Journal Article
. 2002 Feb;415(6871).
doi: 10.1038/415530a.

Gene expression profiling predicts clinical outcome of breast cancer

Laura J van 't Veer 1 Hongyue Dai  Marc J van de Vijver  Yudong D He  Augustinus A M Hart  Mao Mao  Hans L Peterse  Karin van der Kooy  Matthew J Marton  Anke T Witteveen  George J Schreiber  Ron M Kerkhoven  Chris Roberts  Peter S Linsley  René Bernards  Stephen H Friend  
Affiliations
  • PMID: 11823860
  •     2826 citations

Abstract

Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumours according to their clinical behaviour. Chemotherapy or hormonal therapy reduces the risk of distant metastases by approximately one-third; however, 70-80% of patients receiving this treatment would have survived without it. None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). In addition, we established a signature that identifies tumours of BRCA1 carriers. The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy.

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J Cancer Res Clin Oncol, 2004 Jun 19; 130(9). PMID: 15205947
Review.
New challenges in gene expression data analysis and the extended GEPAS.
Javier Herrero, Juan M Vaquerizas, +4 authors, Joaquín Dopazo.
Nucleic Acids Res, 2004 Jun 25; 32(Web Server issue). PMID: 15215434    Free PMC article.
GOAL: automated Gene Ontology analysis of expression profiles.
Stefano Volinia, Rita Evangelisti, +3 authors, Paolo Gasparini.
Nucleic Acids Res, 2004 Jun 25; 32(Web Server issue). PMID: 15215435    Free PMC article.
The role of cost-effectiveness analysis in the era of pharmacogenomics.
Christopher R Flowers, David Veenstra.
Pharmacoeconomics, 2004 Jun 26; 22(8). PMID: 15217305
Review.
Perspectives and limitations of gene expression profiling in rheumatology: new molecular strategies.
Thomas Häupl, Veit Krenn, +2 authors, Gerd R Burmester.
Arthritis Res Ther, 2004 Jul 01; 6(4). PMID: 15225356    Free PMC article.
Review.
Gene expression patterns as marker for 5-year postoperative prognosis of primary breast cancers.
Masamitsu Onda, Mitsuru Emi, +11 authors, Yusuke Nakamura.
J Cancer Res Clin Oncol, 2004 Jul 06; 130(9). PMID: 15235906
A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue.
Shanaz H Dairkee, Youngran Ji, +3 authors, Stefanie S Jeffrey.
BMC Genomics, 2004 Jul 21; 5(1). PMID: 15260889    Free PMC article.
siRNA-mediated gene silencing: a global genome view.
Dimitri Semizarov, Paul Kroeger, Stephen Fesik.
Nucleic Acids Res, 2004 Jul 24; 32(13). PMID: 15272085    Free PMC article.
Metastatic cancer DNA phenotype identified in normal tissues surrounding metastasizing prostate carcinomas.
Donald C Malins, Naomi K Gilman, +6 authors, Katie M Anderson.
Proc Natl Acad Sci U S A, 2004 Jul 29; 101(31). PMID: 15280533    Free PMC article.
Molecular tumor profiling: translating genomic insights into clinical advances.
Alison H Trainer.
Genome Biol, 2004 Aug 04; 5(8). PMID: 15287965    Free PMC article.
A multigene RT-PCR assay used to predict recurrence in early breast cancer: two presentations with contradictory results.
Willem E Fiets, Johan W R Nortier.
Breast Cancer Res, 2004 Aug 21; 6(5). PMID: 15318922    Free PMC article.
Recent translational research: microarray expression profiling of breast cancer--beyond classification and prognostic markers?
Cindy A Wilson, Judy Dering.
Breast Cancer Res, 2004 Aug 21; 6(5). PMID: 15318924    Free PMC article.
Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.
Chin-Yo Lin, Anders Ström, +14 authors, Edison T Liu.
Genome Biol, 2004 Sep 04; 5(9). PMID: 15345050    Free PMC article.
Highly Cited.
Balancing false positives and false negatives for the detection of differential expression in malignancies.
F De Smet, Y Moreau, +3 authors, B De Moor.
Br J Cancer, 2004 Sep 09; 91(6). PMID: 15354216    Free PMC article.
Methods to find out the expression of activated genes.
Sten Z Cekan.
Reprod Biol Endocrinol, 2004 Sep 24; 2. PMID: 15385048    Free PMC article.
Review.
A combinational feature selection and ensemble neural network method for classification of gene expression data.
Bing Liu, Qinghua Cui, Tianzi Jiang, Songde Ma.
BMC Bioinformatics, 2004 Sep 29; 5. PMID: 15450124    Free PMC article.
Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma.
Jun S Wei, Braden T Greer, +11 authors, Javed Khan.
Cancer Res, 2004 Oct 07; 64(19). PMID: 15466177    Free PMC article.
Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA.
Martin Huber, Tai-Fen Wei, +3 authors, Y Paul Bao.
Nucleic Acids Res, 2004 Oct 12; 32(18). PMID: 15475384    Free PMC article.
Mitochondrial survivin inhibits apoptosis and promotes tumorigenesis.
Takehiko Dohi, Elena Beltrami, +2 authors, Dario C Altieri.
J Clin Invest, 2004 Oct 19; 114(8). PMID: 15489959    Free PMC article.
Highly Cited.
Combining gene expression data from different generations of oligonucleotide arrays.
Kyu-Baek Hwang, Sek Won Kong, Steve A Greenberg, Peter J Park.
BMC Bioinformatics, 2004 Oct 27; 5. PMID: 15504239    Free PMC article.
Real-time RT-PCR correlates with immunocytochemistry for the detection of disseminated epithelial cells in bone marrow aspirates of patients with breast cancer.
I H Benoy, H Elst, +6 authors, L Y Dirix.
Br J Cancer, 2004 Oct 27; 91(10). PMID: 15505629    Free PMC article.
Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays.
Marina Bibikova, Dimitri Talantov, +9 authors, Jian-Bing Fan.
Am J Pathol, 2004 Oct 29; 165(5). PMID: 15509548    Free PMC article.
Genetic inheritance of gene expression in human cell lines.
S A Monks, A Leonardson, +6 authors, E E Schadt.
Am J Hum Genet, 2004 Oct 30; 75(6). PMID: 15514893    Free PMC article.
Highly Cited.
Systematic analysis and nomenclature of mammalian F-box proteins.
Jianping Jin, Timothy Cardozo, +3 authors, J Wade Harper.
Genes Dev, 2004 Nov 03; 18(21). PMID: 15520277    Free PMC article.
Highly Cited.
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 amplification method tolerant to sample degradation.
Gang Wang, Elizabeth Maher, +7 authors, G Mike Makrigiorgos.
Genome Res, 2004 Nov 03; 14(11). PMID: 15520297    Free PMC article.
Gene expression profiling of microdissected pancreatic ductal carcinomas using high-density DNA microarrays.
Robert Grützmann, Christian Pilarsky, +11 authors, Hans Detlev Saeger.
Neoplasia, 2004 Nov 19; 6(5). PMID: 15548371    Free PMC article.
Design of a real time quantitative PCR assay to assess global mRNA amplification of small size specimens for microarray hybridisation.
V Choesmel, F Foucault, J P Thiery, N Blin.
J Clin Pathol, 2004 Nov 26; 57(12). PMID: 15563668    Free PMC article.
Co-stimulation of human breast cancer cells with transforming growth factor-beta and tenascin-C enhances matrix metalloproteinase-9 expression and cancer cell invasion.
Kalembeyi Ilunga, Rika Nishiura, +4 authors, Toshimichi Yoshida.
Int J Exp Pathol, 2004 Nov 30; 85(6). PMID: 15566434    Free PMC article.
Comparing functional annotation analyses with Catmap.
Thomas Breslin, Patrik Edén, Morten Krogh.
BMC Bioinformatics, 2004 Dec 14; 5. PMID: 15588298    Free PMC article.
Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data.
Ronglai Shen, Debashis Ghosh, Arul M Chinnaiyan.
BMC Genomics, 2004 Dec 16; 5(1). PMID: 15598354    Free PMC article.
Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.
Kristen M Carr, Kevin Rosenblatt, Emanuel F Petricoin, Lance A Liotta.
Hum Genomics, 2004 Dec 17; 1(2). PMID: 15601541    Free PMC article.
Review.
Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis.
I Zucchi, E Mento, +10 authors, R Dulbecco.
Proc Natl Acad Sci U S A, 2004 Dec 21; 101(52). PMID: 15608061    Free PMC article.
Gene expression profiling of primary breast cancer.
Roman Rouzier, Peter Wagner, Paolo Morandi, Lajos Pusztai.
Curr Oncol Rep, 2004 Dec 22; 7(1). PMID: 15610685
Review.
Candidate-based proteomics in the search for biomarkers of cardiovascular disease.
Leigh Anderson.
J Physiol, 2004 Dec 22; 563(Pt 1). PMID: 15611012    Free PMC article.
Review.
In situ hybridization in the pathology laboratory: general principles, automation, and emerging research applications for tissue-based studies of gene expression.
David G Hicks, Gabe Longoria, +3 authors, Raymond Tubbs.
J Mol Histol, 2004 Dec 23; 35(6). PMID: 15614613
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.
Gastric adenocarcinoma: review and considerations for future directions.
Bryan J Dicken, David L Bigam, +3 authors, Stewart M Hamilton.
Ann Surg, 2004 Dec 29; 241(1). PMID: 15621988    Free PMC article.
Highly Cited. Review.
Distinct organ-specific metastatic potential of individual breast cancer cells and primary tumors.
Andy J Minn, Yibin Kang, +7 authors, Joan Massagué.
J Clin Invest, 2005 Jan 05; 115(1). PMID: 15630443    Free PMC article.
Highly Cited.
Breast cancer oestrogen independence mediated by BCAR1 or BCAR3 genes is transmitted through mechanisms distinct from the oestrogen receptor signalling pathway or the epidermal growth factor receptor signalling pathway.
Lambert C J Dorssers, Ton van Agthoven, +3 authors, Koen J Dechering.
Breast Cancer Res, 2005 Jan 12; 7(1). PMID: 15642172    Free PMC article.
TGF-beta and the Smad signaling pathway support transcriptomic reprogramming during epithelial-mesenchymal cell transition.
Ulrich Valcourt, Marcin Kowanetz, +2 authors, Aristidis Moustakas.
Mol Biol Cell, 2005 Feb 04; 16(4). PMID: 15689496    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.
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival.
Howard Y Chang, Dimitry S A Nuyten, +10 authors, Marc J van de Vijver.
Proc Natl Acad Sci U S A, 2005 Feb 11; 102(10). PMID: 15701700    Free PMC article.
Highly Cited.
Genomic approaches in the management and treatment of breast cancer.
J C Chang, S G Hilsenbeck, S A W Fuqua.
Br J Cancer, 2005 Feb 17; 92(4). PMID: 15714204    Free PMC article.
Review.
Utilizing prognostic and predictive factors in breast cancer.
Deepa S Subramaniam, Claudine Isaacs.
Curr Treat Options Oncol, 2005 Feb 19; 6(2). PMID: 15717996
Review.
Expression of AMAP1, an ArfGAP, provides novel targets to inhibit breast cancer invasive activities.
Yasuhito Onodera, Shigeru Hashimoto, +10 authors, Hisataka Sabe.
EMBO J, 2005 Feb 19; 24(5). PMID: 15719014    Free PMC article.
Gene expression profiling of breast cancer in ethnic populations: an aid to gene discovery for the benefit of all.
Steve Goodison.
Breast J, 2005 Feb 26; 11(2). PMID: 15730452    Free PMC article.
Review.
Show me the genes - I will tell you who/how to treat!
Fatima Cardoso.
Breast Cancer Res, 2005 Mar 04; 7(2). PMID: 15743515    Free PMC article.
A microarray-based gastric carcinoma prewarning system.
Da-Xiang Cui, Li Zhang, +12 authors, Hua-Jian Gao.
World J Gastroenterol, 2005 Mar 12; 11(9). PMID: 15761963    Free PMC article.
Gene expression signature of estrogen receptor alpha status in breast cancer.
Martín C Abba, Yuhui Hu, +5 authors, C Marcelo Aldaz.
BMC Genomics, 2005 Mar 15; 6. PMID: 15762987    Free PMC article.
In silico microdissection of microarray data from heterogeneous cell populations.
Harri Lähdesmäki, Llya Shmulevich, +2 authors, Wei Zhang.
BMC Bioinformatics, 2005 Mar 16; 6. PMID: 15766384    Free PMC article.
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.
Gene expression analysis of immune-mediated arrest of tumorigenesis in a transgenic mouse model of HER-2/neu-positive basal-like mammary carcinoma.
Annalisa Astolfi, Lorena Landuzzi, +10 authors, Pier-Luigi Lollini.
Am J Pathol, 2005 Mar 29; 166(4). PMID: 15793299    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
Transcript AA454543 is a novel prognostic marker for hepatocellular carcinoma after curative partial hepatectomy.
Siu Tim Cheung, Jenny C Y Ho, +4 authors, Sheung Tat Fan.
Neoplasia, 2005 Apr 07; 7(2). PMID: 15810144    Free PMC article.
Histopathologic indicators of breast cancer biology: insights from population mammographic screening.
L R Webster, A M Bilous, +5 authors, R L Balleine.
Br J Cancer, 2005 Apr 07; 92(8). PMID: 15812557    Free PMC article.
SPBP is a phosphoserine-specific repressor of estrogen receptor alpha.
Valentina Gburcik, Nathalie Bot, Marcello Maggiolini, Didier Picard.
Mol Cell Biol, 2005 Apr 16; 25(9). PMID: 15831449    Free PMC article.
Modifiers of mammary tumor progression and metastasis on mouse chromosomes 7, 9, and 17.
Mindy Lancaster, Jessica Rouse, Kent W Hunter.
Mamm Genome, 2005 Apr 30; 16(2). PMID: 15859357
Application of proteomics in the study of tumor metastasis.
Zhen Cai, Jen-Fu Chiu, Qing-Yu He.
Genomics Proteomics Bioinformatics, 2005 May 03; 2(3). PMID: 15862116    Free PMC article.
Review.
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.
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.
Maintenance of cell type diversification in the human breast.
Agla Jael Rubner Fridriksdottir, René Villadsen, Thorarinn Gudjonsson, Ole William Petersen.
J Mammary Gland Biol Neoplasia, 2005 May 12; 10(1). PMID: 15886887
Review.
Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors.
Uma R Chandran, Rajiv Dhir, +3 authors, John Gilbertson.
BMC Cancer, 2005 May 17; 5. PMID: 15892885    Free PMC article.
Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer.
Gennadi V Glinsky, Olga Berezovska, Anna B Glinskii.
J Clin Invest, 2005 Jun 03; 115(6). PMID: 15931389    Free PMC article.
Highly Cited.
Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays.
Kuang-Hung Pan, Chih-Jian Lih, Stanley N Cohen.
Proc Natl Acad Sci U S A, 2005 Jun 14; 102(25). PMID: 15951424    Free PMC article.
An integrative genomics approach to infer causal associations between gene expression and disease.
Eric E Schadt, John Lamb, +18 authors, Aldons J Lusis.
Nat Genet, 2005 Jun 21; 37(7). PMID: 15965475    Free PMC article.
Highly Cited.
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Juan M Vaquerizas, Lucía Conde, +6 authors, Joaquín Dopazo.
Nucleic Acids Res, 2005 Jun 28; 33(Web Server issue). PMID: 15980548    Free PMC article.
Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt.
Ahmed Ashour Ahmed, James D Brenton.
Breast Cancer Res, 2005 Jul 01; 7(3). PMID: 15987437    Free PMC article.
Review.
The promise of microarrays in the management and treatment of breast cancer.
Jenny C Chang, Susan G Hilsenbeck, Suzanne A W Fuqua.
Breast Cancer Res, 2005 Jul 01; 7(3). PMID: 15987438    Free PMC article.
Review.
Signal transduction pathway profiling of individual tumor samples.
Thomas Breslin, Morten Krogh, Carsten Peterson, Carl Troein.
BMC Bioinformatics, 2005 Jul 01; 6. PMID: 15987529    Free PMC article.
p63, cytokeratin 5, and P-cadherin: three molecular markers to distinguish basal phenotype in breast carcinomas.
Irina Matos, Rozany Dufloth, +2 authors, Fernando Schmitt.
Virchows Arch, 2005 Jul 14; 447(4). PMID: 16012853
Heat shock proteins in cancer: diagnostic, prognostic, predictive, and treatment implications.
Daniel R Ciocca, Stuart K Calderwood.
Cell Stress Chaperones, 2005 Jul 26; 10(2). PMID: 16038406    Free PMC article.
Highly Cited. Review.
Classification and selection of biomarkers in genomic data using LASSO.
Debashis Ghosh, Arul M Chinnaiyan.
J Biomed Biotechnol, 2005 Jul 28; 2005(2). PMID: 16046820    Free PMC article.
Storing, linking, and mining microarray databases using SRS.
Antoine Veldhoven, Don de Lange, +3 authors, Guido Jenster.
BMC Bioinformatics, 2005 Jul 29; 6. PMID: 16048644    Free PMC article.
Genes that mediate breast cancer metastasis to lung.
Andy J Minn, Gaorav P Gupta, +7 authors, Joan Massagué.
Nature, 2005 Jul 29; 436(7050). PMID: 16049480    Free PMC article.
Highly Cited.
Primary chemotherapy with gemcitabine, epirubicin and taxol (GET) in operable breast cancer: a phase II study.
P F Conte, S Donati, +16 authors, L Crino.
Br J Cancer, 2005 Jul 30; 93(4). PMID: 16052214    Free PMC article.
From the Cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response.
Josée Laganière, Geneviève Deblois, +3 authors, Vincent Giguère.
Proc Natl Acad Sci U S A, 2005 Aug 10; 102(33). PMID: 16087863    Free PMC article.
Highly Cited.
Predictors of primary breast cancers responsiveness to preoperative epirubicin/cyclophosphamide-based chemotherapy: translation of microarray data into clinically useful predictive signatures.
Olga Modlich, Hans-Bernd Prisack, +2 authors, Hans Bojar.
J Transl Med, 2005 Aug 11; 3. PMID: 16091131    Free PMC article.
Genomic medicine: genetic variation and its impact on the future of health care.
Huntington F Willard, Misha Angrist, Geoffrey S Ginsburg.
Philos Trans R Soc Lond B Biol Sci, 2005 Aug 13; 360(1460). PMID: 16096102    Free PMC article.
Review.
A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced Renilla luciferase-antigen fusion proteins.
Peter D Burbelo, Radoslav Goldman, Thomas L Mattson.
BMC Biotechnol, 2005 Aug 20; 5. PMID: 16109166    Free PMC article.
stam--a Bioconductor compliant R package for structured analysis of microarray data.
Claudio Lottaz, Rainer Spang.
BMC Bioinformatics, 2005 Aug 27; 6. PMID: 16122395    Free PMC article.
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival.
Lance D Miller, Johanna Smeds, +8 authors, Jonas Bergh.
Proc Natl Acad Sci U S A, 2005 Sep 06; 102(38). PMID: 16141321    Free PMC article.
Highly Cited.
L2L: a simple tool for discovering the hidden significance in microarray expression data.
John C Newman, Alan M Weiner.
Genome Biol, 2005 Sep 20; 6(9). PMID: 16168088    Free PMC article.
Early detection of breast cancer based on gene-expression patterns in peripheral blood cells.
Praveen Sharma, Narinder S Sahni, +14 authors, Anders Lönneborg.
Breast Cancer Res, 2005 Sep 20; 7(5). PMID: 16168108    Free PMC article.
No common denominator for breast cancer lymph node metastasis.
B Weigelt, L F A Wessels, +6 authors, L J van't Veer.
Br J Cancer, 2005 Sep 29; 93(8). PMID: 16189523    Free PMC article.
Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis.
Laura España, Berta Martín, +4 authors, Angels Sierra.
Am J Pathol, 2005 Sep 30; 167(4). PMID: 16192647    Free PMC article.
A unique gene expression signature discriminates familial Alzheimer's disease mutation carriers from their wild-type siblings.
Yosuke Nagasaka, Karin Dillner, +9 authors, Caroline Graff.
Proc Natl Acad Sci U S A, 2005 Oct 04; 102(41). PMID: 16199521    Free PMC article.
Numbers of mutations to different types of colorectal cancer.
Peter Calabrese, Jukka-Pekka Mecklin, +3 authors, Darryl Shibata.
BMC Cancer, 2005 Oct 06; 5. PMID: 16202134    Free PMC article.
A cancer-specific transcriptional signature in human neoplasia.
Francesco Nicassio, Fabrizio Bianchi, +7 authors, Pier Paolo Di Fiore.
J Clin Invest, 2005 Oct 15; 115(11). PMID: 16224537    Free PMC article.
Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles.
Elza C de Bruin, Simone van de Pas, +10 authors, Lucy T C Peltenburg.
BMC Genomics, 2005 Oct 18; 6. PMID: 16225673    Free PMC article.
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes.
Patrick Warnat, Roland Eils, Benedikt Brors.
BMC Bioinformatics, 2005 Nov 08; 6. PMID: 16271137    Free PMC article.
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts.
Yudi Pawitan, Judith Bjöhle, +17 authors, Jonas Bergh.
Breast Cancer Res, 2005 Nov 11; 7(6). PMID: 16280042    Free PMC article.
Highly Cited.
Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.
Aaron G Lewis, James Flanagan, +8 authors, Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer.
Breast Cancer Res, 2005 Nov 11; 7(6). PMID: 16280053    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.
Platelet genomics and proteomics in human health and disease.
Iain C Macaulay, Philippa Carr, +3 authors, Nicholas A Watkins.
J Clin Invest, 2005 Dec 03; 115(12). PMID: 16322782    Free PMC article.
Review.
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.
Federica Cavallo, Annalisa Astolfi, +4 authors, Raffaele Calogero.
BMC Bioinformatics, 2005 Dec 15; 6 Suppl 4. PMID: 16351756    Free PMC article.
Predicting the sites of metastases.
Brian Z Ring, Douglas T Ross.
Genome Biol, 2005 Dec 17; 6(12). PMID: 16356275    Free PMC article.
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.
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis.
Adil Elfilali, Séverine Lair, +3 authors, Emmanuel Barillot.
Nucleic Acids Res, 2005 Dec 31; 34(Database issue). PMID: 16381943    Free PMC article.
Gene selection and classification of microarray data using random forest.
Ramón Díaz-Uriarte, Sara Alvarez de Andrés.
BMC Bioinformatics, 2006 Jan 10; 7. PMID: 16398926    Free PMC article.
Highly Cited.
An approach for clustering gene expression data with error information.
Brian Tjaden.
BMC Bioinformatics, 2006 Jan 18; 7. PMID: 16409635    Free PMC article.
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers.
Jen-Tsan Chi, Zhen Wang, +13 authors, Patrick O Brown.
PLoS Med, 2006 Jan 19; 3(3). PMID: 16417408    Free PMC article.
Highly Cited.
Gene expression profiling of primary cultures of ovarian epithelial cells identifies novel molecular classifiers of ovarian cancer.
C Le Page, V Ouellet, +5 authors, A-M Mes-Masson.
Br J Cancer, 2006 Jan 20; 94(3). PMID: 16421595    Free PMC article.
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.
Ming Yi, Jay D Horton, +2 authors, Robert M Stephens.
BMC Bioinformatics, 2006 Jan 21; 7. PMID: 16423281    Free PMC article.
Expression of cyclin-dependent kinases and CDC25a phosphatase is related with recurrences and survival in women with peri- and post-menopausal breast cancer.
Serena Bonin, Davide Brunetti, +2 authors, Giorgio Stanta.
Virchows Arch, 2006 Jan 28; 448(5). PMID: 16440198
Gene expression in breast cancer.
Virginia G Kaklamani, William J Gradishar.
Curr Treat Options Oncol, 2006 Feb 04; 7(2). PMID: 16455023
Review.
High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization.
Tara L Naylor, Joel Greshock, +5 authors, Barbara L Weber.
Breast Cancer Res, 2006 Feb 07; 7(6). PMID: 16457699    Free PMC article.
Metastasis predictive signature profiles pre-exist in normal tissues.
Haiyan Yang, Nigel Crawford, +3 authors, Kent W Hunter.
Clin Exp Metastasis, 2006 Feb 14; 22(7). PMID: 16475030    Free PMC article.
Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays.
Bernardo R Peixoto, Ricardo Z N Vêncio, +3 authors, Eduardo M Reis.
BMC Genomics, 2006 Mar 01; 7. PMID: 16504121    Free PMC article.
