre Ozkumur, Sunmin Ahn, +6 authors, M Selim Unlü.
Biosens Bioelectron, 2010 Jan 26; 25(7). PMID: 20097056    Free PMC article.
One Decade Later: What has Gene Expression Profiling Told us About Neuronal Cell Types, Brain Function and Disease?
Elva Díaz.
Curr Genomics, 2010 Feb 02; 10(5). PMID: 20119529    Free PMC article.
A microarray gene analysis of peripheral whole blood in normal adult male rats after long-term GH gene therapy.
Ying Qin, Ya-Ping Tian.
Cell Mol Biol Lett, 2010 Feb 02; 15(2). PMID: 20119855    Free PMC article.
Ontological evaluation of transcriptional differences between sperm of infertile males and fertile donors using microarray analysis.
Sandra García-Herrero, Nicolás Garrido, +3 authors, Marcos Meseguer.
J Assist Reprod Genet, 2010 Feb 04; 27(2-3). PMID: 20127162    Free PMC article.
Deep SAGE analysis of the Caenorhabditis elegans transcriptome.
Peter Ruzanov, Donald L Riddle.
Nucleic Acids Res, 2010 Feb 05; 38(10). PMID: 20129939    Free PMC article.
[Biomarker for diagnosis of rejection after heart transplantation].
Matthias Frick, Herwig Antretter, Otmar Pachinger, Gerhard Pölzl.
Herz, 2010 Feb 09; 35(1). PMID: 20140784
Review.
Genetics of psychiatric disorders methods: molecular approaches.
Dimitrios Avramopoulos.
Psychiatr Clin North Am, 2010 Feb 18; 33(1). PMID: 20159337    Free PMC article.
Review.
Grafting of antibodies inside integrated microfluidic-microoptic devices by means of automated microcontact printing.
Elie Bou Chakra, Benjamin Hannes, +6 authors, Michel Cabrera.
Sens Actuators B Chem, 2010 Feb 18; 140(1). PMID: 20161128    Free PMC article.
Statecharts for gene network modeling.
Yong-Jun Shin, Mehrdad Nourani.
PLoS One, 2010 Feb 27; 5(2). PMID: 20186343    Free PMC article.
A genomic approach to human autoimmune diseases.
Virginia Pascual, Damien Chaussabel, Jacques Banchereau.
Annu Rev Immunol, 2010 Mar 03; 28. PMID: 20192809    Free PMC article.
Review.
RNA-Seq analysis to capture the transcriptome landscape of a single cell.
Fuchou Tang, Catalin Barbacioru, +5 authors, M Azim Surani.
Nat Protoc, 2010 Mar 06; 5(3). PMID: 20203668    Free PMC article.
Highly Cited.
Pathway-BasedFeature Selection Algorithm for Cancer Microarray Data.
Nirmalya Bandyopadhyay, Tamer Kahveci, +2 authors, Sanjay Ranka.
Adv Bioinformatics, 2009 Jan 01;. PMID: 20204186    Free PMC article.
Using the DFCI gene index databases for biological discovery.
Corina Antonescu, Valentin Antonescu, Razvan Sultana, John Quackenbush.
Curr Protoc Bioinformatics, 2010 Mar 06; Chapter 1. PMID: 20205187    Free PMC article.
Genomics and bioinformatics resources for crop improvement.
Keiichi Mochida, Kazuo Shinozaki.
Plant Cell Physiol, 2010 Mar 09; 51(4). PMID: 20208064    Free PMC article.
Review.
Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray.
Tara J Holman, Michael H Wilson, +4 authors, Michael J Holdsworth.
Plant Methods, 2010 Mar 17; 6. PMID: 20230623    Free PMC article.
Analysis of DNA strand-specific differential expression with high density tiling microarrays.
Luis Quintales, Mar Sánchez, Francisco Antequera.
BMC Bioinformatics, 2010 Mar 18; 11. PMID: 20233458    Free PMC article.
Standards affecting the consistency of gene expression arrays in clinical applications.
Steven A Enkemann.
Cancer Epidemiol Biomarkers Prev, 2010 Mar 25; 19(4). PMID: 20332273    Free PMC article.
Review.
Detection of HIV cDNA point mutations with rolling-circle amplification arrays.
Lingwei Wu, Quanjun Liu, Zhongwei Wu, Zuhong Lu.
Molecules, 2010 Mar 26; 15(2). PMID: 20335932    Free PMC article.
Fabricating nanoscale DNA patterns with gold nanowires.
Yulin Chen, Sheng-Chin Kung, +3 authors, Robert M Corn.
Anal Chem, 2010 Mar 27; 82(8). PMID: 20337428    Free PMC article.
ProbFAST: Probabilistic functional analysis system tool.
Israel T Silva, Ricardo Z N Vêncio, +2 authors, Wilson A Silva.
BMC Bioinformatics, 2010 Apr 01; 11. PMID: 20353576    Free PMC article.
Evaluation of a novel approach for the measurement of RNA quality.
Timothy M Wilkes, Alison S Devonshire, Stephen Lr Ellison, Carole A Foy.
BMC Res Notes, 2010 Apr 03; 3. PMID: 20359344    Free PMC article.
Modern approaches to understanding stress and disease susceptibility: A review with special emphasis on respiratory disease.
Palok Aich, Andrew A Potter, Philip J Griebel.
Int J Gen Med, 2009 Jan 01; 2. PMID: 20360883    Free PMC article.
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance.
Bernie J Daigle, Alicia Deng, +5 authors, Russ B Altman.
PLoS Comput Biol, 2010 Apr 03; 6(3). PMID: 20361040    Free PMC article.
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.
Chuming Chen, Peter B McGarvey, Hongzhan Huang, Cathy H Wu.
Adv Bioinformatics, 2010 Apr 07;. PMID: 20369061    Free PMC article.
Transcriptomics in ecotoxicology.
Kristin Schirmer, Beat B Fischer, Danielle J Madureira, Smitha Pillai.
Anal Bioanal Chem, 2010 Apr 07; 397(3). PMID: 20369230    Free PMC article.
Review.
Matrix factorisation methods applied in microarray data analysis.
Andrew V Kossenkov, Michael F Ochs.
Int J Data Min Bioinform, 2010 Apr 09; 4(1). PMID: 20376923    Free PMC article.
Review.
Photonic Crystal Surfaces as a General Purpose Platform for Label-Free and Fluorescent Assays.
Brian T Cunningham.
JALA Charlottesv Va, 2010 Apr 13; 15(2). PMID: 20383277    Free PMC article.
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis.
Marc Lohse, Adriano Nunes-Nesi, +11 authors, Björn Usadel.
Plant Physiol, 2010 Apr 15; 153(2). PMID: 20388663    Free PMC article.
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds.
Juan C Triviño, Florencio Pazos.