The impact of expression profiling on prognostic and predictive testing in breast cancer.
J S Reis-Filho, C Westbury, J-Y Pierga.
J Clin Pathol, 2006 Mar 01; 59(3). PMID: 16505270    Free PMC article.
Review.
Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology.
Johan Lindberg, Erik af Klint, +5 authors, Joakim Lundeberg.
Arthritis Res Ther, 2006 Mar 02; 8(2). PMID: 16507157    Free PMC article.
Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use.
Raffaella Corvi, Hans-Jürgen Ahr, +21 authors, Leonard M Schechtman.
Environ Health Perspect, 2006 Mar 02; 114(3). PMID: 16507466    Free PMC article.
Genetic regulators of large-scale transcriptional signatures in cancer.
Adam S Adler, Meihong Lin, +3 authors, Howard Y Chang.
Nat Genet, 2006 Mar 07; 38(4). PMID: 16518402    Free PMC article.
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms.
Rainer König, Gunnar Schramm, +5 authors, Roland Eils.
BMC Bioinformatics, 2006 Mar 10; 7. PMID: 16524469    Free PMC article.
A new method for gene discovery in large-scale microarray data.
Kentaro Yano, Kazuhide Imai, Akifumi Shimizu, Takao Hanashita.
Nucleic Acids Res, 2006 Mar 16; 34(5). PMID: 16537840    Free PMC article.
Gene expression analyses reveal molecular relationships among 20 regions of the human CNS.
Richard B Roth, Peter Hevezi, +4 authors, Albert Zlotnik.
Neurogenetics, 2006 Mar 31; 7(2). PMID: 16572319
Highly Cited.
Systematic analysis of the transcriptional switch inducing migration of border cells.
Lodovica Borghese, Georgina Fletcher, +4 authors, Pernille Rørth.
Dev Cell, 2006 Apr 04; 10(4). PMID: 16580994    Free PMC article.
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer.
Liat Ein-Dor, Or Zuk, Eytan Domany.
Proc Natl Acad Sci U S A, 2006 Apr 06; 103(15). PMID: 16585533    Free PMC article.
Highly Cited.
A systems approach to clinical oncology: focus on breast cancer.
Mark Abramovitz, Brian Leyland-Jones.
Proteome Sci, 2006 Apr 06; 4. PMID: 16595007    Free PMC article.
Distinction between hereditary and sporadic breast cancer on the basis of clinicopathological data.
P van der Groep, A Bouter, +7 authors, P J van Diest.
J Clin Pathol, 2006 Apr 11; 59(6). PMID: 16603649    Free PMC article.
The cell-specific activity of the estrogen receptor alpha may be fine-tuned by phosphorylation-induced structural gymnastics.
Valentina Gburcik, Didier Picard.
Nucl Recept Signal, 2006 Apr 11; 4. PMID: 16604168    Free PMC article.
Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors.
Chad J Creighton, Kevin E Cordero, +5 authors, James M Rae.
Genome Biol, 2006 Apr 12; 7(4). PMID: 16606439    Free PMC article.
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data.
Xuegong Zhang, Xin Lu, +7 authors, Wing H Wong.
BMC Bioinformatics, 2006 Apr 12; 7. PMID: 16606446    Free PMC article.
Proteomic technology for biomarker profiling in cancer: an update.
Moulay A Alaoui-Jamali, Ying-jie Xu.
J Zhejiang Univ Sci B, 2006 Apr 21; 7(6). PMID: 16625706    Free PMC article.
Review.
Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay.
Laurent Perreard, Cheng Fan, +18 authors, Philip S Bernard.
Breast Cancer Res, 2006 Apr 22; 8(2). PMID: 16626501    Free PMC article.
Lymphatic or hematogenous dissemination: how does a metastatic tumor cell decide?
Sunny Y Wong, Richard O Hynes.
Cell Cycle, 2006 Apr 22; 5(8). PMID: 16627996    Free PMC article.
Review.
Molecular biology of breast cancer.
Miguel Martín.
Clin Transl Oncol, 2006 Apr 25; 8(1). PMID: 16632434
Review.
GenePING: secure, scalable management of personal genomic data.
Ben Adida, Isaac S Kohane.
BMC Genomics, 2006 Apr 28; 7. PMID: 16638151    Free PMC article.
The molecular portraits of breast tumors are conserved across microarray platforms.
Zhiyuan Hu, Cheng Fan, +28 authors, Charles M Perou.
BMC Genomics, 2006 Apr 29; 7. PMID: 16643655    Free PMC article.
Highly Cited.
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.
RNA interference-mediated silencing of mitotic kinesin KIF14 disrupts cell cycle progression and induces cytokinesis failure.
Michael Carleton, Mao Mao, +7 authors, Peter S Linsley.
Mol Cell Biol, 2006 May 02; 26(10). PMID: 16648480    Free PMC article.
The activity status of cofilin is directly related to invasion, intravasation, and metastasis of mammary tumors.
Weigang Wang, Ghassan Mouneimne, +6 authors, John S Condeelis.
J Cell Biol, 2006 May 03; 173(3). PMID: 16651380    Free PMC article.
Highly Cited.
A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets.
Carmen Lai, Marcel J T Reinders, Laura J van't Veer, Lodewyk F A Wessels.
BMC Bioinformatics, 2006 May 04; 7. PMID: 16670007    Free PMC article.
Characterizing disease states from topological properties of transcriptional regulatory networks.
David P Tuck, Harriet M Kluger, Yuval Kluger.
BMC Bioinformatics, 2006 May 04; 7. PMID: 16670008    Free PMC article.
Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia with a normal karyotype: a Cancer and Leukemia Group B study.
Michael D Radmacher, Guido Marcucci, +11 authors, Cancer and Leukemia Group B.
Blood, 2006 May 04; 108(5). PMID: 16670265    Free PMC article.
Expression profiling and prediction of distant metastases in head and neck squamous cell carcinoma.
B J M Braakhuis, A Senft, +6 authors, R H Brakenhoff.
J Clin Pathol, 2006 May 09; 59(12). PMID: 16679350    Free PMC article.
Genetic variation in putative regulatory loci controlling gene expression in breast cancer.
Vessela N Kristensen, Hege Edvardsen, +11 authors, Anne-Lise Børresen-Dale.
Proc Natl Acad Sci U S A, 2006 May 11; 103(20). PMID: 16684880    Free PMC article.
Induction of melanoma cell apoptosis and inhibition of tumor growth using a cell-permeable Survivin antagonist.
H Yan, J Thomas, +6 authors, D Grossman.
Oncogene, 2006 May 17; 25(52). PMID: 16702945    Free PMC article.
Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms.
Therese Sørlie, Yulei Wang, +4 authors, Anne-Lise Børresen-Dale.
BMC Genomics, 2006 May 30; 7. PMID: 16729877    Free PMC article.
Highly Cited.
BRCA1 and BRCA2: chemosensitivity, treatment outcomes and prognosis.
William D Foulkes.
Fam Cancer, 2006 Jun 01; 5(2). PMID: 16736282
Review.
Noise-injected neural networks show promise for use on small-sample expression data.
Jianping Hua, James Lowey, Zixiang Xiong, Edward R Dougherty.
BMC Bioinformatics, 2006 Jun 02; 7. PMID: 16737545    Free PMC article.
A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients.
Laurel A Habel, Steven Shak, +12 authors, Charles P Quesenberry.
Breast Cancer Res, 2006 Jun 02; 8(3). PMID: 16737553    Free PMC article.
Highly Cited.
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.
Prognostic factors in prostate cancer.
A Buhmeida, S Pyrhönen, M Laato, Y Collan.
Diagn Pathol, 2006 Jun 09; 1. PMID: 16759347    Free PMC article.
A clinical prognostic prediction of lymph node-negative breast cancer by gene expression profiles.
Dingfeng Jiang, Naiqing Zhao.
J Cancer Res Clin Oncol, 2006 Jun 09; 132(9). PMID: 16761122
Kernel-based distance metric learning for microarray data classification.
Huilin Xiong, Xue-wen Chen.
BMC Bioinformatics, 2006 Jun 16; 7. PMID: 16774678    Free PMC article.
Bone sialoprotein mediates the tumor cell-targeted prometastatic activity of transforming growth factor beta in a mouse model of breast cancer.
Jeong-Seok Nam, Adam M Suchar, +9 authors, Lalage M Wakefield.
Cancer Res, 2006 Jun 17; 66(12). PMID: 16778210    Free PMC article.
The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis.
Susan J Cleator, Trevor J Powles, +6 authors, Mitch Dowsett.
Breast Cancer Res, 2006 Jun 23; 8(3). PMID: 16790077    Free PMC article.
Bioinformatics and cancer: an essential alliance.
Joaquín Dopazo.
Clin Transl Oncol, 2006 Jun 23; 8(6). PMID: 16790393
Review.
Cyclin D1 determines mitochondrial function in vivo.
Toshiyuki Sakamaki, Mathew C Casimiro, +19 authors, Richard Pestell.
Mol Cell Biol, 2006 Jul 01; 26(14). PMID: 16809779    Free PMC article.
Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study.
Per Hall, Alexander Ploner, +12 authors, Jonas Bergh.
BMC Med, 2006 Jul 04; 4. PMID: 16813654    Free PMC article.
Array-CGH and breast cancer.
Erik H van Beers, Petra M Nederlof.
Breast Cancer Res, 2006 Jul 05; 8(3). PMID: 16817944    Free PMC article.
Review.
Parallel analysis of transcript and translation profiles: identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications.
Haiyan Yang, Li-Rong Yu, +9 authors, Kent W Hunter.
J Proteome Res, 2006 Jul 11; 5(7). PMID: 16823962    Free PMC article.
When will tumor gene expression profiling be incorporated into clinical breast cancer decision making?
Chad J Creighton, James M Rae.
Breast Cancer Res, 2006 Jul 13; 8(4). PMID: 16834787    Free PMC article.
HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics.
Roel G W Verhaak, Mathijs A Sanders, +6 authors, Peter J M Valk.
BMC Bioinformatics, 2006 Jul 14; 7. PMID: 16836741    Free PMC article.
TOM: a web-based integrated approach for identification of candidate disease genes.
Simona Rossi, Daniele Masotti, +5 authors, Stefano Volinia.
Nucleic Acids Res, 2006 Jul 18; 34(Web Server issue). PMID: 16845011    Free PMC article.
Next station in microarray data analysis: GEPAS.
David Montaner, Joaquín Tárraga, +12 authors, Joaquín Dopazo.
Nucleic Acids Res, 2006 Jul 18; 34(Web Server issue). PMID: 16845056    Free PMC article.
Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer.
Valgerdur Birgisdottir, Olafur A Stefansson, +3 authors, Jorunn E Eyfjord.
Breast Cancer Res, 2006 Jul 19; 8(4). PMID: 16846527    Free PMC article.
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.
L Carrivick, S Rogers, +3 authors, C Cooper.
J R Soc Interface, 2006 Jul 20; 3(8). PMID: 16849266    Free PMC article.
Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer.
Marcia V Fournier, Katherine J Martin, +4 authors, Mina J Bissell.
Cancer Res, 2006 Jul 20; 66(14). PMID: 16849555    Free PMC article.
Chemokine (C-C motif) ligand 2 mediates the prometastatic effect of dysadherin in human breast cancer cells.
Jeong-Seok Nam, Mi-Jin Kang, +6 authors, Lalage M Wakefield.
Cancer Res, 2006 Jul 20; 66(14). PMID: 16849564    Free PMC article.
Breast cancer prognosis by combinatorial analysis of gene expression data.
Gabriela Alexe, Sorin Alexe, +4 authors, Peter L Hammer.
Breast Cancer Res, 2006 Jul 25; 8(4). PMID: 16859500    Free PMC article.
BRIT1 regulates early DNA damage response, chromosomal integrity, and cancer.
Rekha Rai, Hui Dai, +8 authors, Shiaw-Yih Lin.
Cancer Cell, 2006 Jul 29; 10(2). PMID: 16872911    Free PMC article.
p38gamma mitogen-activated protein kinase integrates signaling crosstalk between Ras and estrogen receptor to increase breast cancer invasion.
Xiaomei Qi, Jun Tang, +3 authors, Guan Chen.
Cancer Res, 2006 Aug 04; 66(15). PMID: 16885352    Free PMC article.
[The significance of "normal tissue" in the development of breast cancer: new concepts of early carcinogenesis].
H Bürger, C Kersting, +2 authors, W Böcker.
Pathologe, 2006 Aug 10; 27(5). PMID: 16896674
Comparison of gene expression profiles in core biopsies and corresponding surgical breast cancer samples.
Rosanna Zanetti-Dällenbach, Vincent Vuaroqueaux, +6 authors, Serenella Eppenberger-Castori.
Breast Cancer Res, 2006 Aug 22; 8(4). PMID: 16919157    Free PMC article.
Non-angiogenic functions of VEGF in breast cancer.
Arthur M Mercurio, Elizabeth A Lipscomb, Robin E Bachelder.
J Mammary Gland Biol Neoplasia, 2006 Aug 23; 10(4). PMID: 16924371
Review.
Selecting normalization genes for small diagnostic microarrays.
Jochen Jaeger, Rainer Spang.
BMC Bioinformatics, 2006 Aug 24; 7. PMID: 16925821    Free PMC article.
Genetic prognostic index influences patient outcome for node-positive breast cancer.
Shin-Ichi Asaka, Takashi Fujimoto, +2 authors, Masamitsu Onda.
Surg Today, 2006 Aug 29; 36(9). PMID: 16937283
Identifying genes that contribute most to good classification in microarrays.
Stuart G Baker, Barnett S Kramer.
BMC Bioinformatics, 2006 Sep 09; 7. PMID: 16959042    Free PMC article.
Feature selection using Haar wavelet power spectrum.
Prabakaran Subramani, Rajendra Sahu, Shekhar Verma.
BMC Bioinformatics, 2006 Oct 07; 7. PMID: 17022808    Free PMC article.
A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification.
Manju R Mamtani, Tushar P Thakre, +4 authors, Hemant Kulkarni.
BMC Bioinformatics, 2006 Oct 13; 7. PMID: 17032455    Free PMC article.
Molecular screening for breast cancer prevention, early detection, and treatment planning: combining biomarkers from DNA, RNA, and protein.
Katherine Stemke-Hale, Bryan Hennessy, Gordon B Mills, Rahul Mitra.
Curr Oncol Rep, 2006 Oct 17; 8(6). PMID: 17040626
Review.
Gene expression signatures of morphologically normal breast tissue identify basal-like tumors.
Greg Finak, Svetlana Sadekova, +8 authors, Morag Park.
Breast Cancer Res, 2006 Oct 24; 8(5). PMID: 17054791    Free PMC article.
CD44+/CD24- breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis.
Carol Sheridan, Hiromitsu Kishimoto, +6 authors, Harikrishna Nakshatri.
Breast Cancer Res, 2006 Oct 26; 8(5). PMID: 17062128    Free PMC article.
Highly Cited.
Classification of ductal carcinoma in situ by gene expression profiling.
Juliane Hannemann, Arno Velds, +3 authors, Marc J van de Vijver.
Breast Cancer Res, 2006 Oct 31; 8(5). PMID: 17069663    Free PMC article.
Predicting a local recurrence after breast-conserving therapy by gene expression profiling.
Dimitry S A Nuyten, Bas Kreike, +8 authors, Marc J van de Vijver.
Breast Cancer Res, 2006 Oct 31; 8(5). PMID: 17069664    Free PMC article.
Converting a breast cancer microarray signature into a high-throughput diagnostic test.
Annuska M Glas, Arno Floore, +9 authors, Laura J Van't Veer.
BMC Genomics, 2006 Nov 01; 7. PMID: 17074082    Free PMC article.
Highly Cited.
Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity.
J Peter Svensson, Lukas J A Stalpers, +6 authors, Micheline Giphart-Gassler.
PLoS Med, 2006 Nov 02; 3(10). PMID: 17076557    Free PMC article.
High-throughput genomic technology in research and clinical management of breast cancer. Exploiting the potential of gene expression profiling: is it ready for the clinic?
Andrew H Sims, Kai Ren Ong, Robert B Clarke, Anthony Howell.
Breast Cancer Res, 2006 Nov 02; 8(5). PMID: 17076877    Free PMC article.
Review.
A consensus prognostic gene expression classifier for ER positive breast cancer.
Andrew E Teschendorff, Ali Naderi, +5 authors, Carlos Caldas.
Genome Biol, 2006 Nov 02; 7(10). PMID: 17076897    Free PMC article.
Clinical proteomics: present and future prospects.
Nicole M Verrills.
Clin Biochem Rev, 2006 Nov 02; 27(2). PMID: 17077880    Free PMC article.
GATA3 protein as a MUC1 transcriptional regulator in breast cancer cells.
Martín C Abba, María I Nunez, +3 authors, C Marcelo Aldaz.
Breast Cancer Res, 2006 Nov 03; 8(6). PMID: 17078870    Free PMC article.
Mining expressed sequence tags identifies cancer markers of clinical interest.
Fabien Campagne, Lucy Skrabanek.
BMC Bioinformatics, 2006 Nov 03; 7. PMID: 17078886    Free PMC article.
Identification of differentially expressed genes in HPV-positive and HPV-negative oropharyngeal squamous cell carcinomas.
Ivan Martinez, Jun Wang, +2 authors, Saleem A Khan.
Eur J Cancer, 2006 Nov 03; 43(2). PMID: 17079134    Free PMC article.
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target.
S Horvath, B Zhang, +17 authors, P S Mischel.
Proc Natl Acad Sci U S A, 2006 Nov 09; 103(46). PMID: 17090670    Free PMC article.
Highly Cited.
Vimentin and laminin expression is associated with basal-like phenotype in both sporadic and BRCA1-associated breast carcinomas.
Socorro María Rodríguez-Pinilla, David Sarrió, +5 authors, José Palacios.
J Clin Pathol, 2006 Nov 16; 60(9). PMID: 17105822    Free PMC article.
Molecular subtypes of breast cancer in relation to paclitaxel response and outcomes in women with metastatic disease: results from CALGB 9342.
Lyndsay N Harris, Gloria Broadwater, +10 authors, Lynn Dressler.
Breast Cancer Res, 2006 Nov 30; 8(6). PMID: 17129383    Free PMC article.
GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland.
Hosein Kouros-Mehr, Euan M Slorach, Mark D Sternlicht, Zena Werb.
Cell, 2006 Nov 30; 127(5). PMID: 17129787    Free PMC article.
Highly Cited.
Improved breast cancer prognosis through the combination of clinical and genetic markers.
Yijun Sun, Steve Goodison, +2 authors, William Farmerie.
Bioinformatics, 2006 Nov 30; 23(1). PMID: 17130137    Free PMC article.
Global expression-based classification of lymph node metastasis and extracapsular spread of oral tongue squamous cell carcinoma.
Xiaofeng Zhou, Stephane Temam, +4 authors, David T Wong.
Neoplasia, 2006 Nov 30; 8(11). PMID: 17132224    Free PMC article.
Novel patterns of genome rearrangement and their association with survival in breast cancer.
James Hicks, Alexander Krasnitz, +20 authors, Anders Zetterberg.
Genome Res, 2006 Dec 05; 16(12). PMID: 17142309    Free PMC article.
Highly Cited.
Heterogeneity of mammary lesions represent molecular differences.
Ruria Namba, Jeannie E Maglione, +7 authors, Jeffrey P Gregg.
BMC Cancer, 2006 Dec 07; 6. PMID: 17147824    Free PMC article.
Gene expression patterns associated with p53 status in breast cancer.
Melissa A Troester, Jason I Herschkowitz, +4 authors, Charles M Perou.
BMC Cancer, 2006 Dec 08; 6. PMID: 17150101    Free PMC article.
Dissection of a metastatic gene expression signature into distinct components.
Paul Roepman, Erica de Koning, +4 authors, Frank C P Holstege.
Genome Biol, 2006 Dec 13; 7(12). PMID: 17156469    Free PMC article.
The type III TGF-beta receptor suppresses breast cancer progression.
Mei Dong, Tam How, +7 authors, Gerard C Blobe.
J Clin Invest, 2006 Dec 13; 117(1). PMID: 17160136    Free PMC article.
Distinguishing lung tumours from normal lung based on a small set of genes.
Tatiana Dracheva, Reena Philip, +7 authors, Jin Jen.
Lung Cancer, 2006 Dec 13; 55(2). PMID: 17161497    Free PMC article.
Measuring proliferation in breast cancer: practicalities and applications.
Mark J Beresford, George D Wilson, Andreas Makris.
Breast Cancer Res, 2006 Dec 14; 8(6). PMID: 17164010    Free PMC article.
Review.
Classification methods for the development of genomic signatures from high-dimensional data.
Hojin Moon, Hongshik Ahn, +3 authors, James J Chen.
Genome Biol, 2006 Dec 22; 7(12). PMID: 17181863    Free PMC article.
Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE.
Satoshi Niijima, Satoru Kuhara.
BMC Bioinformatics, 2006 Dec 26; 7. PMID: 17187691    Free PMC article.
Mad2 overexpression promotes aneuploidy and tumorigenesis in mice.
Rocío Sotillo, Eva Hernando, +4 authors, Robert Benezra.
Cancer Cell, 2006 Dec 27; 11(1). PMID: 17189715    Free PMC article.
Highly Cited.
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer.
Yan Lu, William Lemon, +9 authors, Ming You.
PLoS Med, 2006 Dec 30; 3(12). PMID: 17194181    Free PMC article.
Highly Cited.
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.
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer.
Sallyann L O'Brien, Ailís Fagan, +11 authors, William M Gallagher.
Int J Cancer, 2007 Jan 06; 120(7). PMID: 17205517    Free PMC article.
Heterologous tissue culture expression signature predicts human breast cancer prognosis.
Eun Sung Park, Ju-Seog Lee, +4 authors, J Frederic Mushinski.
PLoS One, 2007 Jan 09; 2(1). PMID: 17206280    Free PMC article.
An approach to the validation of novel molecular markers of breast cancer via TMA-based FISH scanning.
Raymond R Tubbs, Eric Swain, James D Pettay, David G Hicks.
J Mol Histol, 2007 Jan 11; 38(2). PMID: 17211577
Molecular markers of early Parkinson's disease based on gene expression in blood.
Clemens R Scherzer, Aron C Eklund, +12 authors, Steven R Gullans.
Proc Natl Acad Sci U S A, 2007 Jan 12; 104(3). PMID: 17215369    Free PMC article.
Highly Cited.
Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease.
Manuel Aivado, Dimitrios Spentzos, +17 authors, Towia A Libermann.
Proc Natl Acad Sci U S A, 2007 Jan 16; 104(4). PMID: 17220270    Free PMC article.
Molecular profiling of cervical cancer progression.
T Hagemann, T Bozanovic, +7 authors, P O A Van Trappen.
Br J Cancer, 2007 Jan 24; 96(2). PMID: 17242701    Free PMC article.
HER-2/neu status and response to CMF: retrospective study in a series of operable breast cancer treated with primary CMF chemotherapy.
Catalina Falo, Abelardo Moreno, +3 authors, Agustín Escobedo.
J Cancer Res Clin Oncol, 2007 Jan 25; 133(7). PMID: 17245595
Genomic signatures in non-small-cell lung cancer: targeting the targeted therapies.
Holly K Dressman, Andrea Bild, +2 authors, Anil Potti.
Curr Oncol Rep, 2007 Jan 27; 8(4). PMID: 17254524
Review.
Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers.
Mervi Jumppanen, Sofia Gruvberger-Saal, +8 authors, Jorma Isola.
Breast Cancer Res, 2007 Feb 01; 9(1). PMID: 17263897    Free PMC article.
Integrative analysis of a cancer somatic mutome.
Pilar Hernández, Xavier Solé, +4 authors, Miguel Angel Pujana.
Mol Cancer, 2007 Feb 07; 6. PMID: 17280605    Free PMC article.
Fish 'n' chips: the use of microarrays for aquatic toxicology.
Nancy D Denslow, Natàlia Garcia-Reyero, David S Barber.
Mol Biosyst, 2007 Feb 20; 3(3). PMID: 17308663    Free PMC article.
Review.
A new inhibitor of apoptosis from vaccinia virus and eukaryotes.
Caroline Gubser, Daniele Bergamaschi, +3 authors, Geoffrey L Smith.
PLoS Pathog, 2007 Feb 27; 3(2). PMID: 17319741    Free PMC article.
A new molecular breast cancer subclass defined from a large scale real-time quantitative RT-PCR study.
Maïa Chanrion, Hélène Fontaine, +5 authors, Jean-Marie Darbon.
BMC Cancer, 2007 Mar 07; 7. PMID: 17338809    Free PMC article.
Interpretation of microarray data in cancer.
S Michiels, S Koscielny, C Hill.
Br J Cancer, 2007 Mar 08; 96(8). PMID: 17342085    Free PMC article.
Review.
Automated detection of regions of interest for tissue microarray experiments: an image texture analysis.
Bilge Karaçali, Aydin Tözeren.
BMC Med Imaging, 2007 Mar 14; 7. PMID: 17349041    Free PMC article.
An overview of prognostic factors for long-term survivors of breast cancer.
Isabelle Soerjomataram, Marieke W J Louwman, +2 authors, Jan Willem W Coebergh.
Breast Cancer Res Treat, 2007 Mar 23; 107(3). PMID: 17377838    Free PMC article.
Highly Cited. Review.
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.
Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.
Lance D Miller, Edison T Liu.
Breast Cancer Res, 2007 Apr 03; 9(2). PMID: 17397520    Free PMC article.
Review.
Enhanced NF kappa B and AP-1 transcriptional activity associated with antiestrogen resistant breast cancer.
Yamei Zhou, Christina Yau, +6 authors, Christopher C Benz.
BMC Cancer, 2007 Apr 05; 7. PMID: 17407600    Free PMC article.
CARD15 status and familial predisposition for Crohn's disease and colonic gene expression.
Claudio Csillag, Ole Haagen Nielsen, +3 authors, Finn Cilius Nielsen.
Dig Dis Sci, 2007 Apr 06; 52(8). PMID: 17410442
Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markers.
Xinan Yang, Xiao Sun.
BMC Bioinformatics, 2007 Apr 07; 8. PMID: 17411443    Free PMC article.
Lung metastasis genes couple breast tumor size and metastatic spread.
Andy J Minn, Gaorav P Gupta, +10 authors, Joan Massagué.
Proc Natl Acad Sci U S A, 2007 Apr 11; 104(16). PMID: 17420468    Free PMC article.
Highly Cited.
Identification of a robust gene signature that predicts breast cancer outcome in independent data sets.
James E Korkola, Ekaterina Blaveri, +7 authors, Frederic M Waldman.
BMC Cancer, 2007 Apr 13; 7. PMID: 17428335    Free PMC article.
Stat5 activation inhibits prolactin-induced AP-1 activity: distinct prolactin-initiated signals in tumorigenesis dependent on cell context.
J H Gutzman, D E Rugowski, S E Nikolai, L A Schuler.
Oncogene, 2007 Apr 18; 26(43). PMID: 17438530    Free PMC article.
Dysadherin: a new player in cancer progression.
Jeong-Seok Nam, Setsuo Hirohashi, Lalage M Wakefield.
Cancer Lett, 2007 Apr 20; 255(2). PMID: 17442482    Free PMC article.
Review.
Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity.
Lao H Saal, Peter Johansson, +14 authors, Ramon Parsons.
Proc Natl Acad Sci U S A, 2007 Apr 25; 104(18). PMID: 17452630    Free PMC article.
Highly Cited.
Ki-67 as prognostic marker in early breast cancer: a meta-analysis of published studies involving 12,155 patients.
E de Azambuja, F Cardoso, +7 authors, M Paesmans.
Br J Cancer, 2007 Apr 25; 96(10). PMID: 17453008    Free PMC article.
Highly Cited.
The macrophage-stimulating protein pathway promotes metastasis in a mouse model for breast cancer and predicts poor prognosis in humans.
Alana L Welm, Julie B Sneddon, +4 authors, J Michael Bishop.
Proc Natl Acad Sci U S A, 2007 Apr 26; 104(18). PMID: 17456594    Free PMC article.
Feature selection and molecular classification of cancer using genetic programming.
Jianjun Yu, Jindan Yu, +4 authors, Arul M Chinnaiyan.
Neoplasia, 2007 Apr 27; 9(4). PMID: 17460773    Free PMC article.
Molecular profiling in breast cancer.
Shannon R Morris, Lisa A Carey.
Rev Endocr Metab Disord, 2007 Apr 28; 8(3). PMID: 17464566
Review.
Do we need to redefine a cancer metastasis and staging definitions?
Danny R Welch.
Breast Dis, 2007 May 03; 26. PMID: 17473362    Free PMC article.
Review.
Nectin-4 is a new histological and serological tumor associated marker for breast cancer.
Stéphanie Fabre-Lafay, Florence Monville, +16 authors, Marc Lopez.
BMC Cancer, 2007 May 04; 7. PMID: 17474988    Free PMC article.
Three methods for optimization of cross-laboratory and cross-platform microarray expression data.
Phillip Stafford, Marcel Brun.
Nucleic Acids Res, 2007 May 05; 35(10). PMID: 17478523    Free PMC article.
Identification of novel amplification gene targets in mouse and human breast cancer at a syntenic cluster mapping to mouse ch8A1 and human ch13q34.
Martin C Abba, Victoria T Fabris, +6 authors, C Marcelo Aldaz.
Cancer Res, 2007 May 08; 67(9). PMID: 17483321    Free PMC article.
Towards a holistic, yet gene-centered analysis of gene expression profiles: a case study of human lung cancers.
Yuchun Guo, Gabriel S Eichler, +2 authors, Sui Huang.
J Biomed Biotechnol, 2007 May 10; 2006(5). PMID: 17489018    Free PMC article.
Detecting multivariate differentially expressed genes.
Roland Nilsson, José M Peña, Johan Björkegren, Jesper Tegnér.
BMC Bioinformatics, 2007 May 11; 8. PMID: 17490475    Free PMC article.
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors.
Jason I Herschkowitz, Karl Simin, +23 authors, Charles M Perou.
Genome Biol, 2007 May 12; 8(5). PMID: 17493263    Free PMC article.
Highly Cited.
Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis.
Yingchun Liu, Markus Ringnér.
Genome Biol, 2007 May 15; 8(5). PMID: 17498287    Free PMC article.
TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer.
Anita Langerød, Hongjuan Zhao, +6 authors, Stefanie S Jeffrey.
Breast Cancer Res, 2007 May 17; 9(3). PMID: 17504517    Free PMC article.
Highly Cited.
Metastasis: recent discoveries and novel treatment strategies.
Suzanne A Eccles, Danny R Welch.
Lancet, 2007 May 22; 369(9574). PMID: 17512859    Free PMC article.
Highly Cited. Review.
Molecular profile of peripheral blood mononuclear cells from patients with rheumatoid arthritis.
Christopher J Edwards, Jeffrey L Feldman, +8 authors, Debra D Pittman.
Mol Med, 2007 May 23; 13(1-2). PMID: 17515956    Free PMC article.
Phosphorylation of FAK, PI-3K, and impaired actin organization in CK-positive micrometastatic breast cancer cells.
Galatea Kallergi, Dimitris Mavroudis, Vassilis Georgoulias, Christos Stournaras.
Mol Med, 2007 May 23; 13(1-2). PMID: 17515959    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.
The cofilin pathway in breast cancer invasion and metastasis.
Weigang Wang, Robert Eddy, John Condeelis.
Nat Rev Cancer, 2007 May 25; 7(6). PMID: 17522712    Free PMC article.
Highly Cited. Review.
Specific isolation of disseminated cancer cells: a new method permitting sensitive detection of target molecules of diagnostic and therapeutic value.
Siri Tveito, Gunhild M Maelandsmo, +2 authors, Oystein Fodstad.
Clin Exp Metastasis, 2007 May 29; 24(5). PMID: 17530423
Low E2F1 transcript levels are a strong determinant of favorable breast cancer outcome.
Vincent Vuaroqueaux, Patrick Urban, +8 authors, Serenella Eppenberger-Castori.
Breast Cancer Res, 2007 May 31; 9(3). PMID: 17535433    Free PMC article.
Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers.
Sendurai A Mani, Jing Yang, +7 authors, Robert A Weinberg.
Proc Natl Acad Sci U S A, 2007 Jun 01; 104(24). PMID: 17537911    Free PMC article.
Highly Cited.
Whole-genome cartography of estrogen receptor alpha binding sites.
Chin-Yo Lin, Vinsensius B Vega, +20 authors, Edison T Liu.
PLoS Genet, 2007 Jun 05; 3(6). PMID: 17542648    Free PMC article.
Highly Cited.
Vascular endothelial growth factor mediates intracrine survival in human breast carcinoma cells through internally expressed VEGFR1/FLT1.
Tae-Hee Lee, Seyha Seng, +4 authors, Shalom Avraham.
PLoS Med, 2007 Jun 07; 4(6). PMID: 17550303    Free PMC article.
Highly Cited.
Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools.
Robert A Ach, Arno Floore, +9 authors, Laura J Van't Veer.
BMC Genomics, 2007 Jun 08; 8. PMID: 17553173    Free PMC article.
Molecular response to aromatase inhibitor treatment in primary breast cancer.
Alan Mackay, Ander Urruticoechea, +10 authors, Mitch Dowsett.
Breast Cancer Res, 2007 Jun 09; 9(3). PMID: 17555561    Free PMC article.
Tumour dormancy in breast cancer: an update.
Muriel Brackstone, Jason L Townson, Ann F Chambers.
Breast Cancer Res, 2007 Jun 15; 9(3). PMID: 17561992    Free PMC article.
Modeling metastatic breast cancer in mice.
Jos Jonkers, Patrick W B Derksen.
J Mammary Gland Biol Neoplasia, 2007 Jun 26; 12(2-3). PMID: 17587153
Review.
Amplification patterns of three genomic regions predict distant recurrence in breast carcinoma.
Lisa M Davis, Cole Harris, +10 authors, John Hozier.
J Mol Diagn, 2007 Jun 27; 9(3). PMID: 17591932    Free PMC article.
Identification of estrogen-responsive genes involved in breast cancer metastases to the bone.
Jun Wang, Jennifer Jarrett, +2 authors, Anait S Levenson.
Clin Exp Metastasis, 2007 Jun 27; 24(6). PMID: 17593529
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.
Strategy for encoding and comparison of gene expression signatures.
Yajun Yi, Chun Li, Clay Miller, Alfred L George.
Genome Biol, 2007 Jul 07; 8(7). PMID: 17612401    Free PMC article.
Optimization of oligonucleotide microarray fabricated by spotting 65-mer.
Myoyong Lee, Jeffrey M Trent, Michael L Bittner.
Anal Biochem, 2007 Jul 10; 368(1). PMID: 17618862    Free PMC article.
Apert p.Ser252Trp mutation in FGFR2 alters osteogenic potential and gene expression of cranial periosteal cells.
Roberto D Fanganiello, Andréa L Sertié, +10 authors, Maria Rita Passos-Bueno.
Mol Med, 2007 Jul 12; 13(7-8). PMID: 17622301    Free PMC article.
Hereditary breast cancer: pathobiology, clinical translation, and potential for targeted cancer therapeutics.
Wendy S Rubinstein.
Fam Cancer, 2007 Jul 13; 7(1). PMID: 17624601
Review.
Src promotes estrogen-dependent estrogen receptor alpha proteolysis in human breast cancer.
Isabel Chu, Angel Arnaout, +8 authors, Joyce M Slingerland.
J Clin Invest, 2007 Jul 14; 117(8). PMID: 17627304    Free PMC article.
Tumor metastasis to bone.
Mandeep S Virk, Jay R Lieberman.
Arthritis Res Ther, 2007 Jul 20; 9 Suppl 1. PMID: 17634144    Free PMC article.
Review.
Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome.
Jessica Shin, Stefano Monti, +4 authors, Thomas S Kupper.
Blood, 2007 Jul 20; 110(8). PMID: 17638852    Free PMC article.
Classification of heterogeneous microarray data by maximum entropy kernel.
Wataru Fujibuchi, Tsuyoshi Kato.
BMC Bioinformatics, 2007 Jul 27; 8. PMID: 17651507    Free PMC article.
Moving toward a system genetics view of disease.
Solveig K Sieberts, Eric E Schadt.
Mamm Genome, 2007 Jul 27; 18(6-7). PMID: 17653589    Free PMC article.
Review.
DNA microarrays: a powerful genomic tool for biomedical and clinical research.
Victor Trevino, Francesco Falciani, Hugo A Barrera-Saldaña.
Mol Med, 2007 Jul 31; 13(9-10). PMID: 17660860    Free PMC article.
Review.
Identification of structural aberrations in cancer by SNP array analysis.
Stefan Heinrichs, A Thomas Look.
Genome Biol, 2007 Aug 02; 8(7). PMID: 17666119    Free PMC article.
Review.
An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer.
Andrew E Teschendorff, Ahmad Miremadi, +2 authors, Carlos Caldas.
Genome Biol, 2007 Aug 09; 8(8). PMID: 17683518    Free PMC article.
Highly Cited.
BCoR-L1 variation and breast cancer.
Felicity Lose, Jeremy Arnold, +7 authors, Amanda B Spurdle.
Breast Cancer Res, 2007 Aug 19; 9(4). PMID: 17697391    Free PMC article.
Activation of the RalGEF/Ral pathway promotes prostate cancer metastasis to bone.
JuanJuan Yin, Claire Pollock, +4 authors, Kathleen Kelly.
Mol Cell Biol, 2007 Aug 22; 27(21). PMID: 17709381    Free PMC article.
Quantification of the impact of feature selection on the variance of cross-validation error estimation.
Yufei Xiao, Jianping Hua, Edward R Dougherty.
EURASIP J Bioinform Syst Biol, 2007 Aug 24;. PMID: 17713587    Free PMC article.
Collagen-binding proteoglycan fibromodulin can determine stroma matrix structure and fluid balance in experimental carcinoma.
Ake Oldberg, Sebastian Kalamajski, +5 authors, Kristofer Rubin.
Proc Natl Acad Sci U S A, 2007 Aug 24; 104(35). PMID: 17715296    Free PMC article.
Stratification bias in low signal microarray studies.
Brian J Parker, Simon Günter, Justin Bedo.
BMC Bioinformatics, 2007 Sep 04; 8. PMID: 17764577    Free PMC article.
A systems biology approach for pathway level analysis.
Sorin Draghici, Purvesh Khatri, +5 authors, Roberto Romero.
Genome Res, 2007 Sep 06; 17(10). PMID: 17785539    Free PMC article.
Highly Cited.
Strategic plans to promote head and neck cancer translational research within the radiation therapy oncology group: a report from the translational research program.
Christine H Chung, Stuart Wong, +4 authors, Quynh-Thu Le.
Int J Radiat Oncol Biol Phys, 2007 Oct 18; 69(2 Suppl). PMID: 17848300    Free PMC article.
Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers.
Christina Yau, Vita Fedele, +11 authors, Christopher C Benz.
Breast Cancer Res, 2007 Sep 14; 9(5). PMID: 17850661    Free PMC article.
Dual actin-bundling and protein kinase C-binding activities of fascin regulate carcinoma cell migration downstream of Rac and contribute to metastasis.
Yosuke Hashimoto, Maddy Parsons, Josephine C Adams.
Mol Biol Cell, 2007 Sep 15; 18(11). PMID: 17855511    Free PMC article.
Breast cancer molecular signatures as determined by SAGE: correlation with lymph node status.
Martín C Abba, Hongxia Sun, +8 authors, C Marcelo Aldaz.
Mol Cancer Res, 2007 Sep 15; 5(9). PMID: 17855657    Free PMC article.
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.
Martin Buess, Dimitry S A Nuyten, +3 authors, Patrick O Brown.
Genome Biol, 2007 Sep 18; 8(9). PMID: 17868458    Free PMC article.
Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy.
Anna L Stratford, Golareh Habibi, +13 authors, Sandra E Dunn.
Breast Cancer Res, 2007 Sep 19; 9(5). PMID: 17875215    Free PMC article.
Effectiveness of gene expression profiling for response prediction of rectal cancer to preoperative radiotherapy.
Eiki Ojima, Yasuhiro Inoue, +2 authors, Masato Kusunoki.
J Gastroenterol, 2007 Sep 19; 42(9). PMID: 17876542
Integrated analysis of independent gene expression microarray datasets improves the predictability of breast cancer outcome.
Zhe Zhang, Dechang Chen, David A Fenstermacher.
BMC Genomics, 2007 Sep 22; 8. PMID: 17883867    Free PMC article.
Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer.
Jack X Yu, Anieta M Sieuwerts, +5 authors, John A Foekens.
BMC Cancer, 2007 Sep 27; 7. PMID: 17894856    Free PMC article.
A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.
Hyungwon Choi, Ronglai Shen, Arul M Chinnaiyan, Debashis Ghosh.
BMC Bioinformatics, 2007 Sep 29; 8. PMID: 17900369    Free PMC article.
A convenient clinically relevant model of human breast cancer bone metastasis.
Teresa Garcia, Amanda Jackson, +4 authors, Philippe Pujuguet.
Clin Exp Metastasis, 2007 Sep 29; 25(1). PMID: 17902030
CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells.
Rene Opavsky, Shu-Huei Wang, +13 authors, Christoph Plass.
PLoS Genet, 2007 Oct 03; 3(9). PMID: 17907813    Free PMC article.
Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas.
Bas Kreike, Marieke van Kouwenhove, +4 authors, Marc J van de Vijver.
Breast Cancer Res, 2007 Oct 04; 9(5). PMID: 17910759    Free PMC article.
Highly Cited.
The patient experience.
Nadia Harbeck, Renate Haidinger.
Breast Cancer Res Treat, 2007 Nov 21; 105 Suppl 1. PMID: 17912639    Free PMC article.
Review.
A multi-gene approach to differentiate papillary thyroid carcinoma from benign lesions: gene selection using support vector machines with bootstrapping.
Krzysztof Fujarewicz, Michal Jarzab, +7 authors, Andrzej Swierniak.
Endocr Relat Cancer, 2007 Oct 05; 14(3). PMID: 17914110    Free PMC article.
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype.
Cherie Blenkiron, Leonard D Goldstein, +10 authors, Eric A Miska.
Genome Biol, 2007 Oct 10; 8(10). PMID: 17922911    Free PMC article.
Highly Cited.
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.
Suet F Chin, Andrew E Teschendorff, +13 authors, Carlos Caldas.
Genome Biol, 2007 Oct 11; 8(10). PMID: 17925008    Free PMC article.
Highly Cited.
Minichromosome maintenance proteins 2 and 5 in non-benign epithelial ovarian tumours: relationship with cell cycle regulators and prognostic implications.
H Gakiopoulou, P Korkolopoulou, +11 authors, E Patsouris.
Br J Cancer, 2007 Oct 18; 97(8). PMID: 17940502    Free PMC article.
Network-based classification of breast cancer metastasis.
Han-Yu Chuang, Eunjung Lee, +2 authors, Trey Ideker.
Mol Syst Biol, 2007 Oct 18; 3. PMID: 17940530    Free PMC article.
Highly Cited.
Protein subnetwork markers improve prediction of cancer outcome.
Charles Auffray.
Mol Syst Biol, 2007 Oct 18; 3. PMID: 17940531    Free PMC article.
Module-based outcome prediction using breast cancer compendia.
Martin H van Vliet, Christiaan N Klijn, Lodewyk F A Wessels, Marcel J T Reinders.
PLoS One, 2007 Oct 18; 2(10). PMID: 17940611    Free PMC article.
Mechanisms of oncogenic cooperation in cancer initiation and metastasis.
Laura G Pedraza-Fariña.
Yale J Biol Med, 2007 Oct 18; 79(3-4). PMID: 17940619    Free PMC article.
Review.
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets.
Michael Gormley, William Dampier, +2 authors, Aydin Tozeren.
BMC Bioinformatics, 2007 Oct 30; 8. PMID: 17963508    Free PMC article.
Increased COX2 expression enhances tumor-induced osteoclastic lesions in breast cancer bone metastasis.
Zhigang Li, Christian Schem, +2 authors, Ming Zhang.
Clin Exp Metastasis, 2007 Oct 30; 25(4). PMID: 17965942
Breast cancer progression: insights into multifaceted matrix metalloproteinases.
Vincent Chabottaux, Agnès Noel.
Clin Exp Metastasis, 2007 Oct 31; 24(8). PMID: 17968664
Review.
Comparison of RNA amplification techniques meeting the demands for the expression profiling of clinical cancer samples.
Martin Lauss, Klemens Vierlinger, +3 authors, Christa Noehammer.
Virchows Arch, 2007 Nov 01; 451(6). PMID: 17972098
New concepts in breast cancer metastasis: tumor initiating cells and the microenvironment.
Jonathan P Sleeman, Natascha Cremers.
Clin Exp Metastasis, 2007 Nov 01; 24(8). PMID: 17972145
Review.
Gene arrays for diagnosis, prognosis and treatment of breast cancer metastasis.
Keltouma Driouch, Thomas Landemaine, +2 authors, Rosette Lidereau.
Clin Exp Metastasis, 2007 Nov 02; 24(8). PMID: 17973194
Review.
Jagged1-mediated Notch activation induces epithelial-to-mesenchymal transition through Slug-induced repression of E-cadherin.
Kevin G Leong, Kyle Niessen, +4 authors, Aly Karsan.
J Exp Med, 2007 Nov 07; 204(12). PMID: 17984306    Free PMC article.
Highly Cited.
Genomic signatures of breast cancer metastasis.
V Urquidi, S Goodison.
Cytogenet Genome Res, 2007 Nov 15; 118(2-4). PMID: 18000362    Free PMC article.
Subclass mapping: identifying common subtypes in independent disease data sets.
Yujin Hoshida, Jean-Philippe Brunet, +2 authors, Jill P Mesirov.
PLoS One, 2007 Nov 22; 2(11). PMID: 18030330    Free PMC article.
Systems biology and cancer stem cells.
Nathan D Price, Greg Foltz, +2 authors, Qiang Tian.
J Cell Mol Med, 2007 Nov 23; 12(1). PMID: 18031300    Free PMC article.
Review.
Analyses of the role of endogenous SPARC in mouse models of prostate and breast cancer.
Sunny Y Wong, Denise Crowley, Roderick T Bronson, Richard O Hynes.
Clin Exp Metastasis, 2007 Dec 07; 25(2). PMID: 18058030    Free PMC article.
Use of the Oncotype DX 21-gene assay to guide adjuvant decision making in early-stage breast cancer.
Alison K Conlin, Andrew D Seidman.
Mol Diagn Ther, 2007 Dec 15; 11(6). PMID: 18078353
Review.
Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis.
Nigel P S Crawford, Xiaolan Qian, +10 authors, Kent W Hunter.
PLoS Genet, 2007 Dec 18; 3(11). PMID: 18081427    Free PMC article.
Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors.
Eike Staub, Joern Groene, +11 authors, André Rosenthal.
Mol Cancer, 2007 Dec 18; 6. PMID: 18081933    Free PMC article.
Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers.
Catherine I Dumur, Maureen Lyons-Weiler, +12 authors, Federico A Monzon.
J Mol Diagn, 2007 Dec 18; 10(1). PMID: 18083688    Free PMC article.
Systems biology and its potential role in radiobiology.
Ludwig Feinendegen, Philip Hahnfeldt, +2 authors, Eberhard O Voit.
Radiat Environ Biophys, 2007 Dec 19; 47(1). PMID: 18087710
Review.
Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis.
Phillip G Febbo, Mike G Mulligan, +5 authors, Stephen C Taylor.
BMC Genomics, 2007 Dec 20; 8. PMID: 18088408    Free PMC article.
Complementary hierarchical clustering.
Gen Nowak, Robert Tibshirani.
Biostatistics, 2007 Dec 21; 9(3). PMID: 18093965    Free PMC article.
Adipose gene expression prior to weight loss can differentiate and weakly predict dietary responders.
David M Mutch, M Ramzi Temanni, +11 authors, Karine Clément.
PLoS One, 2007 Dec 21; 2(12). PMID: 18094752    Free PMC article.
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.
Robert Clarke, Habtom W Ressom, +4 authors, Yue Wang.
Nat Rev Cancer, 2007 Dec 22; 8(1). PMID: 18097463    Free PMC article.
Highly Cited. Review.
Early onset of breast cancer in a group of British black women.
R L Bowen, S W Duffy, +2 authors, J L Jones.
Br J Cancer, 2008 Jan 10; 98(2). PMID: 18182985    Free PMC article.
Partial least squares Cox regression for genome-wide data.
Ståle Nygård, Ornulf Borgan, Ole Christian Lingjaerde, Hege Leite Størvold.
Lifetime Data Anal, 2008 Jan 12; 14(2). PMID: 18188699
Can clinically relevant prognostic subsets of breast cancer patients with four or more involved axillary lymph nodes be identified through immunohistochemical biomarkers? A tissue microarray feasibility study.