BMC Syst Biol, 2010 Apr 22; 4. PMID: 20406431    Free PMC article.
Nanoparticle diffraction gratings for DNA detection on photopatterned glass substrates.
Iuliana E Sendroiu, Robert M Corn.
Biointerphases, 2008 Sep 01; 3(3). PMID: 20408697    Free PMC article.
Genomic approaches with natural fish populations.
M F Oleksiak.
J Fish Biol, 2010 Apr 23; 76(5). PMID: 20409163    Free PMC article.
Review.
Arabidopsis and the plant immune system.
Marc T Nishimura, Jeffery L Dangl.
Plant J, 2010 Apr 23; 61(6). PMID: 20409278    Free PMC article.
Review.
Simultaneous determination of multiple mRNA levels utilizing MALDI-TOF mass spectrometry and biotinylated dideoxynucleotides.
Daniel Scott Duffield, Li Cai, Sobin Kim.
RNA, 2010 Apr 23; 16(6). PMID: 20410241    Free PMC article.
Mosquito transcriptome profiles and filarial worm susceptibility in Armigeres subalbatus.
Matthew T Aliota, Jeremy F Fuchs, +4 authors, Bruce M Christensen.
PLoS Negl Trop Dis, 2010 Apr 28; 4(4). PMID: 20421927    Free PMC article.
Gene expression studies in major depression.
Divya Mehta, Andreas Menke, Elisabeth B Binder.
Curr Psychiatry Rep, 2010 Apr 29; 12(2). PMID: 20425299    Free PMC article.
Review.
Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells.
Michael Pierre, Benoît DeHertogh, +5 authors, Eric Depiereux.
BMC Cancer, 2010 May 04; 10. PMID: 20433688    Free PMC article.
Statistical design and analysis of RNA sequencing data.
Paul L Auer, R W Doerge.
Genetics, 2010 May 05; 185(2). PMID: 20439781    Free PMC article.
Highly Cited.
Gene-expression-based prognostic assays for breast cancer.
Chungyeul Kim, Soonmyung Paik.
Nat Rev Clin Oncol, 2010 May 05; 7(6). PMID: 20440284
Review.
Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq.
Qiang Gan, Iouri Chepelev, +4 authors, Xin Chen.
Cell Res, 2010 May 05; 20(7). PMID: 20440302    Free PMC article.
Methods for molecular surveillance of influenza.
Ruixue Wang, Jeffery K Taubenberger.
Expert Rev Anti Infect Ther, 2010 May 12; 8(5). PMID: 20455681    Free PMC article.
Review.
Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response.
Yu Gao, Laurence Flori, +7 authors, Claire Rogel-Gaillard.
BMC Genomics, 2010 May 13; 11. PMID: 20459780    Free PMC article.
Feature detection techniques for preprocessing proteomic data.
Kimberly F Sellers, Jeffrey C Miecznikowski.
Int J Biomed Imaging, 2010 May 15; 2010. PMID: 20467457    Free PMC article.
Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation.
Martin Cadeiras, Manuel von Bayern, +8 authors, Mario C Deng.
J Cell Mol Med, 2010 May 26; 15(4). PMID: 20497491    Free PMC article.
Metabolomics in premature labor: a novel approach to identify patients at risk for preterm delivery.
Roberto Romero, Shali Mazaki-Tovi, +10 authors, Chris Beecher.
J Matern Fetal Neonatal Med, 2010 May 28; 23(12). PMID: 20504069    Free PMC article.
Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).
Vincent P Klink, Christopher C Overall, +2 authors, Benjamin F Matthews.
J Biomed Biotechnol, 2010 May 29; 2010. PMID: 20508855    Free PMC article.
Current gene expression studies in esophageal carcinoma.
Wei Guo, Yao-Guang Jiang.
Curr Genomics, 2010 Jun 02; 10(8). PMID: 20514215    Free PMC article.
Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3.
Ramona Schmid, Patrick Baum, +7 authors, Karsten Quast.
BMC Genomics, 2010 Jun 08; 11. PMID: 20525181    Free PMC article.
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation.
Shih Chi Peng, David Shan Hill Wong, +5 authors, Chuan Yi Tang.
BMC Bioinformatics, 2010 Jun 10; 11. PMID: 20529327    Free PMC article.
Application of equilibrium models of solution hybridization to microarray design and analysis.
Raad Z Gharaibeh, Joshua M Newton, Jennifer W Weller, Cynthia J Gibas.
PLoS One, 2010 Jun 16; 5(6). PMID: 20548788    Free PMC article.
Revealing the dynamics of polymicrobial infections: implications for antibiotic therapy.
Geraint B Rogers, Lucas R Hoffman, +3 authors, Kenneth D Bruce.
Trends Microbiol, 2010 Jun 18; 18(8). PMID: 20554204    Free PMC article.
Review.
Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced surface plasmon resonance imaging on glassified gold surfaces.
Lida K Gifford, Iuliana E Sendroiu, Robert M Corn, Andrej Lupták.
J Am Chem Soc, 2010 Jun 23; 132(27). PMID: 20565098    Free PMC article.
Magnetic biosensor technologies for medical applications: a review.
J Llandro, J J Palfreyman, A Ionescu, C H W Barnes.
Med Biol Eng Comput, 2010 Jun 25; 48(10). PMID: 20574723
Review.
Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.
Ming Li, William Gray, +6 authors, Robbert J C Slebos.
J Proteome Res, 2010 Jul 01; 9(8). PMID: 20586475    Free PMC article.
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.
Marc Bailly-Bechet, Alfredo Braunstein, +2 authors, Riccardo Zecchina.
BMC Bioinformatics, 2010 Jul 01; 11. PMID: 20587029    Free PMC article.
Microarrayed allergen molecules for the diagnosis of allergic diseases.
Adriano Mari, Claudia Alessandri, +3 authors, Danila Zennaro.
Curr Allergy Asthma Rep, 2010 Jul 03; 10(5). PMID: 20596902
Review.
Evolution of neuronal and endothelial transcriptomes in primates.
Thomas Giger, Philipp Khaitovich, +8 authors, Svante Pääbo.
Genome Biol Evol, 2010 Jul 14; 2. PMID: 20624733    Free PMC article.
Designing a sensitive and quantifiable nanocolloid assay with dielectrophoretic crossover frequencies.
Sagnik Basuray, Hsueh-Chia Chang.
Biomicrofluidics, 2010 Jul 21; 4(1). PMID: 20644668    Free PMC article.
Consistency of predictive signature genes and classifiers generated using different microarray platforms.
X Fan, E K Lobenhofer, +21 authors, W Tong.
Pharmacogenomics J, 2010 Aug 03; 10(4). PMID: 20676064    Free PMC article.
Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients.
A Oberthuer, D Juraeva, +8 authors, B Brors.
Pharmacogenomics J, 2010 Aug 03; 10(4). PMID: 20676065    Free PMC article.