Simon J Crabb, Chris D Bajdik, +4 authors, Karen A Gelmon.
Breast Cancer Res, 2008 Jan 16; 10(1). PMID: 18194560    Free PMC article.
Data mining in genomics.
Jae K Lee, Paul D Williams, Sooyoung Cheon.
Clin Lab Med, 2008 Jan 16; 28(1). PMID: 18194724    Free PMC article.
Loss of Endocan tumorigenic properties after alternative splicing of exon 2.
Florence Depontieu, Bogdan-Dragos Grigoriu, +4 authors, Philippe Lassalle.
BMC Cancer, 2008 Jan 22; 8. PMID: 18205914    Free PMC article.
Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data.
Cecilia Ritz, Patrik Edén.
BMC Genomics, 2008 Jan 22; 9. PMID: 18205949    Free PMC article.
Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets.
Josane F Sousa, Enilza M Espreafico.
BMC Cancer, 2008 Jan 24; 8. PMID: 18211678    Free PMC article.
Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures.
Chih-Hung Jen, Tsun-Po Yang, +4 authors, Hsei-Wei Wang.
BMC Bioinformatics, 2008 Jan 29; 9. PMID: 18221568    Free PMC article.
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation.
David D Smith, Pål Saetrom, +4 authors, Garrett P Larson.
BMC Bioinformatics, 2008 Jan 30; 9. PMID: 18226260    Free PMC article.
Impacts of excision repair cross-complementing gene 1 (ERCC1), dihydropyrimidine dehydrogenase, and epidermal growth factor receptor on the outcomes of patients with advanced gastric cancer.
J Matsubara, T Nishina, +10 authors, K Shirao.
Br J Cancer, 2008 Jan 31; 98(4). PMID: 18231104    Free PMC article.
A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival.
Jianjun Yu, Jindan Yu, +5 authors, Marc E Lippman.
Neoplasia, 2008 Jan 31; 10(1). PMID: 18231641    Free PMC article.
Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder.
Malene Herbsleb, Ole F Christensen, +4 authors, Lars Dyrskjøt.
BMC Cancer, 2008 Feb 02; 8. PMID: 18237400    Free PMC article.
GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model.
Hosein Kouros-Mehr, Seth K Bechis, +6 authors, Zena Werb.
Cancer Cell, 2008 Feb 05; 13(2). PMID: 18242514    Free PMC article.
Highly Cited.
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.
Microenvironmental regulation of cancer development.
Min Hu, Kornelia Polyak.
Curr Opin Genet Dev, 2008 Feb 20; 18(1). PMID: 18282701    Free PMC article.
Highly Cited. Review.
Nuclear receptor location analyses in mammalian genomes: from gene regulation to regulatory networks.
Geneviève Deblois, Vincent Giguère.
Mol Endocrinol, 2008 Feb 23; 22(9). PMID: 18292239    Free PMC article.
Review.
The Diasporin Pathway: a tumor progression-related transcriptional network that predicts breast cancer survival.
Nigel P S Crawford, Renard C Walker, +3 authors, Kent W Hunter.
Clin Exp Metastasis, 2008 Feb 28; 25(4). PMID: 18301994    Free PMC article.
Merging microarray data from separate breast cancer studies provides a robust prognostic test.
Lei Xu, Aik Choon Tan, Raimond L Winslow, Donald Geman.
BMC Bioinformatics, 2008 Feb 29; 9. PMID: 18304324    Free PMC article.
Stathmin activity influences sarcoma cell shape, motility, and metastatic potential.
Barbara Belletti, Milena S Nicoloso, +9 authors, Gustavo Baldassarre.
Mol Biol Cell, 2008 Feb 29; 19(5). PMID: 18305103    Free PMC article.
Update of evidence in chemotherapy for breast cancer.
Hiroyasu Yamashiro, Masakazu Toi.
Int J Clin Oncol, 2008 Mar 01; 13(1). PMID: 18307012
Review.
Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods.
Manuela Zucknick, Sylvia Richardson, Euan A Stronach.
Stat Appl Genet Mol Biol, 2008 Mar 04; 7(1). PMID: 18312212    Free PMC article.
P-cadherin and beta-catenin are useful prognostic markers in breast cancer patients; beta-catenin interacts with heat shock protein Hsp27.
Mariel A Fanelli, Magdalena Montt-Guevara, +6 authors, Daniel R Ciocca.
Cell Stress Chaperones, 2008 Mar 06; 13(2). PMID: 18320359    Free PMC article.
A gene expression signature that can predict the recurrence of tamoxifen-treated primary breast cancer.
Maïa Chanrion, Vincent Negre, +8 authors, Jean-Marie Darbon.
Clin Cancer Res, 2008 Mar 19; 14(6). PMID: 18347175    Free PMC article.
Mechanisms of disease: epithelial-mesenchymal transition--does cellular plasticity fuel neoplastic progression?
Eva A Turley, Mandana Veiseh, Derek C Radisky, Mina J Bissell.
Nat Clin Pract Oncol, 2008 Mar 20; 5(5). PMID: 18349857    Free PMC article.
Highly Cited.
Netrin-1 expression confers a selective advantage for tumor cell survival in metastatic breast cancer.
Julien Fitamant, Céline Guenebeaud, +6 authors, Patrick Mehlen.
Proc Natl Acad Sci U S A, 2008 Mar 21; 105(12). PMID: 18353983    Free PMC article.
Carbonic anhydrase IX and response to postmastectomy radiotherapy in high-risk breast cancer: a subgroup analysis of the DBCG82 b and c trials.
Marianne Kyndi, Flemming B Sørensen, +5 authors, Danish Breast Cancer Cooperative Group.
Breast Cancer Res, 2008 Mar 22; 10(2). PMID: 18355402    Free PMC article.
GATA-3 and the regulation of the mammary luminal cell fate.
Hosein Kouros-Mehr, Jung-whan Kim, Seth K Bechis, Zena Werb.
Curr Opin Cell Biol, 2008 Mar 25; 20(2). PMID: 18358709    Free PMC article.
Review.
Alterations in human breast cancer adhesion-motility in response to changes in cell surface glycoproteins displaying alpha-L-fucose moieties.
Kun Yuan, Dennis Kucik, +3 authors, Gene P Siegal.
Int J Oncol, 2008 Mar 25; 32(4). PMID: 18360707    Free PMC article.
Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection.
Jack Y Yang, Guo-Zheng Li, +2 authors, Youping Deng.
BMC Genomics, 2008 Apr 17; 9 Suppl 1. PMID: 18366616    Free PMC article.
Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses.
René Natowicz, Roberto Incitti, +7 authors, Roman Rouzier.
BMC Bioinformatics, 2008 Mar 28; 9. PMID: 18366635    Free PMC article.
Human breast cancer cell lines contain stem-like cells that self-renew, give rise to phenotypically diverse progeny and survive chemotherapy.
Christine M Fillmore, Charlotte Kuperwasser.
Breast Cancer Res, 2008 Mar 28; 10(2). PMID: 18366788    Free PMC article.
Highly Cited.
ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome.
Christophe Ginestier, Min Hee Hur, +12 authors, Gabriela Dontu.
Cell Stem Cell, 2008 Mar 29; 1(5). PMID: 18371393    Free PMC article.
Highly Cited.
Heterogeneity of breast cancer metastases: comparison of therapeutic target expression and promoter methylation between primary tumors and their multifocal metastases.
Julie M Wu, Mary Jo Fackler, +12 authors, Pedram Argani.
Clin Cancer Res, 2008 Apr 03; 14(7). PMID: 18381931    Free PMC article.
Epigenetic contributions to cancer metastasis.
David I Rodenhiser.
Clin Exp Metastasis, 2008 Apr 04; 26(1). PMID: 18386135
Inflammation and breast cancer: metalloproteinases as common effectors of inflammation and extracellular matrix breakdown in breast cancer.
Carlo V Hojilla, Geoffrey A Wood, Rama Khokha.
Breast Cancer Res, 2008 Apr 09; 10(2). PMID: 18394187    Free PMC article.
Review.
Prognostic significance of cadherin-based adhesion molecules in cutaneous malignant melanoma.
Gretchen M Kreizenbeck, Aaron J Berger, +2 authors, Bonnie E Gould Rothberg.
Cancer Epidemiol Biomarkers Prev, 2008 Apr 10; 17(4). PMID: 18398036    Free PMC article.
Promoter hypermethylation in sentinel lymph nodes as a marker for breast cancer recurrence.
Hetty E Carraway, Shelun Wang, +8 authors, Julie R Lange.
Breast Cancer Res Treat, 2008 Apr 12; 114(2). PMID: 18404369    Free PMC article.
Occurrence of cancer at multiple sites: towards distinguishing multigenesis from metastasis.
Wei-Kang Zhang, Chun Zhang, Jing J Zhang, Shi V Liu.
Biol Direct, 2008 Apr 15; 3. PMID: 18405362    Free PMC article.
Review.
The fibromatosis signature defines a robust stromal response in breast carcinoma.
Andrew H Beck, Inigo Espinosa, +2 authors, Robert B West.
Lab Invest, 2008 Apr 17; 88(6). PMID: 18414401    Free PMC article.
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression.
Sujun Hua, Caleb B Kallen, +11 authors, Kevin P White.
Mol Syst Biol, 2008 Apr 17; 4. PMID: 18414489    Free PMC article.
A gene sets approach for identifying prognostic gene signatures for outcome prediction.
Seon-Young Kim, Yong Sung Kim.
BMC Genomics, 2008 Apr 18; 9. PMID: 18416850    Free PMC article.
Predictive gene lists for breast cancer prognosis: a topographic visualisation study.
Mingmanas Sivaraksa, David Lowe.
BMC Med Genomics, 2008 Apr 19; 1. PMID: 18419801    Free PMC article.
Expression profiling with RNA from formalin-fixed, paraffin-embedded material.
Andrea Oberli, Vlad Popovici, +6 authors, Rolf Jaggi.
BMC Med Genomics, 2008 Apr 22; 1. PMID: 18423048    Free PMC article.
Molecular profiles of progesterone receptor loss in human breast tumors.
Chad J Creighton, C Kent Osborne, +10 authors, Rachel Schiff.
Breast Cancer Res Treat, 2008 Apr 22; 114(2). PMID: 18425577    Free PMC article.
Bromodomain 4 activation predicts breast cancer survival.
Nigel P S Crawford, Jude Alsarraj, +6 authors, Kent W Hunter.
Proc Natl Acad Sci U S A, 2008 Apr 23; 105(17). PMID: 18427120    Free PMC article.
Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies.
Erol E Gulcicek, Christopher M Colangelo, +7 authors, Baolin Wu.
Curr Protoc Bioinformatics, 2008 Apr 23; Chapter 13. PMID: 18428746    Free PMC article.
Review.
Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast-conservation surgery, with or without postoperative radiotherapy.
Emma Niméus-Malmström, Morten Krogh, +8 authors, Mårten Fernö.
Breast Cancer Res, 2008 Apr 24; 10(2). PMID: 18430221    Free PMC article.
Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics.
Montserrat Garcia-Closas, Per Hall, +111 authors, Paul D Pharoah.
PLoS Genet, 2008 Apr 26; 4(4). PMID: 18437204    Free PMC article.
Highly Cited.
Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists.
Jonathan D Mosley, Ruth A Keri.
BMC Med Genomics, 2008 Apr 29; 1. PMID: 18439262    Free PMC article.
LYRIC/AEG-1 overexpression modulates BCCIPalpha protein levels in prostate tumor cells.
S C Ash, D Q Yang, D E Britt.
Biochem Biophys Res Commun, 2008 Apr 29; 371(2). PMID: 18440304    Free PMC article.
Identification of transgelin as a potential novel biomarker for gastric adenocarcinoma based on proteomics technology.
Qiaojia Huang, Qingling Huang, +4 authors, Xu Lin.
J Cancer Res Clin Oncol, 2008 May 01; 134(11). PMID: 18446369
Neutrophil gelatinase-associated lipocalin: new paths for an old shuttle.
Prasad Devarajan.
Cancer Ther, 2008 May 02; 5(B). PMID: 18449360    Free PMC article.
Unraveling the microenvironmental influences on the normal mammary gland and breast cancer.
Britta Weigelt, Mina J Bissell.
Semin Cancer Biol, 2008 May 06; 18(5). PMID: 18455428    Free PMC article.
Highly Cited. Review.
The tumor suppressor semaphorin 3B triggers a prometastatic program mediated by interleukin 8 and the tumor microenvironment.
Charlotte Rolny, Lorena Capparuccia, +7 authors, Luca Tamagnone.
J Exp Med, 2008 May 07; 205(5). PMID: 18458115    Free PMC article.
Insig2 is associated with colon tumorigenesis and inhibits Bax-mediated apoptosis.
Chang Gong Li, Mike Gruidl, +4 authors, Timothy J Yeatman.
Int J Cancer, 2008 May 09; 123(2). PMID: 18464289    Free PMC article.
Joint study of genetic regulators for expression traits related to breast cancer.
Tian Zheng, Shuang Wang, +3 authors, Shaw-Hwa Lo.
BMC Proc, 2008 May 10; 1 Suppl 1. PMID: 18466439    Free PMC article.
PaLS: filtering common literature, biological terms and pathway information.
Andreu Alibés, Andrés Cañada, Ramón Díaz-Uriarte.
Nucleic Acids Res, 2008 May 10; 36(Web Server issue). PMID: 18467422    Free PMC article.
Analysis of the MammaPrint breast cancer assay in a predominantly postmenopausal cohort.
Ben S Wittner, Dennis C Sgroi, +9 authors, Sridhar Ramaswamy.
Clin Cancer Res, 2008 May 17; 14(10). PMID: 18483364    Free PMC article.
Which is better: holdout or full-sample classifier design?
Marcel Brun, Qian Xu, Edward R Dougherty.
EURASIP J Bioinform Syst Biol, 2008 May 17;. PMID: 18483613    Free PMC article.
BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.
Nic Waddell, Anette Ten Haaf, +10 authors, Amanda B Spurdle.
PLoS Genet, 2008 May 24; 4(5). PMID: 18497862    Free PMC article.
Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases.
Lei Xu, Steven S Shen, +7 authors, Richard O Hynes.
Mol Cancer Res, 2008 May 29; 6(5). PMID: 18505921    Free PMC article.
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.
Timothy A Chan, Sabine Glockner, +8 authors, Stephen B Baylin.
PLoS Med, 2008 May 30; 5(5). PMID: 18507500    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.
Meta-analysis confirms BCL2 is an independent prognostic marker in breast cancer.
Grace M Callagy, Mark J Webber, Paul D P Pharoah, Carlos Caldas.
BMC Cancer, 2008 May 31; 8. PMID: 18510726    Free PMC article.
Review.
Molecular imaging of metastatic potential.
Paul T Winnard, Arvind P Pathak, +3 authors, Martin G Pomper.
J Nucl Med, 2008 Jul 01; 49 Suppl 2. PMID: 18523068    Free PMC article.
Review.
Meta-analysis of human cancer microarrays reveals GATA3 is integral to the estrogen receptor alpha pathway.
Brian J Wilson, Vincent Giguère.
Mol Cancer, 2008 Jun 06; 7. PMID: 18533032    Free PMC article.
Cell surface associated alpha-L-fucose moieties modulate human breast cancer neoplastic progression.
Kun Yuan, Catherine M Listinsky, +2 authors, Gene P Siegal.
Pathol Oncol Res, 2008 Jun 17; 14(2). PMID: 18553163
Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification.
Manli Zhu, Aleix M Martinez.
BMC Bioinformatics, 2008 Jun 17; 9. PMID: 18554411    Free PMC article.
Development of a clinically feasible molecular assay to predict recurrence of stage II colon cancer.
Yuqiu Jiang, Graham Casey, +9 authors, Yixin Wang.
J Mol Diagn, 2008 Jun 17; 10(4). PMID: 18556775    Free PMC article.
Penalized feature selection and classification in bioinformatics.
Shuangge Ma, Jian Huang.
Brief Bioinform, 2008 Jun 20; 9(5). PMID: 18562478    Free PMC article.
Review.
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.
Jianchao Yao, Chunqi Chang, +3 authors, Stanley J Roux.
BMC Bioinformatics, 2008 Jun 20; 9. PMID: 18564431    Free PMC article.
[Molecular pathological identification of predictive biomarkers: a new task for diagnostic pathology].
K W Schmid.
Urologe A, 2008 Jun 21; 47(10). PMID: 18566792
In praise of arrays.
Lihua Ying, Minnie Sarwal.
Pediatr Nephrol, 2008 Jun 24; 24(9). PMID: 18568367    Free PMC article.
Review.
Interpretation of genomic data: questions and answers.
Richard Simon.
Semin Hematol, 2008 Jun 28; 45(3). PMID: 18582627    Free PMC article.
Alignment and classification of time series gene expression in clinical studies.
Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph.
Bioinformatics, 2008 Jul 01; 24(13). PMID: 18586707    Free PMC article.
Pathway analysis reveals functional convergence of gene expression profiles in breast cancer.
Ronglai Shen, Arul M Chinnaiyan, Debashis Ghosh.
BMC Med Genomics, 2008 Jul 01; 1. PMID: 18588682    Free PMC article.
Transcriptomic biomarkers for individual risk assessment in new-onset heart failure.
Bettina Heidecker, Edward K Kasper, +6 authors, Joshua M Hare.
Circulation, 2008 Jul 02; 118(3). PMID: 18591436    Free PMC article.
Endocan expression correlated with poor survival in human hepatocellular carcinoma.
Geng-Wen Huang, Yi-Ming Tao, Xiang Ding.
Dig Dis Sci, 2008 Jul 02; 54(2). PMID: 18592377
Molecular dependence of estrogen receptor-negative breast cancer on a notch-survivin signaling axis.
Connie W Lee, Christopher M Raskett, Igor Prudovsky, Dario C Altieri.
Cancer Res, 2008 Jul 03; 68(13). PMID: 18593928    Free PMC article.
KLF6-SV1 overexpression accelerates human and mouse prostate cancer progression and metastasis.
Goutham Narla, Analisa DiFeo, +11 authors, John A Martignetti.
J Clin Invest, 2008 Jul 04; 118(8). PMID: 18596922    Free PMC article.
TDAG51 is an ERK signaling target that opposes ERK-mediated HME16C mammary epithelial cell transformation.
Michael D Oberst, Stacey J Beberman, +3 authors, Kathleen Kelly.
BMC Cancer, 2008 Jul 04; 8. PMID: 18597688    Free PMC article.
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.
Bayesian Weibull tree models for survival analysis of clinico-genomic data.
Jennifer Clarke, Mike West.
Stat Methodol, 2008 Jul 12; 5(3). PMID: 18618012    Free PMC article.
Cyclin-dependent kinase-associated proteins Cks1 and Cks2 are essential during early embryogenesis and for cell cycle progression in somatic cells.
Hanna-Stina Martinsson-Ahlzén, Vasco Liberal, +3 authors, Steven I Reed.
Mol Cell Biol, 2008 Jul 16; 28(18). PMID: 18625720    Free PMC article.
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
B Haibe-Kains, C Desmedt, C Sotiriou, G Bontempi.
Bioinformatics, 2008 Jul 19; 24(19). PMID: 18635567    Free PMC article.
Molecular signatures of metastasis in head and neck cancer.
Stefano Colella, Kristy L Richards, +5 authors, Ralf Krahe.
Head Neck, 2008 Jul 22; 30(10). PMID: 18642293    Free PMC article.
Validation of computational methods in genomics.
Edward R Doughtery, Hua Jianping, Michael L Bittner.
Curr Genomics, 2008 Jul 23; 8(1). PMID: 18645624    Free PMC article.
PRAME expression and clinical outcome of breast cancer.
M T Epping, A A M Hart, +2 authors, R Bernards.
Br J Cancer, 2008 Jul 24; 99(3). PMID: 18648365    Free PMC article.
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.
Vu T Chu, Raphael Gottardo, +2 authors, Ka Yee Yeung.
Genome Biol, 2008 Jul 26; 9(7). PMID: 18652698    Free PMC article.
Mouse modifier genes in mammary tumorigenesis and metastasis.
Scott F Winter, Kent W Hunter.
J Mammary Gland Biol Neoplasia, 2008 Jul 29; 13(3). PMID: 18661105
Review.
Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures.
Pratyaksha Wirapati, Christos Sotiriou, +10 authors, Mauro Delorenzi.
Breast Cancer Res, 2008 Jul 30; 10(4). PMID: 18662380    Free PMC article.
Highly Cited.
Investigating the efficacy of nonlinear dimensionality reduction schemes in classifying gene and protein expression studies.
George Lee, Carlos Rodriguez, Anant Madabhushi.
IEEE/ACM Trans Comput Biol Bioinform, 2008 Aug 02; 5(3). PMID: 18670041    Free PMC article.
Breast cancer stem cells: implications for therapy of breast cancer.
Brian J Morrison, Chris W Schmidt, +2 authors, J Alejandro Lopez.
Breast Cancer Res, 2008 Aug 02; 10(4). PMID: 18671830    Free PMC article.
Review.
Gene expression profiling of papillary thyroid carcinoma identifies transcripts correlated with BRAF mutational status and lymph node metastasis.
Gisele Oler, Cléber P Camacho, +3 authors, Janete M Cerutti.
Clin Cancer Res, 2008 Aug 05; 14(15). PMID: 18676742    Free PMC article.
Genetic polymorphisms of metastasis suppressor gene NME1 and breast cancer survival.
Shimian Qu, Jirong Long, +4 authors, Wei Zheng.
Clin Cancer Res, 2008 Aug 05; 14(15). PMID: 18676749    Free PMC article.
Identification of molecular phenotypes in canine mammary carcinomas with clinical implications: application of the human classification.
A Gama, A Alves, F Schmitt.
Virchows Arch, 2008 Aug 05; 453(2). PMID: 18677512
Prognostic utility of the 21-gene assay in hormone receptor-positive operable breast cancer compared with classical clinicopathologic features.
Lori J Goldstein, Robert Gray, +12 authors, Joseph A Sparano.
J Clin Oncol, 2008 Aug 06; 26(25). PMID: 18678838    Free PMC article.
Highly Cited.
Correlation between expression and differentiation of endocan in colorectal cancer.
Li Zuo, Su-Mei Zhang, +5 authors, Yuan Wang.
World J Gastroenterol, 2008 Aug 06; 14(28). PMID: 18680240    Free PMC article.
Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability.
Martin H van Vliet, Fabien Reyal, +3 authors, Lodewyk F A Wessels.
BMC Genomics, 2008 Aug 08; 9. PMID: 18684329    Free PMC article.
Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity.
David P Chen, Susan C Weber, +3 authors, Atul J Butte.
AMIA Annu Symp Proc, 2008 Aug 13;. PMID: 18693809    Free PMC article.
A decade of genome-wide gene expression profiling in acute myeloid leukemia: flashback and prospects.
Bas J Wouters, Bob Löwenberg, Ruud Delwel.
Blood, 2008 Aug 16; 113(2). PMID: 18703705    Free PMC article.
Review.
Studying chromosome instability in the mouse.
Floris Foijer, Viji M Draviam, Peter K Sorger.
Biochim Biophys Acta, 2008 Aug 19; 1786(1). PMID: 18706976    Free PMC article.
Review.
Multifunctional roles of insulin-like growth factor binding protein 5 in breast cancer.
Mustafa Akkiprik, Yumei Feng, +7 authors, Wei Zhang.
Breast Cancer Res, 2008 Aug 20; 10(4). PMID: 18710598    Free PMC article.
Review.
Prioritization of candidate cancer genes--an aid to oncogenomic studies.
Simon J Furney, Borja Calvo, +2 authors, Nuria Lopez-Bigas.
Nucleic Acids Res, 2008 Aug 20; 36(18). PMID: 18710882    Free PMC article.
Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets.
Katherine J Martin, Denis R Patrick, Mina J Bissell, Marcia V Fournier.
PLoS One, 2008 Aug 21; 3(8). PMID: 18714348    Free PMC article.
Highly Cited.
Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification.
Dimitry S A Nuyten, Trevor Hastie, +2 authors, Marc J van de Vijver.
Eur J Cancer, 2008 Aug 22; 44(15). PMID: 18715778    Free PMC article.
Comparison of prognostic gene expression signatures for breast cancer.
Benjamin Haibe-Kains, Christine Desmedt, +6 authors, Christos Sotiriou.
BMC Genomics, 2008 Aug 23; 9. PMID: 18717985    Free PMC article.
Basal phenotype in breast carcinoma occurring in women aged 35 or younger.
Rita Bori, Gábor Cserni.