Tumor antigen analysis in neuroblastoma by serological interrogation of bioinformatic data.
M Eric Kohler, Bryon D Johnson, +3 authors, Rimas J Orentas.
Cancer Sci, 2010 Aug 20; 101(11). PMID: 20718755    Free PMC article.
Molecular diagnostics in transplantation.
Maarten Naesens, Minnie M Sarwal.
Nat Rev Nephrol, 2010 Aug 26; 6(10). PMID: 20736923
Review.
Transcriptional regulation is only half the story.
Joshua B Plotkin.
Mol Syst Biol, 2010 Aug 27; 6. PMID: 20739928    Free PMC article.
Induced Sézary syndrome PBMCs poorly express immune response genes up-regulated in stimulated memory T cells.
Benjamin F Chong, Patrick Dantzer, +4 authors, Henry K Wong.
J Dermatol Sci, 2010 Aug 31; 60(1). PMID: 20801618    Free PMC article.
Autoassembly protein arrays for analyzing antibody cross-reactivity.
Richard S Gaster, Drew A Hall, Shan X Wang.
Nano Lett, 2010 Sep 02; 11(7). PMID: 20804215    Free PMC article.
Genomics for weed science.
David Horvath.
Curr Genomics, 2010 Sep 03; 11(1). PMID: 20808523    Free PMC article.
Using expression genetics to study the neurobiology of ethanol and alcoholism.
Sean P Farris, Aaron R Wolen, Michael F Miles.
Int Rev Neurobiol, 2010 Sep 04; 91. PMID: 20813241    Free PMC article.
Review.
Genome-scale approaches to investigate oxidative DNA damage.
Shinya Akatsuka, Shinya Toyokuni.
J Clin Biochem Nutr, 2010 Sep 15; 47(2). PMID: 20838563    Free PMC article.
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana.
Gyan Prakash Srivastava, Ping Li, Jingdong Liu, Dong Xu.
BMC Syst Biol, 2010 Sep 25; 4 Suppl 2. PMID: 20840729    Free PMC article.
Undetectable and Decreased Expression of KIAA1949 (Phostensin) Encoded on Chromosome 6p21.33 in Human Breast Cancers Revealed by Transcriptome Analysis.
Yan A Su, Jun Yang, +2 authors, Ping He.
J Cancer, 2010 Sep 16; 1. PMID: 20842223    Free PMC article.
A microarray-based method to perform nucleic acid selections.
Olga Aminova, Matthew D Disney.
Methods Mol Biol, 2010 Sep 22; 669. PMID: 20857369    Free PMC article.
The role of gene expression in ecological speciation.
Scott A Pavey, Hélène Collin, Patrik Nosil, Sean M Rogers.
Ann N Y Acad Sci, 2010 Sep 24; 1206. PMID: 20860685    Free PMC article.
Review.
Linear control theory for gene network modeling.
Yong-Jun Shin, Leonidas Bleris.
PLoS One, 2010 Sep 24; 5(9). PMID: 20862288    Free PMC article.
Functional protein microarray technology.
Shaohui Hu, Zhi Xie, +2 authors, Heng Zhu.
Wiley Interdiscip Rev Syst Biol Med, 2010 Sep 28; 3(3). PMID: 20872749    Free PMC article.
Review.
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Rong Chen, Tara K Sigdel, +11 authors, Atul J Butte.
PLoS Comput Biol, 2010 Oct 05; 6(9). PMID: 20885780    Free PMC article.
Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer.
Yasunori Kinoshita, Takahiro Tayama, +5 authors, Koichi Nishigaki.
BMC Biotechnol, 2010 Oct 07; 10. PMID: 20923572    Free PMC article.
The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment.
Andy G Lynch, James Hadfield, +3 authors, Simon Tavaré.
BMC Genomics, 2010 Oct 12; 11. PMID: 20925945    Free PMC article.
Differential expression analysis of Digital Gene Expression data: RNA-tag filtering, comparison of t-type tests and their genome-wide co-expression based adjustments.
Yinglei Lai.
Int J Bioinform Res Appl, 2010 Oct 14; 6(4). PMID: 20940123    Free PMC article.
Generating and navigating proteome maps using mass spectrometry.
Christian H Ahrens, Erich Brunner, +2 authors, Ruedi Aebersold.
Nat Rev Mol Cell Biol, 2010 Oct 15; 11(11). PMID: 20944666
Review.
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples.
Zhining Wen, Charles Wang, +5 authors, Leming Shi.
BMC Bioinformatics, 2010 Oct 22; 11 Suppl 6. PMID: 20946593    Free PMC article.
Data integration in genetics and genomics: methods and challenges.
Jemila S Hamid, Pingzhao Hu, +3 authors, Joseph Beyene.
Hum Genomics Proteomics, 2009 Jan 01; 2009. PMID: 20948564    Free PMC article.
A python module to normalize microarray data by the quantile adjustment method.
Ibrahima Baber, Jean Philippe Tamby, +5 authors, Doulaye Dembélé.
Infect Genet Evol, 2010 Oct 26; 11(4). PMID: 20970526    Free PMC article.
Reverse phase protein microarrays advance to use in clinical trials.
Claudius Mueller, Lance A Liotta, Virginia Espina.
Mol Oncol, 2010 Oct 27; 4(6). PMID: 20974554    Free PMC article.
Review.
The microarray manual curation tool (MMCT): A Web server for microarray probe evaluations.
Dan Tulpan, Luc Belliveau, Serge Léger.
Bioinformation, 2010 Oct 27; 4(8). PMID: 20975897    Free PMC article.
Studies of complex biological systems with applications to molecular medicine: the need to integrate transcriptomic and proteomic approaches.
Elena Silvestri, Assunta Lombardi, +6 authors, Maria Moreno.
J Biomed Biotechnol, 2010 Oct 29; 2011. PMID: 20981256    Free PMC article.
Review.
Gene expression profiling of human breast tissue samples using SAGE-Seq.
Zhenhua Jeremy Wu, Clifford A Meyer, +9 authors, X Shirley Liu.
Genome Res, 2010 Nov 04; 20(12). PMID: 21045080    Free PMC article.
Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing.
Murray P Cox, Carla J Eaton, D Barry Scott.
Plant Signal Behav, 2010 Nov 04; 5(11). PMID: 21045557    Free PMC article.
Review.
Conversion of a molecular classifier obtained by gene expression profiling into a classifier based on real-time PCR: a prognosis predictor for gliomas.
Satoru Kawarazaki, Kazuya Taniguchi, +7 authors, Kikuya Kato.
BMC Med Genomics, 2010 Nov 11; 3. PMID: 21062501    Free PMC article.
miRNA expression patterns of Triticum dicoccoides in response to shock drought stress.
Melda Kantar, Stuart J Lucas, Hikmet Budak.