Pathol Oncol Res, 2008 Aug 30; 15(1). PMID: 18752048
Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer.
John A Foekens, Anieta M Sieuwerts, +6 authors, John W M Martens.
Proc Natl Acad Sci U S A, 2008 Aug 30; 105(35). PMID: 18755890    Free PMC article.
Highly Cited.
Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis.
Chad J Creighton, Angelo Casa, +5 authors, Adrian V Lee.
J Clin Oncol, 2008 Sep 02; 26(25). PMID: 18757322    Free PMC article.
Highly Cited.
In vitro effect of radiation, antibody to epidermal growth factor receptor and Docetaxel in human head and neck squamous carcinoma cells with mutant P53 and over-expressed EGFR.
Nongnit Laytragoon-Lewin, Hasan Ustun, +5 authors, Freddi Lewin.
J Cancer Res Clin Oncol, 2008 Sep 02; 135(2). PMID: 18758819
The C1C2: a framework for simultaneous model selection and assessment.
Martin Eklund, Ola Spjuth, Jarl Es Wikberg.
BMC Bioinformatics, 2008 Sep 03; 9. PMID: 18761753    Free PMC article.
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.
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer.
Elin Karlsson, Ulla Delle, +4 authors, Khalil Helou.
BMC Cancer, 2008 Sep 10; 8. PMID: 18778486    Free PMC article.
Stemming the tide of cancer for BRCA1/2 mutation carriers.
Henry T Lynch, Joseph N Marcus, Wendy S Rubinstein.
J Clin Oncol, 2008 Sep 10; 26(26). PMID: 18779610    Free PMC article.
Identification of a gene signature in cell cycle pathway for breast cancer prognosis using gene expression profiling data.
Jiangang Liu, Andrew Campen, +6 authors, Shuyu Li.
BMC Med Genomics, 2008 Sep 13; 1. PMID: 18786252    Free PMC article.
Argonaute-2 expression is regulated by epidermal growth factor receptor and mitogen-activated protein kinase signaling and correlates with a transformed phenotype in breast cancer cells.
Brian D Adams, Kevin P Claffey, Bruce A White.
Endocrinology, 2008 Sep 13; 150(1). PMID: 18787018    Free PMC article.
Targeting a metalloprotease-PAR1 signaling system with cell-penetrating pepducins inhibits angiogenesis, ascites, and progression of ovarian cancer.
Anika Agarwal, Lidija Covic, +5 authors, Athan Kuliopulos.
Mol Cancer Ther, 2008 Sep 16; 7(9). PMID: 18790755    Free PMC article.
Systems biology approach to identification of biomarkers for metastatic progression in cancer.
Andrey A Ptitsyn, Michael M Weil, Douglas H Thamm.
BMC Bioinformatics, 2008 Sep 20; 9 Suppl 9. PMID: 18793472    Free PMC article.
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.
Development of resistance to targeted therapies transforms the clinically associated molecular profile subtype of breast tumor xenografts.
Chad J Creighton, Suleiman Massarweh, +6 authors, Rachel Schiff.
Cancer Res, 2008 Sep 17; 68(18). PMID: 18794137    Free PMC article.
The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis.
Andrew H Sims, Graeme J Smethurst, +5 authors, Robert B Clarke.
BMC Med Genomics, 2008 Sep 23; 1. PMID: 18803878    Free PMC article.
Translation of genomics research at the bedside: the promise and the challenge.
Damien Chaussabel.
Clin Immunol, 2008 Sep 23; 129(2). PMID: 18804420    Free PMC article.
Different gene-expression profiles for the poorly differentiated carcinoma and the highly differentiated papillary adenocarcinoma in mammary glands support distinct metabolic pathways.
Tali Eilon, Itamar Barash.
BMC Cancer, 2008 Sep 25; 8. PMID: 18811984    Free PMC article.
Transformation by oncogenic Ras expands the early genomic response to transforming growth factor beta in intestinal epithelial cells.
Carl E Allen, Jianguo Du, +3 authors, John A Barnard.
Neoplasia, 2008 Sep 25; 10(10). PMID: 18813357    Free PMC article.
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
Atsushi Niida, Andrew D Smith, +4 authors, Tetsu Akiyama.
BMC Bioinformatics, 2008 Oct 01; 9. PMID: 18823535    Free PMC article.
The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers.
Vietty Wong, Dong-Yu Wang, +4 authors, Wey Liang Leong.
BMC Cancer, 2008 Oct 02; 8. PMID: 18826606    Free PMC article.
Gene expression profiling of liver metastases from colorectal cancer as potential basis for treatment choice.
M A Pantaleo, A Astolfi, +8 authors, G Biasco.
Br J Cancer, 2008 Oct 02; 99(10). PMID: 18827815    Free PMC article.
Integrative approach for differentially overexpressed genes in gastric cancer by combining large-scale gene expression profiling and network analysis.
A Takeno, I Takemasa, +6 authors, M Monden.
Br J Cancer, 2008 Oct 02; 99(8). PMID: 18827816    Free PMC article.
Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models.
Christina N Bennett, Jeffrey E Green.
Breast Cancer Res, 2008 Oct 03; 10(5). PMID: 18828875    Free PMC article.
Review.
Selecting informative genes for discriminant analysis using multigene expression profiles.
Xin Yan, Tian Zheng.
BMC Genomics, 2008 Oct 10; 9 Suppl 2. PMID: 18831779    Free PMC article.
Tumor classification ranking from microarray data.
Rattikorn Hewett, Phongphun Kijsanayothin.
BMC Genomics, 2008 Oct 10; 9 Suppl 2. PMID: 18831787    Free PMC article.
Gene and pathway identification with Lp penalized Bayesian logistic regression.
Zhenqiu Liu, Ronald B Gartenhaus, +2 authors, Xiaoli Jiao.
BMC Bioinformatics, 2008 Oct 07; 9. PMID: 18834526    Free PMC article.
A method for analyzing censored survival phenotype with gene expression data.
Tongtong Wu, Wei Sun, +2 authors, Ker-Chau Li.
BMC Bioinformatics, 2008 Oct 08; 9. PMID: 18837994    Free PMC article.
Gene expression module-based chemical function similarity search.
Yun Li, Pei Hao, +12 authors, Yixue Li.
Nucleic Acids Res, 2008 Oct 10; 36(20). PMID: 18842630    Free PMC article.
Comparative optimism in models involving both classical clinical and gene expression information.
Caroline Truntzer, Delphine Maucort-Boulch, Pascal Roy.
BMC Bioinformatics, 2008 Oct 16; 9. PMID: 18854055    Free PMC article.
Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.
Hans Neubauer, Susan E Clare, +9 authors, Michael A Cahill.
Breast Cancer Res, 2008 Oct 17; 10(5). PMID: 18922159    Free PMC article.
Suppression of the negative regulator LRIG1 contributes to ErbB2 overexpression in breast cancer.
Jamie K Miller, David L Shattuck, +6 authors, Colleen Sweeney.
Cancer Res, 2008 Oct 17; 68(20). PMID: 18922900    Free PMC article.
Small molecule targeting the Hec1/Nek2 mitotic pathway suppresses tumor cell growth in culture and in animal.
Guikai Wu, Xiao-Long Qiu, +5 authors, Wen-Hwa Lee.
Cancer Res, 2008 Oct 17; 68(20). PMID: 18922912    Free PMC article.
From evidence-based medicine to genomic medicine.
Dhavendra Kumar.
Genomic Med, 2008 Oct 17; 1(3-4). PMID: 18923934    Free PMC article.
Evidence that molecular changes in cells occur before morphological alterations during the progression of breast ductal carcinoma.
Nadia P Castro, Cynthia A B T Osório, +5 authors, Dirce M Carraro.
Breast Cancer Res, 2008 Oct 22; 10(5). PMID: 18928525    Free PMC article.
A candidate molecular signature associated with tamoxifen failure in primary breast cancer.
Julie A Vendrell, Katherine E Robertson, +10 authors, Pascale A Cohen.
Breast Cancer Res, 2008 Oct 22; 10(5). PMID: 18928543    Free PMC article.
New wirings in the survivin networks.
D C Altieri.
Oncogene, 2008 Oct 22; 27(48). PMID: 18931693    Free PMC article.
Review.
Hec1 overexpression hyperactivates the mitotic checkpoint and induces tumor formation in vivo.
Elena Diaz-Rodríguez, Rocio Sotillo, Juan-Manuel Schvartzman, Robert Benezra.
Proc Natl Acad Sci U S A, 2008 Oct 23; 105(43). PMID: 18940925    Free PMC article.
Tumor characteristics as an analytic tool for classifying genetic variants of uncertain clinical significance.
Robert M W Hofstra, Amanda B Spurdle, +5 authors, IARC Unclassified Genetic Variants Working Group.
Hum Mutat, 2008 Oct 28; 29(11). PMID: 18951447    Free PMC article.
Chromosomal instability is associated with higher expression of genes implicated in epithelial-mesenchymal transition, cancer invasiveness, and metastasis and with lower expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin maintenance.
Anna V Roschke, Oleg K Glebov, +3 authors, Ilan R Kirsch.
Neoplasia, 2008 Oct 28; 10(11). PMID: 18953431    Free PMC article.
Gene expression profiling in glioblastoma and immunohistochemical evaluation of IGFBP-2 and CDC20.
Gianluca Marucci, Luca Morandi, +7 authors, Vincenzo Eusebi.
Virchows Arch, 2008 Oct 28; 453(6). PMID: 18953566
Gene expression profiling of breast cancer.
Ting Bao, Nancy E Davidson.
Adv Surg, 2008 Oct 29; 42. PMID: 18953822    Free PMC article.
Review.
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.
Peter A DiMaggio, Scott R McAllister, +3 authors, Herschel A Rabitz.
BMC Bioinformatics, 2008 Oct 29; 9. PMID: 18954459    Free PMC article.
Gene expression data classification using consensus independent component analysis.
Chun-Hou Zheng, De-Shuang Huang, Xiang-Zhen Kong, Xing-Ming Zhao.
Genomics Proteomics Bioinformatics, 2008 Nov 01; 6(2). PMID: 18973863    Free PMC article.
Lost in translation: problems and pitfalls in translating laboratory observations to clinical utility.
Richard Simon.
Eur J Cancer, 2008 Nov 04; 44(18). PMID: 18977655    Free PMC article.
Review.
A phase II trial of vorinostat (suberoylanilide hydroxamic acid) in metastatic breast cancer: a California Cancer Consortium study.
Thehang H Luu, Robert J Morgan, +10 authors, George Somlo.
Clin Cancer Res, 2008 Nov 05; 14(21). PMID: 18981013    Free PMC article.
Robust prognostic value of a knowledge-based proliferation signature across large patient microarray studies spanning different cancer types.
M H W Starmans, B Krishnapuram, +8 authors, P Lambin.
Br J Cancer, 2008 Nov 06; 99(11). PMID: 18985037    Free PMC article.
Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer.
Charles Swanton, Zoltan Szallasi, James D Brenton, Julian Downward.
Breast Cancer Res, 2008 Nov 07; 10(5). PMID: 18986507    Free PMC article.
Review.
Ex vivo characterization of polyclonal memory CD8+ T-cell responses to PRAME-specific peptides in patients with acute lymphoblastic leukemia and acute and chronic myeloid leukemia.
Katayoun Rezvani, Agnes S M Yong, +8 authors, A John Barrett.
Blood, 2008 Nov 08; 113(10). PMID: 18988867    Free PMC article.
Inferring pathway activity toward precise disease classification.
Eunjung Lee, Han-Yu Chuang, +2 authors, Doheon Lee.
PLoS Comput Biol, 2008 Nov 08; 4(11). PMID: 18989396    Free PMC article.
Highly Cited.
A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer.
Fabien Reyal, Martin H van Vliet, +10 authors, Lodewyk F A Wessels.
Breast Cancer Res, 2008 Nov 19; 10(6). PMID: 19014521    Free PMC article.
Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites.
Patricia Severino, Adriana M Alvares, +5 authors, Head and Neck Genome Project GENCAPO.
BMC Res Notes, 2008 Nov 19; 1. PMID: 19014556    Free PMC article.
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification.
Michael Gormley, Aydin Tozeren.
BMC Bioinformatics, 2008 Nov 19; 9. PMID: 19014681    Free PMC article.
Characterization of breast cancers and therapy response by MRS and quantitative gene expression profiling in the choline pathway.
David L Morse, Danielle Carroll, +7 authors, Robert J Gillies.
NMR Biomed, 2008 Nov 20; 22(1). PMID: 19016452    Free PMC article.
Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature.
Andrew Tutt, Alice Wang, +21 authors, Fred Waldman.
BMC Cancer, 2008 Nov 26; 8. PMID: 19025599    Free PMC article.
A functional Notch-survivin gene signature in basal breast cancer.
Connie W Lee, Karl Simin, +5 authors, Dario C Altieri.
Breast Cancer Res, 2008 Nov 26; 10(6). PMID: 19025652    Free PMC article.
A method for constructing a confidence bound for the actual error rate of a prediction rule in high dimensions.
Kevin K Dobbin.
Biostatistics, 2008 Nov 29; 10(2). PMID: 19039030    Free PMC article.
Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells.
Bérengère Marty, Virginie Maire, +15 authors, Thierry Dubois.
Breast Cancer Res, 2008 Dec 06; 10(6). PMID: 19055754    Free PMC article.
"New" molecular taxonomy in breast cancer.
Marta Hergueta-Redondo, José Palacios, Amparo Cano, Gema Moreno-Bueno.
Clin Transl Oncol, 2008 Dec 11; 10(12). PMID: 19068448
Review.
Machine learning-based receiver operating characteristic (ROC) curves for crisp and fuzzy classification of DNA microarrays in cancer research.
Leif E Peterson, Matthew A Coleman.
Int J Approx Reason, 2008 Dec 17; 47(1). PMID: 19079753    Free PMC article.
Statistical issues and analyses of in vivo and in vitro genomic data in order to identify clinically relevant profiles.
Laila M Poisson, Debashis Ghosh.
Cancer Inform, 2007 Jan 01; 3. PMID: 19079768    Free PMC article.
Genetic susceptibility loci for breast cancer by estrogen receptor status.
Montserrat Garcia-Closas, Stephen Chanock.
Clin Cancer Res, 2008 Dec 18; 14(24). PMID: 19088016    Free PMC article.
Review.
Confirmation of gene expression-based prediction of survival in non-small cell lung cancer.
Nancy L Guo, Ying-Wooi Wan, +10 authors, Yong Qian.
Clin Cancer Res, 2008 Dec 18; 14(24). PMID: 19088038    Free PMC article.
Mechanisms of metastasis.
Kent W Hunter, Nigel P S Crawford, Jude Alsarraj.
Breast Cancer Res, 2009 Jan 06; 10 Suppl 1. PMID: 19091006    Free PMC article.
Review.
Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes.
Núria Bonifaci, Antoni Berenguer, +5 authors, Miguel Angel Pujana.
BMC Med Genomics, 2008 Dec 20; 1. PMID: 19094230    Free PMC article.
EZH2 and BMI1 inversely correlate with prognosis and TP53 mutation in breast cancer.
Alexandra M Pietersen, Hugo M Horlings, +7 authors, Maarten van Lohuizen.
Breast Cancer Res, 2008 Dec 23; 10(6). PMID: 19099573    Free PMC article.
The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome.
Jens K Habermann, Jana Doering, +12 authors, Thomas Ried.
Int J Cancer, 2008 Dec 23; 124(7). PMID: 19101988    Free PMC article.
Expression of centromere protein F (CENP-F) associated with higher FDG uptake on PET/CT, detected by cDNA microarray, predicts high-risk patients with primary breast cancer.
Shigeto Ueda, Nobuo Kondoh, +10 authors, Hidetaka Mochizuki.
BMC Cancer, 2008 Dec 24; 8. PMID: 19102762    Free PMC article.
TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
Fabrice Lopez, Julien Textoris, +6 authors, Denis Puthier.
PLoS One, 2008 Dec 24; 3(12). PMID: 19104654    Free PMC article.
Cdc6 and cyclin E2 are PTEN-regulated genes associated with human prostate cancer metastasis.
Zhong Wu, HyungJun Cho, Garret M Hampton, Dan Theodorescu.
Neoplasia, 2008 Dec 25; 11(1). PMID: 19107233    Free PMC article.
Haptoglobin phenotype is not a predictor of recurrence free survival in high-risk primary breast cancer patients.
Marie-Christine W Gast, Harm van Tinteren, +10 authors, Jos H Beijnen.
BMC Cancer, 2008 Dec 26; 8. PMID: 19108738    Free PMC article.
Molecular basis of metastasis.
Anne C Chiang, Joan Massagué.
N Engl J Med, 2008 Dec 26; 359(26). PMID: 19109576    Free PMC article.
Highly Cited. Review.
MTDH activation by 8q22 genomic gain promotes chemoresistance and metastasis of poor-prognosis breast cancer.
Guohong Hu, Robert A Chong, +7 authors, Yibin Kang.
Cancer Cell, 2008 Dec 30; 15(1). PMID: 19111877    Free PMC article.
Highly Cited.
A gene expression signature that defines breast cancer metastases.
Rachel E Ellsworth, Jeff Seebach, +5 authors, Craig D Shriver.
Clin Exp Metastasis, 2008 Dec 30; 26(3). PMID: 19112599
The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH.
Tomoko Furuya, Tetsuji Uchiyama, +6 authors, Kohsuke Sasaki.
BMC Cancer, 2009 Jan 01; 8. PMID: 19115996    Free PMC article.
Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer.
Mads Thomassen, Qihua Tan, Torben A Kruse.
BMC Cancer, 2009 Jan 01; 8. PMID: 19116006    Free PMC article.
A resampling-based meta-analysis for detection of differential gene expression in breast cancer.
Bala Gur-Dedeoglu, Ozlen Konu, +4 authors, Isik G Yulug.
BMC Cancer, 2009 Jan 01; 8. PMID: 19116033    Free PMC article.
The origins of breast cancer prognostic gene expression profiles.
Luanne Lukes, Nigel P S Crawford, Renard Walker, Kent W Hunter.
Cancer Res, 2009 Jan 02; 69(1). PMID: 19118016    Free PMC article.
Common genetic variation in candidate genes and susceptibility to subtypes of breast cancer.
Nasim Mavaddat, Alison M Dunning, +2 authors, Paul D Pharoah.
Cancer Epidemiol Biomarkers Prev, 2009 Jan 07; 18(1). PMID: 19124506    Free PMC article.
Recommendations from the EGAPP Working Group: can tumor gene expression profiling improve outcomes in patients with breast cancer?
Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group.
Genet Med, 2009 Jan 07; 11(1). PMID: 19125125    Free PMC article.
Using pathway signatures as means of identifying similarities among microarray experiments.
Luca Beltrame, Lisa Rizzetto, +4 authors, Duccio Cavalieri.
PLoS One, 2009 Jan 07; 4(1). PMID: 19125200    Free PMC article.
The utility of conventional and molecular pathology in managing breast cancer.
D Craig Allred.
Breast Cancer Res, 2009 Jan 16; 10 Suppl 4. PMID: 19128442    Free PMC article.
Molecular classification and prognostication of adrenocortical tumors by transcriptome profiling.
Thomas J Giordano, Rork Kuick, +7 authors, Gary Hammer.
Clin Cancer Res, 2009 Jan 17; 15(2). PMID: 19147773    Free PMC article.
Highly Cited.
On reliable discovery of molecular signatures.
Roland Nilsson, Johan Björkegren, Jesper Tegnér.
BMC Bioinformatics, 2009 Jan 31; 10. PMID: 19178740    Free PMC article.
Integrating biological knowledge with gene expression profiles for survival prediction of cancer.
Xi Chen, Lily Wang.
J Comput Biol, 2009 Feb 03; 16(2). PMID: 19183004    Free PMC article.
Altered proliferation and differentiation properties of primary mammary epithelial cells from BRCA1 mutation carriers.
Laura N Burga, Nadine M Tung, +8 authors, Gerburg M Wulf.
Cancer Res, 2009 Feb 05; 69(4). PMID: 19190334    Free PMC article.
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
Eran Eden, Roy Navon, +2 authors, Zohar Yakhini.
BMC Bioinformatics, 2009 Feb 05; 10. PMID: 19192299    Free PMC article.
Highly Cited.
Molecular changes in primary breast tumors and the Nottingham Histologic Score.
Rachel E Ellsworth, Jeffrey A Hooke, +2 authors, Craig D Shriver.
Pathol Oncol Res, 2009 Feb 06; 15(4). PMID: 19194786
Prognostic gene signatures for non-small-cell lung cancer.
Paul C Boutros, Suzanne K Lau, +6 authors, Igor Jurisica.
Proc Natl Acad Sci U S A, 2009 Feb 07; 106(8). PMID: 19196983    Free PMC article.
Highly Cited.
[Molecular pathology as an necessity: its role in diagnostic and predictive pathology].
K W Schmid.
Pathologe, 2009 Feb 10; 30(2). PMID: 19198840
Outcome prediction based on microarray analysis: a critical perspective on methods.
Michalis Zervakis, Michalis E Blazadonakis, +3 authors, Dimitris Kafetzopoulos.
BMC Bioinformatics, 2009 Feb 10; 10. PMID: 19200394    Free PMC article.
Diurnal variation of the human adipose transcriptome and the link to metabolic disease.
Andrey Loboda, Walter K Kraft, +16 authors, Pek Yee Lum.
BMC Med Genomics, 2009 Feb 11; 2. PMID: 19203388    Free PMC article.
Supervised risk predictor of breast cancer based on intrinsic subtypes.
Joel S Parker, Michael Mullins, +17 authors, Philip S Bernard.
J Clin Oncol, 2009 Feb 11; 27(8). PMID: 19204204    Free PMC article.
Highly Cited.
Breast cancer subtypes and response to docetaxel in node-positive breast cancer: use of an immunohistochemical definition in the BCIRG 001 trial.
Judith Hugh, John Hanson, +11 authors, Charles Vogel.
J Clin Oncol, 2009 Feb 11; 27(8). PMID: 19204205    Free PMC article.
Highly Cited.
A voting approach to identify a small number of highly predictive genes using multiple classifiers.
Md Rafiul Hassan, M Maruf Hossain, +3 authors, Kotagiri Ramamohanarao.
BMC Bioinformatics, 2009 Feb 28; 10 Suppl 1. PMID: 19208118    Free PMC article.
Knowledge driven decomposition of tumor expression profiles.
Martin H van Vliet, Lodewyk F A Wessels, Marcel J T Reinders.
BMC Bioinformatics, 2009 Feb 28; 10 Suppl 1. PMID: 19208120    Free PMC article.
Improving the efficiency of biomarker identification using biological knowledge.
John H Phan, Qiqin Yin-Goen, Andrew N Young, May D Wang.
Pac Symp Biocomput, 2009 Feb 13;. PMID: 19209720    Free PMC article.
Master regulators used as breast cancer metastasis classifier.
Wei Keat Lim, Eugenia Lyashenko, Andrea Califano.
Pac Symp Biocomput, 2009 Feb 13;. PMID: 19209726    Free PMC article.
[Genome-wide expression profiling as a clinical tool: are we there yet?].
F C Geyer, T Decker, J S Reis-Filho.
Pathologe, 2009 Feb 17; 30(2). PMID: 19219435
Review.
Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care.
Christopher L Tebbit, Jun Zhai, +8 authors, John A Olson.
Breast Cancer Res Treat, 2009 Feb 19; 118(3). PMID: 19224362    Free PMC article.
Biological convergence of cancer signatures.
Xavier Solé, Núria Bonifaci, +11 authors, Miguel Angel Pujana.
PLoS One, 2009 Feb 21; 4(2). PMID: 19229342    Free PMC article.
Genomancy: predicting tumour response to cancer therapy based on the oracle of genetics.
P D Williams, J K Lee, D Theodorescu.
Curr Oncol, 2009 Feb 21; 16(1). PMID: 19229372    Free PMC article.
Role of BRCA2 mutation status on overall survival among breast cancer patients from Sardinia.
Mario Budroni, Rosaria Cesaraccio, +7 authors, Giuseppe Palmieri.
BMC Cancer, 2009 Feb 24; 9. PMID: 19232099    Free PMC article.
Comparison of EGFR and K-RAS gene status between primary tumours and corresponding metastases in NSCLC.
A Kalikaki, A Koutsopoulos, +5 authors, A Voutsina.
Br J Cancer, 2009 Feb 25; 99(6). PMID: 19238633    Free PMC article.
Cell-cycle-phase progression analysis identifies unique phenotypes of major prognostic and predictive significance in breast cancer.
M Loddo, S R Kingsbury, +10 authors, G H Williams.
Br J Cancer, 2009 Feb 26; 100(6). PMID: 19240714    Free PMC article.
Synthesis and biological evaluation of a series of novel inhibitor of Nek2/Hec1 analogues.
Xiao-Long Qiu, Guideng Li, +5 authors, Wen-Hwa Lee.
J Med Chem, 2009 Feb 27; 52(6). PMID: 19243176    Free PMC article.
Protein kinase D1 regulates matrix metalloproteinase expression and inhibits breast cancer cell invasion.
Tim Eiseler, Heike Döppler, +2 authors, Peter Storz.
Breast Cancer Res, 2009 Feb 27; 11(1). PMID: 19243594    Free PMC article.
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.
Amalia Annest, Roger E Bumgarner, Adrian E Raftery, Ka Yee Yeung.
BMC Bioinformatics, 2009 Feb 28; 10. PMID: 19245714    Free PMC article.
Utilizing the molecular gateway: the path to personalized cancer management.
Jonathan B Overdevest, Dan Theodorescu, Jae K Lee.
Clin Chem, 2009 Feb 28; 55(4). PMID: 19246616    Free PMC article.
Review.
Evaluating microarray-based classifiers: an overview.
A-L Boulesteix, C Strobl, T Augustin, M Daumer.
Cancer Inform, 2008 Jan 01; 6. PMID: 19259405    Free PMC article.
Chromosome 20q amplification regulates in vitro response to Kinesin-5 inhibitor.
Aimee L Jackson, Mao Mao, +5 authors, Peter S Linsley.
Cancer Inform, 2008 Jan 01; 6. PMID: 19259408    Free PMC article.
An integrative analysis of microRNA and mRNA expression--a case study.
Li-Xuan Qin.
Cancer Inform, 2008 Jan 01; 6. PMID: 19259417    Free PMC article.
The anti-tumour agent, cisplatin, and its clinically ineffective isomer, transplatin, produce unique gene expression profiles in human cells.
Anne M Galea, Vincent Murray.
Cancer Inform, 2008 Jan 01; 6. PMID: 19259415    Free PMC article.
A radiation-derived gene expression signature predicts clinical outcome for breast cancer patients.
Brian D Piening, Pei Wang, Aravind Subramanian, Amanda G Paulovich.
Radiat Res, 2009 Mar 10; 171(2). PMID: 19267539    Free PMC article.
Silencing of D4-GDI inhibits growth and invasive behavior in MDA-MB-231 cells by activation of Rac-dependent p38 and JNK signaling.
Yaqin Zhang, Leslie A Rivera Rosado, Sun Young Moon, Baolin Zhang.
J Biol Chem, 2009 Mar 10; 284(19). PMID: 19269969    Free PMC article.
Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup.
M Chehani Alles, Margaret Gardiner-Garden, +5 authors, Christopher J Ormandy.
PLoS One, 2009 Mar 10; 4(3). PMID: 19270750    Free PMC article.
The tspair package for finding top scoring pair classifiers in R.
Jeffrey T Leek.
Bioinformatics, 2009 Mar 12; 25(9). PMID: 19276151    Free PMC article.
Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation.
Xiaohui Fan, Leming Shi, +3 authors, Weida Tong.
BMC Proc, 2009 Mar 13; 3 Suppl 2. PMID: 19278560    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.
Regulation of p53 by TopBP1: a potential mechanism for p53 inactivation in cancer.
Kang Liu, Naresh Bellam, +4 authors, Weei-Chin Lin.
Mol Cell Biol, 2009 Mar 18; 29(10). PMID: 19289498    Free PMC article.
Factors influencing the statistical power of complex data analysis protocols for molecular signature development from microarray data.
Constantin F Aliferis, Alexander Statnikov, +3 authors, Frank E Harrell.
PLoS One, 2009 Mar 18; 4(3). PMID: 19290050    Free PMC article.
A compact VEGF signature associated with distant metastases and poor outcomes.
Zhiyuan Hu, Cheng Fan, +10 authors, Charles M Perou.
BMC Med, 2009 Mar 18; 7. PMID: 19291283    Free PMC article.
Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach.
Yijun Sun, Virginia Urquidi, Steve Goodison.
Breast Cancer Res Treat, 2009 Mar 18; 119(3). PMID: 19291396    Free PMC article.
High cyclin B1 expression is associated with poor survival in breast cancer.
K Aaltonen, R-M Amini, +4 authors, C Blomqvist.
Br J Cancer, 2009 Mar 19; 100(7). PMID: 19293801    Free PMC article.
Prediction of breast cancer metastasis by genomic profiling: where do we stand?
Ulrich Pfeffer, Francesco Romeo, Douglas M Noonan, Adriana Albini.
Clin Exp Metastasis, 2009 Mar 25; 26(6). PMID: 19308665    Free PMC article.
Review.
Tissue biomarkers for prognosis in cutaneous melanoma: a systematic review and meta-analysis.
Bonnie E Gould Rothberg, Michael B Bracken, David L Rimm.
J Natl Cancer Inst, 2009 Mar 26; 101(7). PMID: 19318635    Free PMC article.
Systematic Review.
Bringing diagnostic technologies to the clinical laboratory: Rigor, regulation, and reality.
Gordon Whiteley.
Proteomics Clin Appl, 2008 Jan 01; 2(10-11). PMID: 19325937    Free PMC article.
Comparative expression pathway analysis of human and canine mammary tumors.
Paolo Uva, Luigi Aurisicchio, +13 authors, Emanuele de Rinaldis.
BMC Genomics, 2009 Mar 31; 10. PMID: 19327144    Free PMC article.
A signature-based method for indexing cell cycle phase distribution from microarray profiles.
Hideaki Mizuno, Yoshito Nakanishi, +2 authors, Kunio Kitada.
BMC Genomics, 2009 Apr 01; 10. PMID: 19331659    Free PMC article.
A multi-marker assay to distinguish malignant melanomas from benign nevi.
Mohammed Kashani-Sabet, Javier Rangel, +7 authors, Richard W Sagebiel.
Proc Natl Acad Sci U S A, 2009 Apr 01; 106(15). PMID: 19332774    Free PMC article.
A network view of disease and compound screening.
Eric E Schadt, Stephen H Friend, David A Shaywitz.
Nat Rev Drug Discov, 2009 Apr 02; 8(4). PMID: 19337271
Highly Cited. Review.
The subcellular localization of IGFBP5 affects its cell growth and migration functions in breast cancer.
Mustafa Akkiprik, Limei Hu, +2 authors, Wei Zhang.
BMC Cancer, 2009 Apr 04; 9. PMID: 19341485    Free PMC article.
Optimizing molecular signatures for predicting prostate cancer recurrence.
Yijun Sun, Steve Goodison.
Prostate, 2009 Apr 04; 69(10). PMID: 19343730    Free PMC article.
Breaking down barriers: the importance of the stromal microenvironment in acquiring invasiveness in young women's breast cancer.
Pepper Schedin, Virginia Borges.
Breast Cancer Res, 2009 Apr 07; 11(2). PMID: 19344495    Free PMC article.
Gene expression profiles and breast cancer metastasis: a genetic perspective.
Kent W Hunter, Jude Alsarraj.
Clin Exp Metastasis, 2009 Apr 07; 26(6). PMID: 19347591    Free PMC article.
Review.
[Individualizing treatment for locally advanced rectal cancer].
T Liersch, H Rothe, B M Ghadimi, H Becker.
Chirurg, 2009 Apr 08; 80(4). PMID: 19350305
Review.
CCAAT/enhancer-binding protein beta: its role in breast cancer and associations with receptor tyrosine kinases.
Cynthia A Zahnow.
Expert Rev Mol Med, 2009 Apr 09; 11. PMID: 19351437    Free PMC article.
Review.
Overexpression and mislocalization of the chromosomal segregation protein separase in multiple human cancers.
Rene Meyer, Viacheslav Fofanov, +3 authors, Debananda Pati.
Clin Cancer Res, 2009 Apr 09; 15(8). PMID: 19351757    Free PMC article.
Translating the metastasis paradigm from scientific theory to clinical oncology.
Fei Dong, Anuradha S Budhu, Xin Wei Wang.
Clin Cancer Res, 2009 Apr 09; 15(8). PMID: 19351761    Free PMC article.
Use of gene expression profiles of peripheral blood lymphocytes to distinguish BRCA1 mutation carriers in high risk breast cancer families.
Marie-Laure Vuillaume, Nancy Uhrhammer, +5 authors, Yves-Jean Bignon.
Cancer Inform, 2009 Apr 09; 7. PMID: 19352458    Free PMC article.
Measurement and quality control issues in multiplex protein assays: a case study.
Allison A Ellington, Iftikhar J Kullo, Kent R Bailey, George G Klee.
Clin Chem, 2009 Apr 18; 55(6). PMID: 19372187    Free PMC article.
Identifying estrogen receptor target genes.
Willem-Jan Welboren, Henk G Stunnenberg, Fred C G J Sweep, Paul N Span.
Mol Oncol, 2007 Sep 01; 1(2). PMID: 19383291    Free PMC article.
Review.
Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer.
Bjørn Naume, Xi Zhao, +10 authors, Therese Sørlie.
Mol Oncol, 2007 Sep 01; 1(2). PMID: 19383292    Free PMC article.
Gene expression profiling of human lymph node metastases and matched primary breast carcinomas: clinical implications.
Mika Suzuki, David Tarin.
Mol Oncol, 2007 Sep 01; 1(2). PMID: 19383293    Free PMC article.
The MINDACT trial: the first prospective clinical validation of a genomic tool.
Fatima Cardoso, Martine Piccart-Gebhart, +2 authors, TRANSBIG Consortium.
Mol Oncol, 2007 Dec 01; 1(3). PMID: 19383299    Free PMC article.
Identification of a subset of breast carcinomas characterized by expression of cytokeratin 15: relationship between CK15+ progenitor/amplified cells and pre-malignant lesions and invasive disease.
Julio E Celis, Irina Gromova, +5 authors, José M A Moreira.
Mol Oncol, 2007 Dec 01; 1(3). PMID: 19383306    Free PMC article.
Targeted proteomic strategy for clinical biomarker discovery.
Ralph Schiess, Bernd Wollscheid, Ruedi Aebersold.
Mol Oncol, 2009 Apr 23; 3(1). PMID: 19383365    Free PMC article.
Highly Cited. Review.
Development of a multiplex quantitative PCR signature to predict progression in non-muscle-invasive bladder cancer.
Rou Wang, David S Morris, +8 authors, Arul M Chinnaiyan.
Cancer Res, 2009 Apr 23; 69(9). PMID: 19383904    Free PMC article.
Is bagging effective in the classification of small-sample genomic and proteomic data?
T T Vu, U M Braga-Neto.
EURASIP J Bioinform Syst Biol, 2009 Apr 25;. PMID: 19390645    Free PMC article.
PrognoScan: a new database for meta-analysis of the prognostic value of genes.
Hideaki Mizuno, Kunio Kitada, Kenta Nakai, Akinori Sarai.
BMC Med Genomics, 2009 Apr 28; 2. PMID: 19393097    Free PMC article.
Highly Cited.
Molecular characterization of apocrine carcinoma of the breast: validation of an apocrine protein signature in a well-defined cohort.
Julio E Celis, Teresa Cabezón, +7 authors, Fritz Rank.
Mol Oncol, 2009 Apr 28; 3(3). PMID: 19393583    Free PMC article.
Transforming growth factor-(beta)s and mammary gland involution; functional roles and implications for cancer progression.
Kathleen C Flanders, Lalage M Wakefield.
J Mammary Gland Biol Neoplasia, 2009 Apr 28; 14(2). PMID: 19396528    Free PMC article.
Four-gene expression ratio test for survival in patients undergoing surgery for mesothelioma.
Gavin J Gordon, Lingsheng Dong, +9 authors, Raphael Bueno.
J Natl Cancer Inst, 2009 Apr 30; 101(9). PMID: 19401544    Free PMC article.
Predicting and controlling the reactivity of immune cell populations against cancer.
Kfir Oved, Eran Eden, +11 authors, Yoram Reiter.
Mol Syst Biol, 2009 Apr 30; 5. PMID: 19401677    Free PMC article.
Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.
M J Smith, A C Culhane, +8 authors, H P Redmond.
Br J Cancer, 2009 Apr 30; 100(9). PMID: 19401702    Free PMC article.
Genomic and proteomic biomarkers for cancer: a multitude of opportunities.
Michael A Tainsky.
Biochim Biophys Acta, 2009 May 02; 1796(2). PMID: 19406210    Free PMC article.
Review.
A mouse mammary gland involution mRNA signature identifies biological pathways potentially associated with breast cancer metastasis.
Torsten Stein, Nathan Salomonis, +2 authors, Barry A Gusterson.
J Mammary Gland Biol Neoplasia, 2009 May 02; 14(2). PMID: 19408105
Review.
Univariate shrinkage in the cox model for high dimensional data.
Robert J Tibshirani.
Stat Appl Genet Mol Biol, 2009 May 05; 8. PMID: 19409065    Free PMC article.
Downregulation of JUNB mRNA expression in advanced phase chronic myelogenous leukemia.
Koyu Hoshino, Alfonso Quintás-Cardama, +3 authors, Guillermo Garcia-Manero.
Leuk Res, 2009 May 05; 33(10). PMID: 19409613    Free PMC article.
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction.
Chunrong Cheng, Kui Shen, +2 authors, George C Tseng.
Bioinformatics, 2009 May 06; 25(13). PMID: 19414534    Free PMC article.
Altered gene and protein expression by Nm23-H1 in metastasis suppression.
Jong Heun Lee, Jean-Claude Marshall, Patricia S Steeg, Christine E Horak.
Mol Cell Biochem, 2009 May 06; 329(1-2). PMID: 19415462    Free PMC article.
Review.
Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression.
Cecilia Williams, Luisa Helguero, +2 authors, Jan-Ake Gustafsson.
Breast Cancer Res, 2009 May 12; 11(3). PMID: 19426500    Free PMC article.
Multiplexed measurements of gene signatures in different analytes using the Nanostring nCounter Assay System.
Vladislav A Malkov, Kyle A Serikawa, +4 authors, Thomas Fare.
BMC Res Notes, 2009 May 12; 2. PMID: 19426535    Free PMC article.
Recent advances in systemic therapy: new diagnostics and biological predictors of outcome in early breast cancer.
Catherine Oakman, Silvia Bessi, +3 authors, Angelo Di Leo.
Breast Cancer Res, 2009 May 14; 11(2). PMID: 19435470    Free PMC article.
Review.
The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic silencing in breast cancer.
R Shah, P Smith, +5 authors, T Crook.
Br J Cancer, 2009 May 14; 100(10). PMID: 19436308    Free PMC article.
Analysis of gene expression profiles in HeLa cells in response to overexpression or siRNA-mediated depletion of NASP.
Oleg M Alekseev, Richard T Richardson, Oleg Alekseev, Michael G O'Rand.
Reprod Biol Endocrinol, 2009 May 15; 7. PMID: 19439102    Free PMC article.
Systematic identification of transcription factors associated with patient survival in cancers.
Chao Cheng, Lei M Li, Pedro Alves, Mark Gerstein.
BMC Genomics, 2009 May 16; 10. PMID: 19442316    Free PMC article.
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature.
Seon-Young Kim.
BMC Bioinformatics, 2009 May 19; 10. PMID: 19445687    Free PMC article.
Distinct gene-expression profiles characterize mammary tumors developed in transgenic mice expressing constitutively active and C-terminally truncated variants of STAT5.
Tali Eilon, Itamar Barash.
BMC Genomics, 2009 May 20; 10. PMID: 19450255    Free PMC article.
The role of HER2 in early breast cancer metastasis and the origins of resistance to HER2-targeted therapies.
Jaclyn A Freudenberg, Qiang Wang, +3 authors, Mark I Greene.
Exp Mol Pathol, 2009 May 20; 87(1). PMID: 19450579    Free PMC article.
Review.
Abrogation of TGF-beta signaling enhances chemokine production and correlates with prognosis in human breast cancer.
Brian Bierie, Christine H Chung, +6 authors, Harold L Moses.
J Clin Invest, 2009 May 20; 119(6). PMID: 19451693    Free PMC article.
Feature selection for predicting tumor metastases in microarray experiments using paired design.
Qihua Tan, Mads Thomassen, Torben A Kruse.
Cancer Inform, 2007 Jan 01; 3. PMID: 19455244    Free PMC article.
Combining clinical and genomic covariates via Cov-TGDR.
Shuangge Ma, Jian Huang.
Cancer Inform, 2007 Jan 01; 3. PMID: 19455255    Free PMC article.
A practical multifaceted approach to selecting differentially expressed genes.
Yingye Zheng, Margaret Pepe.
Cancer Inform, 2007 Jan 01; 3. PMID: 19455259    Free PMC article.
Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns.
G Alexe, G S Dalgin, +2 authors, G Bhanot.
Cancer Inform, 2007 Jan 01; 2. PMID: 19458770    Free PMC article.
A novel information retrieval model for high-throughput molecular medicine modalities.
Firas H Wehbe, Steven H Brown, +3 authors, Constantin F Aliferis.
Cancer Inform, 2009 May 22; 8. PMID: 19458790    Free PMC article.
Alpha6beta4 integrin crosslinking induces EGFR clustering and promotes EGF-mediated Rho activation in breast cancer.
Michael Z Gilcrease, Xiao Zhou, +3 authors, Phillip J Morrissey.
J Exp Clin Cancer Res, 2009 May 28; 28. PMID: 19470173    Free PMC article.
Cancer invasion and metastasis: interacting ecosystems.
Marc Mareel, Maria J Oliveira, Indira Madani.
Virchows Arch, 2009 May 28; 454(6). PMID: 19471961
Review.
Profile of estrogen-responsive genes in an estrogen-specific mammary gland outgrowth model.
Bonnie J Deroo, Sylvia C Hewitt, +3 authors, Kenneth S Korach.
Mol Reprod Dev, 2009 Jun 02; 76(8). PMID: 19484750    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.
Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering.
Dikla Dotan-Cohen, Simon Kasif, Avraham A Melkman.
Bioinformatics, 2009 Jun 06; 25(14). PMID: 19497934    Free PMC article.
A longitudinal study of gene expression in healthy individuals.
Chris Karlovich, Guillemette Duchateau-Nguyen, +8 authors, John P Caulfield.
BMC Med Genomics, 2009 Jun 09; 2. PMID: 19500411    Free PMC article.
A systems biology view of cancer.
Reinhard Laubenbacher, Valerie Hower, +5 authors, Steven Akman.
Biochim Biophys Acta, 2009 Jun 10; 1796(2). PMID: 19505535    Free PMC article.
Review.
Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study.
Joëlle Vermeulen, Katleen De Preter, +33 authors, Jo Vandesompele.
Lancet Oncol, 2009 Jun 12; 10(7). PMID: 19515614    Free PMC article.
Can systems biology understand pathway activation? Gene expression signatures as surrogate markers for understanding the complexity of pathway activation.
Hiraku Itadani, Shinji Mizuarai, Hidehito Kotani.
Curr Genomics, 2009 Jun 12; 9(5). PMID: 19517027    Free PMC article.
HtrA serine proteases as potential therapeutic targets in cancer.
Jeremy Chien, Mara Campioni, Viji Shridhar, Alfonso Baldi.
Curr Cancer Drug Targets, 2009 Jun 13; 9(4). PMID: 19519315    Free PMC article.
Review.
Genetic prognostic and predictive markers in colorectal cancer.
Axel Walther, Elaine Johnstone, +3 authors, David Kerr.
Nat Rev Cancer, 2009 Jun 19; 9(7). PMID: 19536109
Highly Cited. Review.
Genomic predictors of outcome and treatment response in breast cancer.
Lara Dunn, Angela Demichele.
Mol Diagn Ther, 2009 Jun 23; 13(2). PMID: 19537843
Review.
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.
Comparison of prognostic gene profiles using qRT-PCR in paraffin samples: a retrospective study in patients with early breast cancer.
Enrique Espinosa, Iker Sánchez-Navarro, +9 authors, Juan Angel Fresno Vara.
PLoS One, 2009 Jun 24; 4(6). PMID: 19547727    Free PMC article.
A novel lung metastasis signature links Wnt signaling with cancer cell self-renewal and epithelial-mesenchymal transition in basal-like breast cancer.
Theresa A DiMeo, Kristen Anderson, +5 authors, Charlotte Kuperwasser.
Cancer Res, 2009 Jun 25; 69(13). PMID: 19549913    Free PMC article.
Highly Cited.
Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer.
Sherene Loi, Christos Sotiriou, +5 authors, Grant A McArthur.
BMC Med Genomics, 2009 Jun 26; 2. PMID: 19552798    Free PMC article.
Integrated analysis of DNA copy number and gene expression microarray data using gene sets.
Renée X Menezes, Marten Boetzer, +2 authors, Judith M Boer.
BMC Bioinformatics, 2009 Jul 01; 10. PMID: 19563656    Free PMC article.
Intrinsic bias in breast cancer gene expression data sets.
Jonathan D Mosley, Ruth A Keri.
BMC Cancer, 2009 Jul 01; 9. PMID: 19563679    Free PMC article.
Estrogen regulation of cyclin E2 requires cyclin D1 but not c-Myc.
C Elizabeth Caldon, C Marcelo Sergio, +4 authors, Elizabeth A Musgrove.
Mol Cell Biol, 2009 Jul 01; 29(17). PMID: 19564413    Free PMC article.
Detection of Colorectal Cancer by Serum and Tissue Protein Profiling: A Prospective Study in a Population at Risk.
Judith Y M N Engwegen, Annekatrien C T M Depla, +8 authors, Jos H Beijnen.
Biomark Insights, 2008 Jan 01; 3. PMID: 19578519    Free PMC article.
Current molecular diagnostics of breast cancer and the potential incorporation of microRNA.
Christine K Zoon, Elizabeth Q Starker, +3 authors, Michael A Tangrea.
Expert Rev Mol Diagn, 2009 Jul 08; 9(5). PMID: 19580430    Free PMC article.
Review.
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery.
Jessica Kao, Keyan Salari, +9 authors, Jonathan R Pollack.
PLoS One, 2009 Jul 08; 4(7). PMID: 19582160    Free PMC article.
Highly Cited.
Computational identification of a p38SAPK-regulated transcription factor network required for tumor cell quiescence.
Alejandro P Adam, Ajish George, +6 authors, Julio A Aguirre-Ghiso.
Cancer Res, 2009 Jul 09; 69(14). PMID: 19584293    Free PMC article.
Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes.
Olafur Andri Stefansson, Jon Gunnlaugur Jonasson, +4 authors, Jorunn Erla Eyfjord.
Breast Cancer Res, 2009 Jul 11; 11(4). PMID: 19589159    Free PMC article.
DNA copy number aberrations in breast cancer by array comparative genomic hybridization.
Jian Li, Kai Wang, +6 authors, Lars Bolund.
Genomics Proteomics Bioinformatics, 2009 Jul 14; 7(1-2). PMID: 19591788    Free PMC article.
Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer.
Monika Pietrowska, Lukasz Marczak, +9 authors, Piotr Widlak.
J Transl Med, 2009 Jul 15; 7. PMID: 19594898    Free PMC article.
Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective.
Sui Huang, Ingemar Ernberg, Stuart Kauffman.
Semin Cell Dev Biol, 2009 Jul 15; 20(7). PMID: 19595782    Free PMC article.
Highly Cited. Review.
A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors.
Jing Zhang, Bing Liu, +7 authors, Sonya Wei Song.
PLoS One, 2009 Jul 18; 4(7). PMID: 19609451    Free PMC article.
The role of X-box binding protein-1 in tumorigenicity.
Ayesha N Shajahan, Rebecca B Riggins, Robert Clarke.
Drug News Perspect, 2009 Jul 18; 22(5). PMID: 19609461    Free PMC article.
Review.
A comparison of RNA amplification techniques at sub-nanogram input concentration.
Julie E Lang, Mark Jesus M Magbanua, +6 authors, Christopher M Haqq.
BMC Genomics, 2009 Jul 22; 10. PMID: 19619282    Free PMC article.
RCP is a human breast cancer-promoting gene with Ras-activating function.
Jinqiu Zhang, Xuejing Liu, +14 authors, Lance David Miller.
J Clin Invest, 2009 Jul 22; 119(8). PMID: 19620787    Free PMC article.
SIK1 couples LKB1 to p53-dependent anoikis and suppresses metastasis.
Hailing Cheng, Pixu Liu, +9 authors, Jean J Zhao.
Sci Signal, 2009 Jul 23; 2(80). PMID: 19622832    Free PMC article.