Planta, 2010 Nov 12; 233(3). PMID: 21069383
Highly Cited.
Algorithm-driven artifacts in median polish summarization of microarray data.
Federico M Giorgi, Anthony M Bolger, Marc Lohse, Bjoern Usadel.
BMC Bioinformatics, 2010 Nov 13; 11. PMID: 21070630    Free PMC article.
Fermenting knowledge: the history of winemaking, science and yeast research.
Paul J Chambers, Isak S Pretorius.
EMBO Rep, 2010 Nov 13; 11(12). PMID: 21072064    Free PMC article.
Genetic and epigenetic alterations after hybridization and genome doubling.
Ovidiu Paun, Michael F Fay, Douglas E Soltis, Mark W Chase.
Taxon, 2007 Aug 01; 56(3). PMID: 21082042    Free PMC article.
Candidate genes involved in tanshinone biosynthesis in hairy roots of Salvia miltiorrhiza revealed by cDNA microarray.
Guanghong Cui, Luqi Huang, Xiaojing Tang, Jingxue Zhao.
Mol Biol Rep, 2010 Nov 18; 38(4). PMID: 21082262
Tumor profiling: development of prognostic and predictive factors to guide brain tumor treatment.
Stephen H Settle, Erik P Sulman.
Curr Oncol Rep, 2010 Nov 18; 13(1). PMID: 21082294
Review.
Molecular Diagnostics in Transfusion Medicine: In Capillary, on a Chip, in Silico, or in Flight?
Henk S P Garritsen, Alex Xiu-Cheng Fan, +6 authors, Bernhard Wörmann.
Transfus Med Hemother, 2009 Jan 01; 36(3). PMID: 21113259    Free PMC article.
Long-term survival of women with basal-like ductal carcinoma in situ of the breast: a population-based cohort study.
Wenjing Zhou, Karin Jirström, +4 authors, Fredrik Wärnberg.
BMC Cancer, 2010 Dec 02; 10. PMID: 21118480    Free PMC article.
Functional identification of neuroprotective molecules.
Cheng Dai, Dong Liang, +3 authors, Valina L Dawson.
PLoS One, 2010 Dec 03; 5(11). PMID: 21124846    Free PMC article.
UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/genomic level.
Shu-Hwa Chen, Chen-Zen Lo, +3 authors, Chung-Yen Lin.
BMC Genomics, 2010 Dec 22; 11 Suppl 4. PMID: 21143815    Free PMC article.
The evolution of bioinformatics in toxicology: advancing toxicogenomics.
Cynthia A Afshari, Hisham K Hamadeh, Pierre R Bushel.
Toxicol Sci, 2010 Dec 24; 120 Suppl 1. PMID: 21177775    Free PMC article.
Review.
Short-segment Barrett's esophagus and cardia intestinal metaplasia: A comparative analysis.
Ying Chang, Bin Liu, +2 authors, Jun Gong.
World J Gastroenterol, 2010 Dec 25; 16(48). PMID: 21182233    Free PMC article.
Statistical method for revealing form-function relations in biological networks.
Andrew Mugler, Boris Grinshpun, Riley Franks, Chris H Wiggins.
Proc Natl Acad Sci U S A, 2010 Dec 25; 108(2). PMID: 21183719    Free PMC article.
Systems approaches to molecular cancer diagnostics.
Shuyi Ma, Cory C Funk, Nathan D Price.
Discov Med, 2010 Dec 30; 10(55). PMID: 21189224    Free PMC article.
Review.
Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
Raad Z Gharaibeh, Anthony A Fodor, Cynthia J Gibas.
PLoS One, 2011 Jan 07; 5(12). PMID: 21209932    Free PMC article.
Using stochastic causal trees to augment Bayesian networks for modeling eQTL datasets.
Kyle C Chipman, Ambuj K Singh.
BMC Bioinformatics, 2011 Jan 08; 12. PMID: 21211042    Free PMC article.
Microarray-based gene expression profiles of silkworm brains.
Ling Gan, Xilong Liu, Zhonghuai Xiang, Ningjia He.
BMC Neurosci, 2011 Jan 21; 12. PMID: 21247463    Free PMC article.
Multiplexed protein analysis using encoded antibody-conjugated microbeads.
Nora Theilacker, Eric E Roller, +2 authors, Xiaohua Huang.
J R Soc Interface, 2011 Jan 21; 8(61). PMID: 21247950    Free PMC article.
Discovery of genes related to diabetic nephropathy in various animal models by current techniques.
Jun Wada, Lin Sun, Yashpal S Kanwar.
Contrib Nephrol, 2011 Jan 22; 169. PMID: 21252517    Free PMC article.
Gene Expression Profiling via Multigene Concatemers.
Kai Jin, Xiaoli Zheng, Yuxian Xia.
PLoS One, 2011 Jan 27; 6(1). PMID: 21267445    Free PMC article.
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity.
Alejandro Tapia, Cristian Vilos, +2 authors, Luigi Devoto.
Reprod Biol Endocrinol, 2011 Jan 29; 9. PMID: 21272326    Free PMC article.
A database for the analysis of immunity genes in Drosophila: PADMA database.
Mark J Lee, Ariful Mondal, +3 authors, Shubha Govind.
Fly (Austin), 2011 Jan 29; 5(2). PMID: 21273816    Free PMC article.
Discovering tumor suppressor genes through genome-wide copy number analysis.
S Michael Rothenberg, Jeff Settleman.
Curr Genomics, 2011 Feb 03; 11(5). PMID: 21286308    Free PMC article.
Fabrication of DNA polymer brush arrays by destructive micropatterning and rolling-circle amplification.
Kristopher D Barbee, Matt Chandrangsu, Xiaohua Huang.
Macromol Biosci, 2011 Feb 10; 11(5). PMID: 21305694    Free PMC article.
Human transcriptome array for high-throughput clinical studies.
Weihong Xu, Junhee Seok, +15 authors, Inflammation and Host Response to Injury Large-Scale Collaborative Research Program.
Proc Natl Acad Sci U S A, 2011 Feb 15; 108(9). PMID: 21317363    Free PMC article.
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns.
Daniel Baron, Emeric Dubois, +9 authors, Rémi Houlgatte.
BMC Genomics, 2011 Feb 18; 12. PMID: 21324190    Free PMC article.
Systems biology: the next frontier for bioinformatics.
Vladimir A Likić, Malcolm J McConville, Trevor Lithgow, Antony Bacic.
Adv Bioinformatics, 2011 Feb 19;. PMID: 21331364    Free PMC article.
Identification and validation of genes involved in cervical tumourigenesis.
Thangarajan Rajkumar, Kesavan Sabitha, +4 authors, Ganesharaja Selvaluxmy.
BMC Cancer, 2011 Feb 23; 11. PMID: 21338529    Free PMC article.