Development of a microarray platform for FFPET profiling: application to the classification of human tumors.
Sven Duenwald, Mingjie Zhou, +10 authors, Matthew Marton.
J Transl Med, 2009 Jul 30; 7. PMID: 19638234    Free PMC article.
MicroRNAs as Novel Biomarkers for Breast Cancer.
H M Heneghan, N Miller, +2 authors, M J Kerin.
J Oncol, 2009 Jul 30; 2009. PMID: 19639033    Free PMC article.
The mRNA expression of SATB1 and SATB2 in human breast cancer.
Neill Patani, Wen Jiang, +2 authors, Kefah Mokbel.
Cancer Cell Int, 2009 Aug 01; 9. PMID: 19642980    Free PMC article.
Pharmacogenetics of solid tumors: directed therapy in breast, lung, and colorectal cancer: a paper from the 2008 william beaumont hospital symposium on molecular pathology.
Christine L H Snozek, Dennis J O'Kane, Alicia Algeciras-Schimnich.
J Mol Diagn, 2009 Aug 01; 11(5). PMID: 19644023    Free PMC article.
Review.
SlimPLS: a method for feature selection in gene expression-based disease classification.
Michael Gutkin, Ron Shamir, Gideon Dror.
PLoS One, 2009 Aug 04; 4(7). PMID: 19649265    Free PMC article.
X chromosome inactivation and autoimmunity.
Wesley H Brooks.
Clin Rev Allergy Immunol, 2009 Aug 05; 39(1). PMID: 19653135
Review.
Survival analysis with high-dimensional covariates.
Daniela M Witten, Robert Tibshirani.
Stat Methods Med Res, 2009 Aug 06; 19(1). PMID: 19654171    Free PMC article.
Review.
Multianalyte tests for the early detection of cancer: speedbumps and barriers.
Michael A Tainsky, Madhumita Chatterjee, +2 authors, Judith Abrams.
Biomark Insights, 2007 Jan 01; 2. PMID: 19662209    Free PMC article.
A gene expression profile for detection of sufficient tumour cells in breast tumour tissue: microarray diagnosis eligibility.
Paul Roepman, Arenda Schuurman, +3 authors, Annuska M Glas.
BMC Med Genomics, 2009 Aug 14; 2. PMID: 19674463    Free PMC article.
State of the art of neoadjuvant chemotherapy in breast cancer: rationale, results and recent developments.
Arnd Honig, Lorenz Rieger, +3 authors, Erich-Franz Solomayer.
Ger Med Sci, 2005 Jan 01; 3. PMID: 19675725    Free PMC article.
Hyperactivated NF-{kappa}B and AP-1 transcription factors promote highly accessible chromatin and constitutive transcription across the interleukin-6 gene promoter in metastatic breast cancer cells.
'Matladi N Ndlovu, Carine Van Lint, +4 authors, Wim Vanden Berghe.
Mol Cell Biol, 2009 Aug 19; 29(20). PMID: 19687301    Free PMC article.
A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response.
Sanjay Chandriani, Eirik Frengen, +4 authors, Michael D Cole.
PLoS One, 2009 Aug 20; 4(8). PMID: 19690609    Free PMC article.
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.
Xue Lin, Bahman Afsari, +4 authors, Donald Geman.
BMC Bioinformatics, 2009 Aug 22; 10. PMID: 19695104    Free PMC article.
Mechanisms and pathways of bone metastasis: challenges and pitfalls of performing molecular research on patient samples.
T R Cawthorn, E Amir, +7 authors, M Clemons.
Clin Exp Metastasis, 2009 Aug 22; 26(8). PMID: 19697143
Analysis of DNA microarray expression data.
Richard Simon.
Best Pract Res Clin Haematol, 2009 Aug 25; 22(2). PMID: 19698933    Free PMC article.
Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response.
Jadwiga R Bienkowska, Gul S Dalgin, +4 authors, John P Carulli.
Genomics, 2009 Aug 25; 94(6). PMID: 19699293    Free PMC article.
Trastuzumab in the management of early and advanced stage breast cancer.
Rupert Bartsch, Catharina Wenzel, Guenther G Steger.
Biologics, 2007 Mar 01; 1(1). PMID: 19707345    Free PMC article.
BRCA1-deficient mammary tumor cells are dependent on EZH2 expression and sensitive to Polycomb Repressive Complex 2-inhibitor 3-deazaneplanocin A.
Julian Puppe, Rinske Drost, +8 authors, Alexandra M Pietersen.
Breast Cancer Res, 2009 Aug 28; 11(4). PMID: 19709408    Free PMC article.
The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor.
Nigel P S Crawford, Hailiu Yang, Katherine R Mattaini, Kent W Hunter.
J Biol Chem, 2009 Aug 28; 284(42). PMID: 19710015    Free PMC article.
Utilization of genomic signatures to identify phenotype-specific drugs.
Seiichi Mori, Jeffrey T Chang, +2 authors, Joseph R Nevins.
PLoS One, 2009 Aug 29; 4(8). PMID: 19714244    Free PMC article.
The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis.
Gerald B W Wertheim, Thomas W Yang, +10 authors, Lewis A Chodosh.
Proc Natl Acad Sci U S A, 2009 Sep 01; 106(37). PMID: 19717424    Free PMC article.
Divide and conquer: progress in the molecular stratification of cancer.
Patrick Tan.
Yonsei Med J, 2009 Sep 01; 50(4). PMID: 19718393    Free PMC article.
Review.
Robust model selection for classification of microarrays.
Ikumi Suzuki, Takashi Takenouchi, +2 authors, Shin Ishii.
Cancer Inform, 2009 Sep 01; 7. PMID: 19718450    Free PMC article.
mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein.
Genome Biol, 2009 Sep 03; 10(9). PMID: 19723326    Free PMC article.
Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".
Aedín C Culhane, John Quackenbush.
Cancer Res, 2009 Sep 03; 69(18). PMID: 19723662    Free PMC article.
Gene expression profiling of canine osteosarcoma reveals genes associated with short and long survival times.
Gayathri T Selvarajah, Jolle Kirpensteijn, +3 authors, Jan A Mol.
Mol Cancer, 2009 Sep 09; 8. PMID: 19735553    Free PMC article.
A gene expression model of intrinsic tumor radiosensitivity: prediction of response and prognosis after chemoradiation.
Steven A Eschrich, Jimmy Pramana, +10 authors, Javier F Torres-Roca.
Int J Radiat Oncol Biol Phys, 2009 Sep 09; 75(2). PMID: 19735873    Free PMC article.
Systems biology modeling of the radiation sensitivity network: a biomarker discovery platform.
Steven Eschrich, Hongling Zhang, +4 authors, Javier F Torres-Roca.
Int J Radiat Oncol Biol Phys, 2009 Sep 09; 75(2). PMID: 19735874    Free PMC article.
Genetic characterization of breast cancer and implications for clinical management.
Felipe C Geyer, Maria A Lopez-Garcia, Maryou B Lambros, Jorge S Reis-Filho.
J Cell Mol Med, 2009 Sep 17; 13(10). PMID: 19754664    Free PMC article.
Review.
Network analysis of genes regulated in renal diseases: implications for a molecular-based classification.
Suresh K Bhavnani, Felix Eichinger, +3 authors, Matthias Kretzler.
BMC Bioinformatics, 2009 Sep 26; 10 Suppl 9. PMID: 19761573    Free PMC article.
PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment.
Angel Janevski, Sitharthan Kamalakaran, +2 authors, Nevenka Dimitrova.
BMC Bioinformatics, 2009 Sep 26; 10 Suppl 9. PMID: 19761577    Free PMC article.
Hec1 contributes to mitotic centrosomal microtubule growth for proper spindle assembly through interaction with Hice1.
Guikai Wu, Randy Wei, +2 authors, Wen-Hwa Lee.
Mol Biol Cell, 2009 Sep 25; 20(22). PMID: 19776357    Free PMC article.
The rapamycin-regulated gene expression signature determines prognosis for breast cancer.
Argun Akcakanat, Li Zhang, Spiridon Tsavachidis, Funda Meric-Bernstam.
Mol Cancer, 2009 Sep 26; 8. PMID: 19778445    Free PMC article.
A microarray analysis of temporal gene expression profiles in thermally injured human skin.
J A Greco, A C Pollins, +2 authors, L B Nanney.
Burns, 2009 Sep 29; 36(2). PMID: 19781859    Free PMC article.
Immutable functional attributes of histologic grade revealed by context-independent gene expression in primary breast cancer cells.
Shanaz H Dairkee, Aejaz Sayeed, +6 authors, Dan H Moore.
Cancer Res, 2009 Oct 01; 69(19). PMID: 19789341    Free PMC article.
Tumor-endothelial interaction links the CD44(+)/CD24(-) phenotype with poor prognosis in early-stage breast cancer.
Martin Buess, Michal Rajski, +2 authors, Christoph Rochlitz.
Neoplasia, 2009 Oct 02; 11(10). PMID: 19794958    Free PMC article.
Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer.
Corey Speers, Anna Tsimelzon, +7 authors, Powel Brown.
Clin Cancer Res, 2009 Oct 08; 15(20). PMID: 19808870    Free PMC article.
A comprehensive analysis of gene expression evolution between humans and mice.
Yupeng Wang, Romdhane Rekaya.
Evol Bioinform Online, 2009 Oct 09; 5. PMID: 19812728    Free PMC article.
Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis.
Paul A Lyons, Eoin F McKinney, +7 authors, Kenneth G C Smith.
Ann Rheum Dis, 2009 Oct 10; 69(6). PMID: 19815495    Free PMC article.
Shining new light on 3D cell motility and the metastatic process.
Paolo P Provenzano, Kevin W Eliceiri, Patricia J Keely.
Trends Cell Biol, 2009 Oct 13; 19(11). PMID: 19819146    Free PMC article.
Review.
Making the case for molecular staging of malignant pleural mesothelioma.
Raphael Bueno.
Semin Thorac Cardiovasc Surg, 2009 Oct 14; 21(2). PMID: 19822292    Free PMC article.
Review.
Preinvasive breast cancer.
Dennis C Sgroi.
Annu Rev Pathol, 2009 Oct 15; 5. PMID: 19824828    Free PMC article.
Review.
Gene expression profiling integrated into network modelling reveals heterogeneity in the mechanisms of BRCA1 tumorigenesis.
R Fernández-Ramires, X Solé, +11 authors, A Osorio.
Br J Cancer, 2009 Oct 15; 101(8). PMID: 19826428    Free PMC article.
Prognostic and predictive factors and genetic analysis of early breast cancer.
Miguel Martín, Fernando González Palacios, +2 authors, José Schneider.
Clin Transl Oncol, 2009 Oct 16; 11(10). PMID: 19828405
Review.
Gene expression profile assays as predictors of distant recurrence-free survival in early-stage breast cancer.
Nicole M Kuderer, Gary H Lyman.
Cancer Invest, 2009 Oct 17; 27(9). PMID: 19832034    Free PMC article.
Review.
Molecular biology of cancer-associated fibroblasts: can these cells be targeted in anti-cancer therapy?
Tamas A Gonda, Andrea Varro, Timothy C Wang, Benjamin Tycko.
Semin Cell Dev Biol, 2009 Oct 21; 21(1). PMID: 19840860    Free PMC article.
Review.
An eight-gene blood expression profile predicts the response to infliximab in rheumatoid arthritis.
Antonio Julià, Alba Erra, +4 authors, Sara Marsal.
PLoS One, 2009 Oct 23; 4(10). PMID: 19847310    Free PMC article.
IRF-1 transcriptionally upregulates PUMA, which mediates the mitochondrial apoptotic pathway in IRF-1-induced apoptosis in cancer cells.
J Gao, M Senthil, +5 authors, J H Yim.
Cell Death Differ, 2009 Oct 24; 17(4). PMID: 19851330    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.
Activation of host wound responses in breast cancer microenvironment.
Melissa A Troester, Myung Hee Lee, +7 authors, Sallie Smith Schneider.
Clin Cancer Res, 2009 Nov 06; 15(22). PMID: 19887484    Free PMC article.
Harnessing gene expression to identify the genetic basis of drug resistance.
Bo-Juen Chen, Helen C Causton, +3 authors, Dana Pe'er.
Mol Syst Biol, 2009 Nov 06; 5. PMID: 19888205    Free PMC article.
Circulating levels of matrix metalloproteinase-9 (MMP-9), neutrophil gelatinase-associated lipocalin (NGAL) and their complex MMP-9/NGAL in breast cancer disease.
Xeni Provatopoulou, Antonia Gounaris, +6 authors, George Zografos.
BMC Cancer, 2009 Nov 06; 9. PMID: 19889214    Free PMC article.
Using the ratio of means as the effect size measure in combining results of microarray experiments.
Pingzhao Hu, Celia M T Greenwood, Joseph Beyene.
BMC Syst Biol, 2009 Nov 07; 3. PMID: 19891778    Free PMC article.
MMP13 as a stromal mediator in controlling persistent angiogenesis in skin carcinoma.
Wiltrud Lederle, Bettina Hartenstein, +4 authors, Margareta M Mueller.
Carcinogenesis, 2009 Nov 07; 31(7). PMID: 19892798    Free PMC article.
Altered serotonin physiology in human breast cancers favors paradoxical growth and cell survival.
Vaibhav P Pai, Aaron M Marshall, +2 authors, Nelson D Horseman.
Breast Cancer Res, 2009 Nov 12; 11(6). PMID: 19903352    Free PMC article.
Epithelial to mesenchymal transition and breast cancer.
Eva Tomaskovic-Crook, Erik W Thompson, Jean Paul Thiery.
Breast Cancer Res, 2009 Nov 17; 11(6). PMID: 19909494    Free PMC article.
Highly Cited. Review.
Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes.
Amal T Qattan, Claire Mulvey, +2 authors, Jasminka Godovac-Zimmermann.
J Proteome Res, 2009 Nov 17; 9(1). PMID: 19911851    Free PMC article.
Tight junctions: a barrier to the initiation and progression of breast cancer?
Kieran Brennan, Gozie Offiah, Elaine A McSherry, Ann M Hopkins.
J Biomed Biotechnol, 2009 Nov 19; 2010. PMID: 19920867    Free PMC article.
Review.
Impact of biospecimens handling on biomarker research in breast cancer.
Loris De Cecco, Valeria Musella, +6 authors, Maria Grazia Daidone.
BMC Cancer, 2009 Nov 26; 9. PMID: 19930681    Free PMC article.
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.
Herman M J Sontrop, Perry D Moerland, +2 authors, Wim F J Verhaegh.
BMC Bioinformatics, 2009 Nov 28; 10. PMID: 19941644    Free PMC article.
Histological and molecular types of breast cancer: is there a unifying taxonomy?
Britta Weigelt, Jorge S Reis-Filho.
Nat Rev Clin Oncol, 2009 Nov 28; 6(12). PMID: 19942925
Highly Cited. Review.
Crosstalk between the DNA damage response, histone modifications and neovascularisation.
Athanassios Vassilopoulos, Chu-Xia Deng, Triantafyllos Chavakis.
Int J Biochem Cell Biol, 2009 Dec 01; 42(2). PMID: 19945543    Free PMC article.
Review.
ZBRK1 acts as a metastatic suppressor by directly regulating MMP9 in cervical cancer.
Li-Fang Lin, Chih-Hung Chuang, +8 authors, Ju-Ming Wang.
Cancer Res, 2009 Dec 10; 70(1). PMID: 19996286    Free PMC article.
Accurate and reliable cancer classification based on probabilistic inference of pathway activity.
Junjie Su, Byung-Jun Yoon, Edward R Dougherty.
PLoS One, 2009 Dec 10; 4(12). PMID: 19997592    Free PMC article.
Refining gene signatures: a Bayesian approach.
Amira Djebbari, Aurélie Labbe.
BMC Bioinformatics, 2009 Dec 17; 10. PMID: 20003289    Free PMC article.
Survival prediction from clinico-genomic models--a comparative study.
Hege M Bøvelstad, Ståle Nygård, Ornulf Borgan.
BMC Bioinformatics, 2009 Dec 17; 10. PMID: 20003386    Free PMC article.
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?
Cyril Benes, Jeff Settleman.
BMC Med, 2009 Dec 17; 7. PMID: 20003409    Free PMC article.
Web-based interrogation of gene expression signatures using EXALT.
Jun Wu, Qingchao Qiu, +5 authors, Yajun Yi.
BMC Bioinformatics, 2009 Dec 17; 10. PMID: 20003458    Free PMC article.
Advances in translational bioinformatics: computational approaches for the hunting of disease genes.
Maricel G Kann.
Brief Bioinform, 2009 Dec 17; 11(1). PMID: 20007728    Free PMC article.
Int6 and Moe1 interact with Cdc48 to regulate ERAD and proper chromosome segregation.
Joel H Otero, Jinfeng Suo, Colin Gordon, Eric C Chang.
Cell Cycle, 2009 Dec 18; 9(1). PMID: 20016281    Free PMC article.
Interaction of the regulatory subunit of the cAMP-dependent protein kinase with PATZ1 (ZNF278).
Weng-Lang Yang, Roald Ravatn, +2 authors, Khew-Voon Chin.
Biochem Biophys Res Commun, 2009 Dec 23; 391(3). PMID: 20026299    Free PMC article.
Expression signature developed from a complex series of mouse models accurately predicts human breast cancer survival.
Mei He, David P Mangiameli, +5 authors, Steven K Libutti.
Clin Cancer Res, 2009 Dec 24; 16(1). PMID: 20028755    Free PMC article.
Current potential and limitations of molecular diagnostic methods in head and neck cancer.
Magdy E Mahfouz, Juan P Rodrigo, +4 authors, Alfio Ferlito.
Eur Arch Otorhinolaryngol, 2009 Dec 29; 267(6). PMID: 20037788
Review.
Role of axillary clearance after a tumor-positive sentinel node in the administration of adjuvant therapy in early breast cancer.
Marieke E Straver, Philip Meijnen, +11 authors, Emiel J T Rutgers.
J Clin Oncol, 2009 Dec 30; 28(5). PMID: 20038733    Free PMC article.
Classification across gene expression microarray studies.
Andreas Buness, Markus Ruschhaupt, Ruprecht Kuner, Achim Tresch.
BMC Bioinformatics, 2010 Jan 01; 10. PMID: 20042109    Free PMC article.
Detection of gene pathways with predictive power for breast cancer prognosis.
Shuangge Ma, Michael R Kosorok.
BMC Bioinformatics, 2010 Jan 02; 11. PMID: 20043860    Free PMC article.
Validation of a web-based predictive nomogram for ipsilateral breast tumor recurrence after breast conserving therapy.
Mona Sanghani, Pauline T Truong, +5 authors, Alphonse G Taghian.
J Clin Oncol, 2010 Jan 06; 28(5). PMID: 20048188    Free PMC article.
IGF-I induced genes in stromal fibroblasts predict the clinical outcome of breast and lung cancer patients.
Michal Rajski, Rosanna Zanetti-Dällenbach, +3 authors, Martin Buess.
BMC Med, 2010 Jan 07; 8. PMID: 20051100    Free PMC article.
Basic and clinical significance of IGF-I-induced signatures in cancer.
Haim Werner, Ilan Bruchim.
BMC Med, 2010 Jan 07; 8. PMID: 20051101    Free PMC article.
Decoding pooled RNAi screens by means of barcode tiling arrays.
Michael Boettcher, Johannes Fredebohm, +4 authors, Jörg D Hoheisel.
BMC Genomics, 2010 Jan 07; 11. PMID: 20051122    Free PMC article.
Identification of cancer-associated gene clusters and genes via clustering penalization.
Shuangge Ma, Jian Huang, Shihao Shen.
Stat Interface, 2010 Jan 09; 2(1). PMID: 20057914    Free PMC article.
Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer.
Wun-Jae Kim, Eun-Jung Kim, +10 authors, Suk-Chul Bae.
Mol Cancer, 2010 Jan 12; 9. PMID: 20059769    Free PMC article.
Highly Cited.
Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast.
M Bauer, G Su, +3 authors, A Friedl.
Oncogene, 2010 Jan 12; 29(12). PMID: 20062080    Free PMC article.
Association between the 21-gene recurrence score assay and risk of locoregional recurrence in node-negative, estrogen receptor-positive breast cancer: results from NSABP B-14 and NSABP B-20.
Eleftherios P Mamounas, Gong Tang, +7 authors, Norman Wolmark.
J Clin Oncol, 2010 Jan 13; 28(10). PMID: 20065188    Free PMC article.
Highly Cited.
Multidisciplinary approach of early breast cancer: the biology applied to radiation oncology.
Céline Bourgier, Mahmut Ozsahin, David Azria.
Radiat Oncol, 2010 Jan 16; 5. PMID: 20074364    Free PMC article.
Review.
Bayesian rule learning for biomedical data mining.
Vanathi Gopalakrishnan, Jonathan L Lustgarten, Shyam Visweswaran, Gregory F Cooper.
Bioinformatics, 2010 Jan 19; 26(5). PMID: 20080512    Free PMC article.
Genomic analyses as a guide to target identification and preclinical testing of mouse models of breast cancer.
Christina N Bennett, Jeffrey E Green.
Toxicol Pathol, 2010 Jan 19; 38(1). PMID: 20080934    Free PMC article.
Review.
Epidermal growth factor receptor expression in breast cancer association with biologic phenotype and clinical outcomes.
Mothaffar F Rimawi, Priya B Shetty, +4 authors, Richard M Elledge.
Cancer, 2010 Jan 19; 116(5). PMID: 20082448    Free PMC article.
Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.
Joseph Andrews, Wendy Kennette, +4 authors, David I Rodenhiser.
PLoS One, 2010 Jan 20; 5(1). PMID: 20084286    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.
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.
Andrew H Beck, Ziming Weng, +8 authors, Robert B West.
PLoS One, 2010 Jan 26; 5(1). PMID: 20098735    Free PMC article.
FiGS: a filter-based gene selection workbench for microarray data.
Taeho Hwang, Choong-Hyun Sun, Taegyun Yun, Gwan-Su Yi.
BMC Bioinformatics, 2010 Jan 27; 11. PMID: 20100357    Free PMC article.
Semiparametric prognosis models in genomic studies.
Shuangge Ma, Jian Huang, +2 authors, Ben-Chang Shia.
Brief Bioinform, 2010 Feb 04; 11(4). PMID: 20123942    Free PMC article.
A population-based gene signature is predictive of breast cancer survival and chemoresponse.
Shruti Rathnagiriswaran, Ying-Wooi Wan, +3 authors, Nancy L Guo.
Int J Oncol, 2010 Feb 04; 36(3). PMID: 20126981    Free PMC article.
MYC regulation of a "poor-prognosis" metastatic cancer cell state.
Anita Wolfer, Ben S Wittner, +14 authors, Sridhar Ramaswamy.
Proc Natl Acad Sci U S A, 2010 Feb 06; 107(8). PMID: 20133671    Free PMC article.
Cancer-specific methylation in the BRCA1 promoter in sporadic breast tumours.
Azhar B Ali, Philip T C Iau, Jen-Hwei Sng.
Med Oncol, 2010 Feb 06; 28(1). PMID: 20135363
Genetic variants on chromosome 5p12 are associated with risk of breast cancer in African American women: the Black Women's Health Study.
Edward A Ruiz-Narvaez, Lynn Rosenberg, +6 authors, Julie R Palmer.
Breast Cancer Res Treat, 2010 Feb 09; 123(2). PMID: 20140701    Free PMC article.
A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics.
Yi Hong, Thomas Downey, +2 authors, Peh Yean Cheah.
Clin Exp Metastasis, 2010 Feb 10; 27(2). PMID: 20143136
Highly Cited.
Testing the additional predictive value of high-dimensional molecular data.
Anne-Laure Boulesteix, Torsten Hothorn.
BMC Bioinformatics, 2010 Feb 11; 11. PMID: 20144191    Free PMC article.
Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue.
Janine Antonov, Vlad Popovici, +9 authors, Rolf Jaggi.
BMC Cancer, 2010 Feb 11; 10. PMID: 20144231    Free PMC article.
An ets2-driven transcriptional program in tumor-associated macrophages promotes tumor metastasis.
Tahera Zabuawala, David A Taffany, +8 authors, Michael C Ostrowski.
Cancer Res, 2010 Feb 11; 70(4). PMID: 20145133    Free PMC article.
Dual KS: Defining Gene Sets with Tissue Set Enrichment Analysis.
Yarong Yang, Eric J Kort, +2 authors, Bin T Teh.
Cancer Inform, 2010 Feb 12; 9. PMID: 20148167    Free PMC article.
Cellular processes of v-Src transformation revealed by gene profiling of primary cells--implications for human cancer.