Estrogen-dependent gene expression in the mouse ovary.
Seng H Liew, Mai A Sarraj, Ann E Drummond, Jock K Findlay.
PLoS One, 2011 Feb 25; 6(2). PMID: 21347412    Free PMC article.
Automatically identifying and annotating mouse embryo gene expression patterns.
Liangxiu Han, Jano I van Hemert, Richard A Baldock.
Bioinformatics, 2011 Mar 02; 27(8). PMID: 21357576    Free PMC article.
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods.
Chao Chen, Kay Grennan, +4 authors, Chunyu Liu.
PLoS One, 2011 Mar 10; 6(2). PMID: 21386892    Free PMC article.
Highly Cited.
Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging.
Iuliana E Sendroiu, Lida K Gifford, Andrej Lupták, Robert M Corn.
J Am Chem Soc, 2011 Mar 12; 133(12). PMID: 21391582    Free PMC article.
The first decade and beyond of transcriptional profiling in schizophrenia.
P Adolfo Sequeira, Maureen V Martin, Marquis P Vawter.
Neurobiol Dis, 2011 Mar 15; 45(1). PMID: 21396449    Free PMC article.
Review.
The impact of quantitative optimization of hybridization conditions on gene expression analysis.
Peter Sykacek, David P Kreil, +4 authors, Gos Micklem.
BMC Bioinformatics, 2011 Mar 16; 12. PMID: 21401920    Free PMC article.
A new normalizing algorithm for BAC CGH arrays with quality control metrics.
Jeffrey C Miecznikowski, Daniel P Gaile, +2 authors, Norma Nowak.
J Biomed Biotechnol, 2011 Mar 16; 2011. PMID: 21403910    Free PMC article.
Collection of epithelial cells from rodent mammary gland via laser capture microdissection yielding high-quality RNA suitable for microarray analysis.
John N McGinley, Zongjian Zhu, Weiqin Jiang, Henry J Thompson.
Biol Proced Online, 2010 Jan 01; 12(1). PMID: 21406068    Free PMC article.
Making sense of cancer genomic data.
Lynda Chin, William C Hahn, Gad Getz, Matthew Meyerson.
Genes Dev, 2011 Mar 17; 25(6). PMID: 21406553    Free PMC article.
Highly Cited. Review.
A wholly defined Agilent microarray spike-in dataset.
Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon.
Bioinformatics, 2011 Mar 19; 27(9). PMID: 21414985    Free PMC article.
Multiplex cDNA quantification method that facilitates the standardization of gene expression data.
Osamu Gotoh, Yasufumi Murakami, Akira Suyama.
Nucleic Acids Res, 2011 Mar 19; 39(10). PMID: 21415008    Free PMC article.
Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts.
John A Calarco, Mei Zhen, Benjamin J Blencowe.
RNA, 2011 Mar 19; 17(5). PMID: 21415141    Free PMC article.
Review.
Global array-based transcriptomics from minimal input RNA utilising an optimal RNA isolation process combined with SPIA cDNA probes.
Laura Kennedy, Mahesh Pauriah, +8 authors, Gino Miele.
PLoS One, 2011 Mar 30; 6(3). PMID: 21445340    Free PMC article.
Glycan microarrays for decoding the glycome.
Cory D Rillahan, James C Paulson.
Annu Rev Biochem, 2011 Apr 08; 80. PMID: 21469953    Free PMC article.
Highly Cited. Review.
Molecular genetics of Psoriasis (Principles, technology, gene location, genetic polymorphism and gene expression).
Ahmad A Al Robaee.
Int J Health Sci (Qassim), 2011 Apr 09; 4(2). PMID: 21475550    Free PMC article.
Quantification of protein interactions and solution transport using high-density GMR sensor arrays.
Richard S Gaster, Liang Xu, +5 authors, Shan X Wang.
Nat Nanotechnol, 2011 Apr 12; 6(5). PMID: 21478869    Free PMC article.
A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon).
Rungnapa Leelatanawit, Umaporn Uawisetwathana, Sirawut Klinbunga, Nitsara Karoonuthaisiri.
BMC Mol Biol, 2011 Apr 14; 12. PMID: 21486443    Free PMC article.
A computational framework for gene regulatory network inference that combines multiple methods and datasets.
Rita Gupta, Anna Stincone, +4 authors, Francesco Falciani.
BMC Syst Biol, 2011 Apr 15; 5. PMID: 21489290    Free PMC article.
Integrated analysis of gene expression and copy number data on gene shaving using independent component analysis.
Jinhua Sheng, Hong-Wen Deng, Vince D Calhoun, Yu-Ping Wang.
IEEE/ACM Trans Comput Biol Bioinform, 2011 Apr 27; 8(6). PMID: 21519112    Free PMC article.
Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.
Yutao Liu, Drew Munro, +6 authors, Michael A Hauser.
Mol Vis, 2011 Apr 30; 17. PMID: 21528004    Free PMC article.
Gene expression profiling in lungs of chronic asthmatic mice treated with galectin-3: downregulation of inflammatory and regulatory genes.
Esther López, M Paz Zafra, +3 authors, Victoria del Pozo.
Mediators Inflamm, 2011 May 07; 2011. PMID: 21547260    Free PMC article.
Analysis of differential transcriptional profiling in wheat infected by Blumeria graminis f. sp. tritici using GeneChip.
Jun-Mei Wang, Hong-Yan Liu, +2 authors, Zhen-Sheng Kang.
Mol Biol Rep, 2011 May 11; 39(1). PMID: 21556764
Microarray data analysis and mining tools.
Saravanakumar Selvaraj, Jeyakumar Natarajan.
Bioinformation, 2011 May 18; 6(3). PMID: 21584183    Free PMC article.
New approaches to Prunus transcriptome analysis.
Pedro Martínez-Gómez, Carlos H Crisosto, Claudio Bonghi, Manuel Rubio.
Genetica, 2011 May 18; 139(6). PMID: 21584650
Genomic medicine and neurological disease.
Philip M Boone, Wojciech Wiszniewski, James R Lupski.
Hum Genet, 2011 May 20; 130(1). PMID: 21594611    Free PMC article.
Review.
Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses.
Lichieh Julie Chu, Hanyin Yang, +10 authors, Wailap Victor Ng.
J Proteome Res, 2011 May 24; 10(7). PMID: 21598921    Free PMC article.
A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression.
Alfredo A Kalaitzis, Neil D Lawrence.
BMC Bioinformatics, 2011 May 24; 12. PMID: 21599902    Free PMC article.
Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments.
Bryan A Baker, Valeria T Milam.
Nucleic Acids Res, 2011 May 27; 39(15). PMID: 21613238    Free PMC article.
Expression analysis of prestin and selected transcription factors in newborn rats.
Johann Gross, Maximilian Angerstein, +2 authors, Birgit Mazurek.
Cell Mol Neurobiol, 2011 May 27; 31(7). PMID: 21614551
Plant-pathogen interactions: what microarray tells about it?
T D Lodha, J Basak.
Mol Biotechnol, 2011 May 28; 50(1). PMID: 21618071
Review.
Computational methods for transcriptome annotation and quantification using RNA-seq.
Manuel Garber, Manfred G Grabherr, Mitchell Guttman, Cole Trapnell.
Nat Methods, 2011 May 31; 8(6). PMID: 21623353
Highly Cited. Review.
Microarrays, deep sequencing and the true measure of the transcriptome.
John H Malone, Brian Oliver.
BMC Biol, 2011 Jun 02; 9. PMID: 21627854    Free PMC article.
Highly Cited. Review.
D-MaPs - DNA-microarray projects: Web-based software for multi-platform microarray analysis.
Marcelo F Carazzolle, Taís S Herig, Ana C Deckmann, Gonçalo A G Pereira.
Genet Mol Biol, 2009 Jul 01; 32(3). PMID: 21637530    Free PMC article.
Genome-wide detection of novel regulatory RNAs in E. coli.
Rahul Raghavan, Eduardo A Groisman, Howard Ochman.
Genome Res, 2011 Jun 15; 21(9). PMID: 21665928    Free PMC article.
Highly Cited.
Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA.
Atul J Butte, Nigam H Shah.
J Am Med Inform Assoc, 2011 Jun 16; 18(4). PMID: 21672904    Free PMC article.
A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks.
Koji Kyoda, Kotaro Baba, Hiroaki Kitano, Shuichi Onami.
Source Code Biol Med, 2011 Jun 28; 6(1). PMID: 21699737    Free PMC article.
Analysis of gene expression profile of Arabidopsis genes under trichloroethylene stresses with the use of a full-length cDNA microarray.
Bo Zhu, Ri-He Peng, +10 authors, Quan-Hong Yao.
Mol Biol Rep, 2011 Jul 12; 39(4). PMID: 21743994
Defining genome maintenance pathways using functional genomic approaches.
Carol E Bansbach, David Cortez.
Crit Rev Biochem Mol Biol, 2011 Jul 27; 46(4). PMID: 21787120    Free PMC article.
Review.
Gene coexpression network analysis as a source of functional annotation for rice genes.
Kevin L Childs, Rebecca M Davidson, C Robin Buell.
PLoS One, 2011 Jul 30; 6(7). PMID: 21799793    Free PMC article.
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana.
Cheng-Wei Yao, Ban-Dar Hsu, Bor-Sen Chen.
BMC Bioinformatics, 2011 Aug 13; 12. PMID: 21834997    Free PMC article.
Bacterial transcriptomics: what is beyond the RNA horiz-ome?
Marc Güell, Eva Yus, Maria Lluch-Senar, Luis Serrano.
Nat Rev Microbiol, 2011 Aug 13; 9(9). PMID: 21836626
Review.
LeukoCatch, a quick and efficient tool for the preparation of leukocyte extracts from blood.
Daisuke Okuzaki, Shoichi Kimura, +2 authors, Hiroshi Nojima.
BMC Clin Pathol, 2011 Aug 19; 11. PMID: 21849019    Free PMC article.
Discovery and preclinical validation of drug indications using compendia of public gene expression data.
Marina Sirota, Joel T Dudley, +5 authors, Atul J Butte.
Sci Transl Med, 2011 Aug 19; 3(96). PMID: 21849665    Free PMC article.
Highly Cited.
Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
Doris Steger, David Berry, +4 authors, Alexander Loy.
PLoS One, 2011 Aug 23; 6(8). PMID: 21858215    Free PMC article.
An emulsion based microarray method to detect the toxin genes of toxin-producing organisms.
Ying Wang, Jiafeng Lu, +2 authors, Qinyu Ge.
Molecules, 2011 Aug 31; 16(9). PMID: 21876483    Free PMC article.
Molecular beacons: powerful tools for imaging RNA in living cells.
Ricardo Monroy-Contreras, Luis Vaca.
J Nucleic Acids, 2011 Aug 31; 2011. PMID: 21876785    Free PMC article.
Comprehensive assessment of host responses to ionizing radiation by nuclear factor-κB bioluminescence imaging-guided transcriptomic analysis.
Chung-Ta Chang, Ho Lin, +6 authors, Chien-Yun Hsiang.
PLoS One, 2011 Sep 03; 6(8). PMID: 21887294    Free PMC article.
Microarrays for pathogen detection and analysis.
Kevin S McLoughlin.
Brief Funct Genomics, 2011 Sep 21; 10(6). PMID: 21930658    Free PMC article.
Review.
Differential gene expression between wild-type and Gulo-deficient mice supplied with vitamin C.
Yan Jiao, Jifei Zhang, +6 authors, Weikuan Gu.
Genet Mol Biol, 2011 Sep 21; 34(3). PMID: 21931508    Free PMC article.
Multi-membership gene regulation in pathway based microarray analysis.
Stelios P Pavlidis, Annette M Payne, Stephen M Swift.
Algorithms Mol Biol, 2011 Sep 24; 6. PMID: 21939531    Free PMC article.
Unravelling the complexity of metastasis - molecular understanding and targeted therapies.
Nilay Sethi, Yibin Kang.
Nat Rev Cancer, 2011 Sep 24; 11(10). PMID: 21941285
Highly Cited. Review.
Genomic analysis at the single-cell level.
Tomer Kalisky, Paul Blainey, Stephen R Quake.
Annu Rev Genet, 2011 Sep 29; 45. PMID: 21942365    Free PMC article.
Review.
Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform.
Ji Qiu, Joshua LaBaer.
Methods Enzymol, 2011 Sep 29; 500. PMID: 21943897    Free PMC article.
Insight into the heterogeneity of breast cancer through next-generation sequencing.
Hege G Russnes, Nicholas Navin, James Hicks, Anne-Lise Borresen-Dale.
J Clin Invest, 2011 Oct 04; 121(10). PMID: 21965338    Free PMC article.
Highly Cited. Review.
Microarray-based cancer prediction using single genes.
Xiaosheng Wang, Richard Simon.
BMC Bioinformatics, 2011 Oct 11; 12. PMID: 21982331    Free PMC article.
Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis.
Régis Lavigne, Emmanuelle Becker, +4 authors, Charles Pineau.
Mol Cell Proteomics, 2011 Oct 15; 11(2). PMID: 21997732    Free PMC article.
A system for performing high throughput assays of synaptic function.
Chris M Hempel, Michael Sivula, +7 authors, Jeffrey R Cottrell.
PLoS One, 2011 Oct 15; 6(10). PMID: 21998743    Free PMC article.
Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches.
Ronald J Hause, Hyung-Do Kim, Kin K Leung, Richard Baker Jones.
Expert Rev Proteomics, 2011 Oct 18; 8(5). PMID: 21999828    Free PMC article.
Review.
Towards multiple readout application of plasmonic arrays.
Dana Cialla, Karina Weber, +6 authors, Jürgen Popp.
Beilstein J Nanotechnol, 2011 Oct 18; 2. PMID: 22003456    Free PMC article.
Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples.
Anna Dvorkin-Gheva, John A Hassell.
PLoS One, 2011 Oct 25; 6(10). PMID: 22022496    Free PMC article.
Evolving genomic approaches to idiopathic pulmonary fibrosis: moving beyond genes.
Daniel J Kass, Naftali Kaminski.
Clin Transl Sci, 2011 Oct 28; 4(5). PMID: 22029812    Free PMC article.
Review.
Curcumin-the paradigm of a multi-target natural compound with applications in cancer prevention and treatment.
Marie-Hélène Teiten, Serge Eifes, Mario Dicato, Marc Diederich.
Toxins (Basel), 2010 Jan 01; 2(1). PMID: 22069551    Free PMC article.
Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments.
Chang Ding, Jianzhong He.
Microb Biotechnol, 2011 Nov 11; 5(3). PMID: 22070763    Free PMC article.
Review.
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.
Ming Hu, Yu Zhu, +2 authors, Zhaohui S Qin.
Bioinformatics, 2011 Nov 11; 28(1). PMID: 22072384    Free PMC article.
Application of phylogenetic microarrays to interrogation of human microbiota.
Oleg Paliy, Richard Agans.
FEMS Microbiol Ecol, 2011 Nov 19; 79(1). PMID: 22092522    Free PMC article.
Review.
Towards an evidence-based process for the clinical interpretation of copy number variation.
E R Riggs, D M Church, +11 authors, C L Martin.
Clin Genet, 2011 Nov 22; 81(5). PMID: 22097934    Free PMC article.
Review.
Sensitive RNA detection by combining three-way junction formation and primer generation-rolling circle amplification.
Taku Murakami, Jun Sumaoka, Makoto Komiyama.
Nucleic Acids Res, 2011 Dec 01; 40(3). PMID: 22127872    Free PMC article.
Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.
Brian A Kennedy, Xun Lan, +2 authors, Victor X Jin.
Methods Mol Biol, 2011 Dec 02; 802. PMID: 22130890    Free PMC article.
NANOSTRUCTURED PROBES FOR IN VIVO GENE DETECTION.
Gang Bao, Phillip Santangelo, Nitin Nitin, Won Jong Rhee.
Nanomedicine (Chichester), 2010 Jan 01;. PMID: 22138717    Free PMC article.
Empirical comparison of cross-platform normalization methods for gene expression data.
Jason Rudy, Faramarz Valafar.
BMC Bioinformatics, 2011 Dec 14; 12. PMID: 22151536    Free PMC article.
Evaluation of the cell viability of human Wharton's jelly stem cells for use in cell therapy.
Ingrid Garzón, Barbara Pérez-Köhler, +7 authors, Miguel Alaminos.
Tissue Eng Part C Methods, 2011 Dec 15; 18(6). PMID: 22166141    Free PMC article.
Event extraction for DNA methylation.
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii.
J Biomed Semantics, 2011 Dec 15; 2 Suppl 5. PMID: 22166595    Free PMC article.
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana.
Jianhua Ruan, Joseph Perez, +3 authors, Valerie M Sponsel.
BMC Bioinformatics, 2011 Dec 30; 12 Suppl 12. PMID: 22168340    Free PMC article.
Chronic psychosocial stressors and salivary biomarkers in emerging adults.
Andrew W Bergen, Aditi Mallick, +8 authors, Judy A Andrews.
Psychoneuroendocrinology, 2011 Dec 17; 37(8). PMID: 22172638    Free PMC article.
Aberrant signaling pathways in squamous cell lung carcinoma.
Ivy Shi, Nooshin Hashemi Sadraei, Zhong-Hui Duan, Ting Shi.
Cancer Inform, 2011 Dec 17; 10. PMID: 22174565    Free PMC article.
CrossQuery: a web tool for easy associative querying of transcriptome data.
Toni U Wagner, Andreas Fischer, Eva C Thoma, Manfred Schartl.
PLoS One, 2011 Dec 17; 6(12). PMID: 22174941    Free PMC article.
Simultaneous measurement of 10,000 protein-ligand affinity constants using microarray-based kinetic constant assays.
James P Landry, Yiyan Fei, Xiangdong Zhu.
Assay Drug Dev Technol, 2011 Dec 24; 10(3). PMID: 22192305    Free PMC article.
Partition decoupling for multi-gene analysis of gene expression profiling data.
Rosemary Braun, Gregory Leibon, Scott Pauls, Daniel Rockmore.
BMC Bioinformatics, 2012 Jan 03; 12. PMID: 22208906    Free PMC article.
Interrogating genomic and epigenomic data to understand prostate cancer.
Jung Kim, Jindan Yu.
Biochim Biophys Acta, 2012 Jan 14; 1825(2). PMID: 22240201    Free PMC article.
Review.
Use of negative dielectrophoresis for selective elution of protein-bound particles.
Mehdi Javanmard, Sam Emaminejad, Robert W Dutton, Ronald W Davis.
Anal Chem, 2012 Jan 17; 84(3). PMID: 22242790    Free PMC article.
Differential network biology.
Trey Ideker, Nevan J Krogan.
Mol Syst Biol, 2012 Jan 19; 8. PMID: 22252388    Free PMC article.
Highly Cited. Review.
The role of gene expression profiling in early-stage non-small cell lung cancer.
Wenlong Shao, Daoyuan Wang, Jianxing He.
J Thorac Dis, 2010 Jun 01; 2(2). PMID: 22263026    Free PMC article.
Single-cell and regional gene expression analysis in Alzheimer's disease.
Ruby Kwong, Michelle K Lupton, Michal Janitz.
Cell Mol Neurobiol, 2012 Jan 25; 32(4). PMID: 22271178
Review.
Toxicogenomic biomarkers for liver toxicity.
Naoki Kiyosawa, Yosuke Ando, Sunao Manabe, Takashi Yamoto.
J Toxicol Pathol, 2009 Mar 01; 22(1). PMID: 22271975    Free PMC article.
Macro-level modeling of the response of C. elegans reproduction to chronic heat stress.
Patrick D McMullen, Erin Z Aprison, +3 authors, Ilya Ruvinsky.
PLoS Comput Biol, 2012 Feb 01; 8(1). PMID: 22291584    Free PMC article.
Salt tolerance.
Liming Xiong, Jian-Kang Zhu.
Arabidopsis Book, 2002 Jan 01; 1. PMID: 22303210    Free PMC article.
Transcriptional regulation: a genomic overview.
José Luis Riechmann.
Arabidopsis Book, 2002 Jan 01; 1. PMID: 22303220    Free PMC article.
The Arabidopsis cytoskeletal genome.
Richard B Meagher, Marcus Fechheimer.
Arabidopsis Book, 2003 Jan 01; 2. PMID: 22303225    Free PMC article.
Accurate measurement of the relative abundance of different DNA species in complex DNA mixtures.
Sangkyun Jeong, Hyunjoo Yu, Karl Pfeifer.
DNA Res, 2012 Feb 16; 19(3). PMID: 22334570    Free PMC article.
DNA sensors with diamond as a promising alternative transducer material.
Veronique Vermeeren, Sylvia Wenmackers, Patrick Wagner, Luc Michiels.
Sensors (Basel), 2009 Jan 01; 9(7). PMID: 22346717    Free PMC article.
Optimizing the specificity of nucleic acid hybridization.
David Yu Zhang, Sherry Xi Chen, Peng Yin.
Nat Chem, 2012 Feb 23; 4(3). PMID: 22354435    Free PMC article.
Microarray analysis of differentially expressed genes between cysts and trophozoites of Acanthamoeba castellanii.
Eun-Kyung Moon, Ying-Hua Xuan, +2 authors, Hyun-Hee Kong.
Korean J Parasitol, 2012 Feb 23; 49(4). PMID: 22355200    Free PMC article.
Use of non-amplified RNA samples for microarray analysis of gene expression.
Hiroko Sudo, Atsuko Mizoguchi, +2 authors, Satoko Takizawa.
PLoS One, 2012 Feb 23; 7(2). PMID: 22355363    Free PMC article.
Sequence similarity based identification of abiotic stress responsive genes in chickpea.
Manish Roorkiwal, Prakash Chand Sharma.
Bioinformation, 2012 Feb 24; 8(2). PMID: 22359442    Free PMC article.
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
Hazuki Takahashi, Timo Lassmann, Mitsuyoshi Murata, Piero Carninci.
Nat Protoc, 2012 Mar 01; 7(3). PMID: 22362160    Free PMC article.
Highly Cited.
Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.
Sudhakar Thalapati, Anil K Batchu, Sarla Neelamraju, Rajeshwari Ramanan.
Funct Integr Genomics, 2012 Mar 01; 12(2). PMID: 22367483
Translating the brain transcriptome in neuroAIDS: from non-human primates to humans.
Jessica M Winkler, Amrita Datta Chaudhuri, Howard S Fox.
J Neuroimmune Pharmacol, 2012 Mar 01; 7(2). PMID: 22367717    Free PMC article.
Review.
iGepros: an integrated gene and protein annotation server for biological nature exploration.
Guangyong Zheng, Haibo Wang, Chaochun Wei, Yixue Li.
BMC Bioinformatics, 2012 Mar 01; 12 Suppl 14. PMID: 22373022    Free PMC article.
Partitioning transcript variation in Drosophila: abundance, isoforms, and alleles.
Yajie Yang, Rita M Graze, +5 authors, Lauren M McIntyre.
G3 (Bethesda), 2012 Mar 03; 1(6). PMID: 22384353    Free PMC article.
Life on a microarray: assessing live cell functions in a microarray format.
Krisztián Papp, Zoltán Szittner, József Prechl.
Cell Mol Life Sci, 2012 Mar 07; 69(16). PMID: 22391673
Review.
Apparent thixotropic properties of saline/glycerol drops with biotinylated antibodies on streptavidin-coated glass slides: implications for bacterial capture on antibody microarrays.
David M Albin, Andrew G Gehring, Sue A Reed, Shu-I Tu.
Sensors (Basel), 2009 Jan 01; 9(2). PMID: 22399952    Free PMC article.
Microelectrode array biosensor for studying carbohydrate-mediated interactions.
Jeffrey W Chamberlain, Karl Maurer, +3 authors, Daniel M Ratner.
Biosens Bioelectron, 2012 Mar 13; 34(1). PMID: 22405843    Free PMC article.
Genomic basis for light control of plant development.
Jigang Li, William Terzaghi, Xing Wang Deng.
Protein Cell, 2012 Mar 20; 3(2). PMID: 22426979    Free PMC article.
Review.
Progress and prospects for stem cell engineering.
Randolph S Ashton, Albert J Keung, Joseph Peltier, David V Schaffer.
Annu Rev Chem Biomol Eng, 2011 Jan 01; 2. PMID: 22432628    Free PMC article.
Review.
A platform for combined DNA and protein microarrays based on total internal reflection fluorescence.
Alexander Asanov, Angélica Zepeda, Luis Vaca.
Sensors (Basel), 2012 Mar 23; 12(2). PMID: 22438738    Free PMC article.
Omics and therapy - a basis for precision medicine.
Joseph P Garay, Joe W Gray.
Mol Oncol, 2012 Mar 27; 6(2). PMID: 22445068    Free PMC article.
Review.
Science behind human saliva.
Manjul Tiwari.
J Nat Sci Biol Med, 2011 Jan 01; 2(1). PMID: 22470235    Free PMC article.
A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data.
Erlandson F Saraiva, Francisco Louzada, +2 authors, Juliana Cobre.
Comput Math Methods Med, 2012 Apr 05; 2012. PMID: 22474543    Free PMC article.
A normalization strategy for comparing tag count data.
Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu.
Algorithms Mol Biol, 2012 Apr 06; 7(1). PMID: 22475125    Free PMC article.
Identification of common tumor signatures based on gene set enrichment analysis.
Xiaosheng Wang.
In Silico Biol, 2011 Jan 01; 11(1-2). PMID: 22475747    Free PMC article.
Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data.
Katrina M Waters, Tao Liu, +7 authors, Brian D Thrall.
PLoS One, 2012 Apr 06; 7(3). PMID: 22479638    Free PMC article.
Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.
Samuel W Baushke, Robert D Stedtfeld, +5 authors, Syed A Hashsham.
J Microbiol Methods, 2012 Apr 28; 90(1). PMID: 22537822    Free PMC article.
Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays.
Vered Padler-Karavani, Xuezheng Song, +17 authors, Ajit Varki.
J Biol Chem, 2012 May 03; 287(27). PMID: 22549775    Free PMC article.
Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe.
Bo-Ruei Chen, Devin C Hale, Peter J Ciolek, Kurt W Runge.
BMC Genomics, 2012 May 05; 13. PMID: 22554201    Free PMC article.
The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science.
Isak S Pretorius, Christopher D Curtin, Paul J Chambers.
Bioeng Bugs, 2012 May 11; 3(3). PMID: 22572786    Free PMC article.
Review.
Overview of electrochemical DNA biosensors: new approaches to detect the expression of life.
Stefano Cagnin, Marcelo Caraballo, +6 authors, Gerolamo Lanfranchi.
Sensors (Basel), 2009 Jan 01; 9(4). PMID: 22574066