Bart M Maślikowski, Benjamin D Néel, +4 authors, Pierre-André Bédard.
BMC Cancer, 2010 Feb 16; 10. PMID: 20152043    Free PMC article.
A fuzzy gene expression-based computational approach improves breast cancer prognostication.
Benjamin Haibe-Kains, Christine Desmedt, +3 authors, Gianluca Bontempi.
Genome Biol, 2010 Feb 17; 11(2). PMID: 20156340    Free PMC article.
Bimodal gene expression patterns in breast cancer.
Marina Bessarabova, Eugene Kirillov, +3 authors, Tatiana Nikolskaya.
BMC Genomics, 2010 Mar 03; 11 Suppl 1. PMID: 20158879    Free PMC article.
The COXEN principle: translating signatures of in vitro chemosensitivity into tools for clinical outcome prediction and drug discovery in cancer.
Steven C Smith, Alexander S Baras, Jae K Lee, Dan Theodorescu.
Cancer Res, 2010 Feb 18; 70(5). PMID: 20160033    Free PMC article.
Review.
Approaches to biomarkers in human colorectal cancer: looking back, to go forward.
Rod K Nibbe, Mark R Chance.
Biomark Med, 2010 Feb 18; 3(4). PMID: 20161020    Free PMC article.
Comparison of breast cancer to healthy control tissue discovers novel markers with potential for prognosis and early detection.
Michèl Schummer, Ann Green, +6 authors, Nicole Urban.
PLoS One, 2010 Feb 18; 5(2). PMID: 20161755    Free PMC article.
Search for the smallest random forest.
Heping Zhang, Minghui Wang.
Stat Interface, 2010 Feb 19; 2(3). PMID: 20165560    Free PMC article.
Identification of genes associated with local aggressiveness and metastatic behavior in soft tissue tumors.
Isabela Werneck Cunha, Katia Candido Carvalho, +10 authors, Luiz Fernando Lima Reis.
Transl Oncol, 2010 Feb 19; 3(1). PMID: 20165692    Free PMC article.
High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma.
Kellie J Archer, Valeria R Mas, Daniel G Maluf, Robert A Fisher.
Mol Genet Genomics, 2010 Feb 19; 283(4). PMID: 20165882    Free PMC article.
Distinct and redundant functions of cyclin E1 and cyclin E2 in development and cancer.
C Elizabeth Caldon, Elizabeth A Musgrove.
Cell Div, 2010 Feb 26; 5. PMID: 20180967    Free PMC article.
Performance of feature selection methods.
Edward R Dougherty, Jianping Hua, Chao Sima.
Curr Genomics, 2010 Mar 02; 10(6). PMID: 20190952    Free PMC article.
Gene expression profiles identify inflammatory signatures in dendritic cells.
Anna Torri, Ottavio Beretta, +3 authors, Maria Foti.
PLoS One, 2010 Mar 03; 5(2). PMID: 20195376    Free PMC article.
Gene expression in histologically normal epithelium from breast cancer patients and from cancer-free prophylactic mastectomy patients shares a similar profile.
K Graham, A de las Morenas, +10 authors, C L Rosenberg.
Br J Cancer, 2010 Mar 04; 102(8). PMID: 20197764    Free PMC article.
Statistical expression deconvolution from mixed tissue samples.
Jennifer Clarke, Pearl Seo, Bertrand Clarke.
Bioinformatics, 2010 Mar 06; 26(8). PMID: 20202973    Free PMC article.
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.
LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer.
Yoon-La Choi, Melanie Bocanegra, +6 authors, Jonathan R Pollack.
Cancer Res, 2010 Mar 11; 70(6). PMID: 20215510    Free PMC article.
Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244).
Jonathan R Dry, Sandra Pavey, +26 authors, Paul D Smith.
Cancer Res, 2010 Mar 11; 70(6). PMID: 20215513    Free PMC article.
Highly Cited.
Gene Expression Profiling in Hereditary, BRCA1-linked Breast Cancer: Preliminary Report.
Volha Dudaladava, Michał Jarzab, +8 authors, Katarzyna Lisowska.
Hered Cancer Clin Pract, 2006 Jan 01; 4(1). PMID: 20223001    Free PMC article.
Integrative mixture of experts to combine clinical factors and gene markers.
Kim-Anh Lê Cao, Emmanuelle Meugnier, Geoffrey J McLachlan.
Bioinformatics, 2010 Mar 13; 26(9). PMID: 20223834    Free PMC article.
Impact of missing value imputation on classification for DNA microarray gene expression data--a model-based study.
Youting Sun, Ulisses Braga-Neto, Edward R Dougherty.
EURASIP J Bioinform Syst Biol, 2009 Jan 01; 2009. PMID: 20224634    Free PMC article.
Lung cancer progression and metastasis from the prognostic point of view.
Kentaro Inamura, Yuichi Ishikawa.
Clin Exp Metastasis, 2010 Mar 13; 27(6). PMID: 20225084
Review.
Selection of extreme phenotypes: the role of clinical observation in translational research.
José Luis Pérez-Gracia, Alfonso Gúrpide, +4 authors, Ignacio Melero Bermejo.
Clin Transl Oncol, 2010 Mar 17; 12(3). PMID: 20231122    Free PMC article.
Review.
The pathology of hereditary breast cancer.
Emiliano Honrado, Javier Benítez, José Palacios.
Hered Cancer Clin Pract, 2004 Jan 01; 2(3). PMID: 20233467    Free PMC article.
A robust gene selection method for microarray-based cancer classification.
Xiaosheng Wang, Osamu Gotoh.
Cancer Inform, 2010 Mar 18; 9. PMID: 20234770    Free PMC article.
Indirect two-sided relative ranking: a robust similarity measure for gene expression data.
Louis Licamele, Lise Getoor.
BMC Bioinformatics, 2010 Mar 20; 11. PMID: 20236517    Free PMC article.
18F-FDG PET of locally invasive breast cancer and association of estrogen receptor status with standardized uptake value: microarray and immunohistochemical analysis.
Joseph R Osborne, Elisa Port, +5 authors, Steven Larson.
J Nucl Med, 2010 Mar 20; 51(4). PMID: 20237034    Free PMC article.
Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets.
Kosuke Yoshihara, Atsushi Tajima, +14 authors, Kenichi Tanaka.
PLoS One, 2010 Mar 20; 5(3). PMID: 20300634    Free PMC article.
The Nm23-H1 metastasis suppressor as a translational target.
Jean-Claude Marshall, Joshua Collins, Natascia Marino, Patricia Steeg.
Eur J Cancer, 2010 Mar 23; 46(7). PMID: 20304626    Free PMC article.
Review.
Tumor size and survival in breast cancer--a reappraisal.
William D Foulkes, Jorge S Reis-Filho, Steven A Narod.
Nat Rev Clin Oncol, 2010 Mar 24; 7(6). PMID: 20309006
Review.
Optimized ranking and selection methods for feature selection with application in microarray experiments.
Xinping Cui, Haibing Zhao, Jason Wilson.
J Biopharm Stat, 2010 Mar 24; 20(2). PMID: 20309756    Free PMC article.
A genome-wide association study of prognosis in breast cancer.
Elizabeth M Azzato, Paul D P Pharoah, +8 authors, Peter Kraft.
Cancer Epidemiol Biomarkers Prev, 2010 Mar 25; 19(4). PMID: 20332263    Free PMC article.
Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures.
James Chen, Lee Sam, +5 authors, Yves A Lussier.
J Biomed Inform, 2010 Mar 31; 43(3). PMID: 20350617    Free PMC article.
Biomarkers and surrogate end points--the challenge of statistical validation.
Marc Buyse, Daniel J Sargent, +2 authors, Aimery de Gramont.
Nat Rev Clin Oncol, 2010 Apr 07; 7(6). PMID: 20368727
Review.
Lack of evidence for KRAS oncogenic mutations in triple-negative breast cancer.
Alfonso Sánchez-Muñoz, Elena Gallego, +5 authors, Emilio Alba.
BMC Cancer, 2010 Apr 14; 10. PMID: 20385028    Free PMC article.
HOXA9 regulates BRCA1 expression to modulate human breast tumor phenotype.
Penney M Gilbert, Janna K Mouw, +11 authors, Valerie M Weaver.
J Clin Invest, 2010 Apr 15; 120(5). PMID: 20389018    Free PMC article.
Clinical outcome of breast cancer patients with N3a (≥10 positive lymph nodes) disease: has it changed over years?
Gul Basaran, Cabuk Devrim, +9 authors, Serdar N Turhal.
Med Oncol, 2010 Apr 15; 28(3). PMID: 20390469
Gene expression analysis with an integrated CMOS microarray by time-resolved fluorescence detection.
Ta-chien D Huang, Sunirmal Paul, +4 authors, Kenneth L Shepard.
Biosens Bioelectron, 2010 Apr 16; 26(5). PMID: 20392628    Free PMC article.
Migrastatin analogues target fascin to block tumour metastasis.
Lin Chen, Shengyu Yang, +2 authors, Xin-Yun Huang.
Nature, 2010 Apr 16; 464(7291). PMID: 20393565    Free PMC article.
Highly Cited.
Genetically engineered mouse models in cancer research.
Jessica C Walrath, Jessica J Hawes, Terry Van Dyke, Karlyne M Reilly.
Adv Cancer Res, 2010 Apr 20; 106. PMID: 20399958    Free PMC article.
Review.
A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.
Eoin F McKinney, Paul A Lyons, +11 authors, Kenneth G C Smith.
Nat Med, 2010 Apr 20; 16(5). PMID: 20400961    Free PMC article.
Highly Cited.
Genomic alterations of primary tumor and blood in invasive ductal carcinoma of breast.
Ja Seong Bae, Jin Soo Choi, +5 authors, Sang Seol Jung.
World J Surg Oncol, 2010 Apr 23; 8. PMID: 20409316    Free PMC article.
Phosphoinositide signalling in cancer: beyond PI3K and PTEN.
Tom D Bunney, Matilda Katan.
Nat Rev Cancer, 2010 Apr 24; 10(5). PMID: 20414202
Highly Cited. Review.
FABIA: factor analysis for bicluster acquisition.
Sepp Hochreiter, Ulrich Bodenhofer, +11 authors, Djork-Arné Clevert.
Bioinformatics, 2010 Apr 27; 26(12). PMID: 20418340    Free PMC article.
Power of deep sequencing and agilent microarray for gene expression profiling study.
Lin Feng, Hang Liu, +9 authors, Yong Zhang.
Mol Biotechnol, 2010 May 01; 45(2). PMID: 20432071
Gene-expression-based prognostic assays for breast cancer.
Chungyeul Kim, Soonmyung Paik.
Nat Rev Clin Oncol, 2010 May 05; 7(6). PMID: 20440284
Review.
Transcriptional evidence for the "Reverse Warburg Effect" in human breast cancer tumor stroma and metastasis: similarities with oxidative stress, inflammation, Alzheimer's disease, and "Neuron-Glia Metabolic Coupling".
Stephanos Pavlides, Aristotelis Tsirigos, +9 authors, Michael P Lisanti.
Aging (Albany NY), 2010 May 06; 2(4). PMID: 20442453    Free PMC article.
Epithelial-to-mesenchymal transitions and circulating tumor cells.
Arnaud Bonnomet, Anne Brysse, +4 authors, Christine Gilles.
J Mammary Gland Biol Neoplasia, 2010 May 08; 15(2). PMID: 20449641
Review.
Histological types of breast cancer: how special are they?
Britta Weigelt, Felipe C Geyer, Jorge S Reis-Filho.
Mol Oncol, 2010 May 11; 4(3). PMID: 20452298    Free PMC article.
Highly Cited. Review.
Transcriptomic "portraits" of canine mammary cancer cell lines with various phenotypes.
M Król, K M Pawłowski, +6 authors, T Motyl.
J Appl Genet, 2010 May 11; 51(2). PMID: 20453304
Breast cancer diagnosis using a microfluidic multiplexed immunohistochemistry platform.
Minseok S Kim, Taemin Kim, +6 authors, Je-Kyun Park.
PLoS One, 2010 May 11; 5(5). PMID: 20454672    Free PMC article.
A semi-parametric Bayesian model for unsupervised differential co-expression analysis.
Johannes M Freudenberg, Siva Sivaganesan, Michael Wagner, Mario Medvedovic.
BMC Bioinformatics, 2010 May 13; 11. PMID: 20459663    Free PMC article.
Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities.
Dinesh Kumar Singh, Chin-Jen Ku, +3 authors, Steven J Altschuler.
Mol Syst Biol, 2010 May 13; 6. PMID: 20461076    Free PMC article.
Molecular basis for therapy resistance.
Per E Lønning.
Mol Oncol, 2010 May 15; 4(3). PMID: 20466604    Free PMC article.
Review.
The effects of globin on microarray-based gene expression analysis of mouse blood.
Mary E Winn, Matthew A Zapala, +3 authors, Nicholas J Schork.
Mamm Genome, 2010 May 18; 21(5-6). PMID: 20473674    Free PMC article.
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer.
Raj Chari, Bradley P Coe, +2 authors, Wan L Lam.
BMC Syst Biol, 2010 May 19; 4. PMID: 20478067    Free PMC article.
Incorporating gene co-expression network in identification of cancer prognosis markers.
Shuangge Ma, Mingyu Shi, +2 authors, Ben-Chang Shia.
BMC Bioinformatics, 2010 May 22; 11. PMID: 20487548    Free PMC article.
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context.
Gad Abraham, Adam Kowalczyk, +2 authors, Justin Zobel.
BMC Bioinformatics, 2010 May 27; 11. PMID: 20500821    Free PMC article.
Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma.
Jo Eyles, Anne-Laure Puaux, +12 authors, Jean-Pierre Abastado.
J Clin Invest, 2010 May 27; 120(6). PMID: 20501944    Free PMC article.
Highly Cited.
Basal-like breast cancer displays distinct patterns of promoter methylation.
Ji Shin Lee, Mary Jo Fackler, +5 authors, Saraswati Sukumar.
Cancer Biol Ther, 2010 May 28; 9(12). PMID: 20505321    Free PMC article.
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression.
Zhiao Shi, Catherine K Derow, Bing Zhang.
BMC Syst Biol, 2010 May 29; 4. PMID: 20507583    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.
Characterization of molecular subtypes of Korean breast cancer: an ethnically and clinically distinct population.
Wonshik Han, Monica Nicolau, Dong-Young Noh, Stefanie S Jeffrey.
Int J Oncol, 2010 Jun 02; 37(1). PMID: 20514396    Free PMC article.
Classification versus association models: should the same methods apply?
Ziding Feng.
Scand J Clin Lab Invest Suppl, 2010 Jun 03; 242. PMID: 20515278    Free PMC article.
Using functional genetics to understand breast cancer biology.
Alan Ashworth, Rene Bernards.
Cold Spring Harb Perspect Biol, 2010 Jun 04; 2(7). PMID: 20519343    Free PMC article.
Review.
The pathology of EMT in mouse mammary tumorigenesis.
Robert Darrell Cardiff.
J Mammary Gland Biol Neoplasia, 2010 Jun 04; 15(2). PMID: 20521088    Free PMC article.
Review.
Assessing risk prediction models in case-control studies using semiparametric and nonparametric methods.
Ying Huang, Margaret Sullivan Pepe.
Stat Med, 2010 Jun 09; 29(13). PMID: 20527013    Free PMC article.
A boosting method for maximizing the partial area under the ROC curve.
Osamu Komori, Shinto Eguchi.
BMC Bioinformatics, 2010 Jun 12; 11. PMID: 20537139    Free PMC article.
Micro-RNAs and breast cancer.
John Le Quesne, Carlos Caldas.
Mol Oncol, 2010 Jun 12; 4(3). PMID: 20537965    Free PMC article.
Review.
Triple-negative breast cancer: present challenges and new perspectives.
Franca Podo, Lutgarde M C Buydens, +16 authors, FEMME Consortium.
Mol Oncol, 2010 Jun 12; 4(3). PMID: 20537966    Free PMC article.
Highly Cited. Review.
Genetic susceptibility to breast cancer.
Nasim Mavaddat, Antonis C Antoniou, Douglas F Easton, Montserrat Garcia-Closas.
Mol Oncol, 2010 Jun 15; 4(3). PMID: 20542480    Free PMC article.
Highly Cited. Review.
Does applicability domain exist in microarray-based genomic research?
Li Shao, Leihong Wu, +2 authors, Xiaohui Fan.
PLoS One, 2010 Jun 16; 5(6). PMID: 20548774    Free PMC article.
Molecular circuits of solid tumors: prognostic and predictive tools for bedside use.
Charles Ferté, Fabrice André, Jean-Charles Soria.
Nat Rev Clin Oncol, 2010 Jun 17; 7(7). PMID: 20551944
Review.
Up-regulation of cell cycle arrest protein BTG2 correlates with increased overall survival in breast cancer, as detected by immunohistochemistry using tissue microarray.
Elin Möllerström, Anikó Kovács, +8 authors, Khalil Helou.
BMC Cancer, 2010 Jun 18; 10. PMID: 20553615    Free PMC article.
Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.
Bettina Heidecker, Joshua M Hare.
J Cardiovasc Transl Res, 2008 Sep 01; 1(3). PMID: 20559924    Free PMC article.
Review.
An algorithm for classifying tumors based on genomic aberrations and selecting representative tumor models.
Xin Lu, Ke Zhang, +2 authors, Dimitri Semizarov.
BMC Med Genomics, 2010 Jun 24; 3. PMID: 20569491    Free PMC article.
Angiogenesis-associated sequence variants relative to breast cancer recurrence and survival.
LaCreis R Kidd, Guy N Brock, +4 authors, James L Wittliff.
Cancer Causes Control, 2010 Jun 24; 21(10). PMID: 20571871    Free PMC article.
Mouse models of cancers: opportunities to address heterogeneity of human cancer and evaluate therapeutic strategies.
Eran R Andrechek, Joseph R Nevins.
J Mol Med (Berl), 2010 Jun 25; 88(11). PMID: 20574808    Free PMC article.
Review.
Expectations, validity, and reality in gene expression profiling.
Kyoungmi Kim, Stanislav O Zakharkin, David B Allison.
J Clin Epidemiol, 2010 Jun 29; 63(9). PMID: 20579843    Free PMC article.
Review.
Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity.
Frédéric Chibon, Pauline Lagarde, +17 authors, Alain Aurias.
Nat Med, 2010 Jun 29; 16(7). PMID: 20581836
Highly Cited.
An 8-gene qRT-PCR-based gene expression score that has prognostic value in early breast cancer.
Iker Sánchez-Navarro, Angelo Gámez-Pozo, +11 authors, Enrique Espinosa.
BMC Cancer, 2010 Jun 30; 10. PMID: 20584321    Free PMC article.
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.
The gene expression profile in the synovium as a predictor of the clinical response to infliximab treatment in rheumatoid arthritis.
Johan Lindberg, Carla A Wijbrandts, +7 authors, Paul P Tak.
PLoS One, 2010 Jul 02; 5(6). PMID: 20593016    Free PMC article.
AACR centennial series: the biology of cancer metastasis: historical perspective.
James E Talmadge, Isaiah J Fidler.
Cancer Res, 2010 Jul 09; 70(14). PMID: 20610625    Free PMC article.
Highly Cited. Review.
Measurement of biomarker proteins for point-of-care early detection and monitoring of cancer.
James F Rusling, Challa V Kumar, J Silvio Gutkind, Vyomesh Patel.
Analyst, 2010 Jul 09; 135(10). PMID: 20614087    Free PMC article.
Highly Cited. Review.
Mammostrat as a tool to stratify breast cancer patients at risk of recurrence during endocrine therapy.
John M S Bartlett, Jeremy Thomas, +12 authors, Udi Chetty.
Breast Cancer Res, 2010 Jul 10; 12(4). PMID: 20615243    Free PMC article.
The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer.
J Yu, Q Cao, +13 authors, A M Chinnaiyan.
Oncogene, 2010 Jul 14; 29(39). PMID: 20622896    Free PMC article.
Stability of ranked gene lists in large microarray analysis studies.
Gregor Stiglic, Peter Kokol.
J Biomed Biotechnol, 2010 Jul 14; 2010. PMID: 20625502    Free PMC article.
Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts.
Mariana O Baratti, Yuri B Moreira, +3 authors, Sara T Olalla-Saad.
BMC Med Genomics, 2010 Jul 17; 3. PMID: 20633296    Free PMC article.
Local-learning-based feature selection for high-dimensional data analysis.
Yijun Sun, Sinisa Todorovic, Steve Goodison.
IEEE Trans Pattern Anal Mach Intell, 2010 Jul 17; 32(9). PMID: 20634556    Free PMC article.
Dissecting the transcriptional networks underlying breast cancer: NR4A1 reduces the migration of normal and breast cancer cell lines.
Annika N Alexopoulou, Maria Leao, +7 authors, Parmjit S Jat.
Breast Cancer Res, 2010 Jul 21; 12(4). PMID: 20642837    Free PMC article.
Technology as a force for improved diagnosis and treatment of breast disease.
Claire M B Holloway, Alexandra Easson, +5 authors, David R McCready.
Can J Surg, 2010 Jul 22; 53(4). PMID: 20646402    Free PMC article.
Review.
Ceramide galactosyltransferase (UGT8) is a molecular marker of breast cancer malignancy and lung metastases.
P Dzięgiel, T Owczarek, +6 authors, M Ugorski.
Br J Cancer, 2010 Jul 22; 103(4). PMID: 20648017    Free PMC article.
Predictive relevance of HOXB13 protein expression for tamoxifen benefit in breast cancer.
Piiha-Lotta Jerevall, Agneta Jansson, +3 authors, Olle Stål.
Breast Cancer Res, 2010 Jul 24; 12(4). PMID: 20649975    Free PMC article.
A Quick and Parallel Analytical Method Based on Quantum Dots Labeling for ToRCH-Related Antibodies.
Hao Yang, Qing Guo, +5 authors, Daxiang Cui.
Nanoscale Res Lett, 2009 Jan 01; 4(12). PMID: 20652102    Free PMC article.
Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer.
Aslaug Aamodt Muggerud, Michael Hallett, +8 authors, Fredrik Wärnberg.
Mol Oncol, 2010 Jul 29; 4(4). PMID: 20663721    Free PMC article.
BCL2 in breast cancer: a favourable prognostic marker across molecular subtypes and independent of adjuvant therapy received.
S-J Dawson, N Makretsov, +17 authors, P Pharoah.
Br J Cancer, 2010 Jul 29; 103(5). PMID: 20664598    Free PMC article.
Highly Cited.
PTK6 regulates IGF-1-induced anchorage-independent survival.
Hanna Y Irie, Yashaswi Shrestha, +13 authors, Joan S Brugge.
PLoS One, 2010 Jul 30; 5(7). PMID: 20668531    Free PMC article.
Finding biomarker signatures in pooled sample designs: a simulation framework for methodological comparisons.
Anna Telaar, Gerd Nürnberg, Dirk Repsilber.
Adv Bioinformatics, 2010 Jul 31;. PMID: 20671968    Free PMC article.
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.
W Shi, M Bessarabova, +19 authors, Y Nikolsky.
Pharmacogenomics J, 2010 Aug 03; 10(4). PMID: 20676069    Free PMC article.
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Leming Shi, Gregory Campbell, +200 authors, MAQC Consortium.
Nat Biotechnol, 2010 Aug 03; 28(8). PMID: 20676074    Free PMC article.
Highly Cited.
Homeobox transcription factor muscle segment homeobox 2 (Msx2) correlates with good prognosis in breast cancer patients and induces apoptosis in vitro.
Fiona Lanigan, Gabriela Gremel, +4 authors, William M Gallagher.
Breast Cancer Res, 2010 Aug 05; 12(4). PMID: 20682066    Free PMC article.
The histone demethylase JMJD2B is regulated by estrogen receptor alpha and hypoxia, and is a key mediator of estrogen induced growth.
Jun Yang, Adrian M Jubb, +7 authors, Adrian L Harris.
Cancer Res, 2010 Aug 05; 70(16). PMID: 20682797    Free PMC article.
Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues.
Kellie J Archer, Zhongming Zhao, +3 authors, Valeria R Mas.
Int J Comput Biol Drug Des, 2010 Aug 10; 3(1). PMID: 20693610    Free PMC article.
Impact of RNA degradation on gene expression profiling.
Lennart Opitz, Gabriela Salinas-Riester, +6 authors, Jochen Gaedcke.
BMC Med Genomics, 2010 Aug 11; 3. PMID: 20696062    Free PMC article.
Phosphorylation of estrogen receptor beta at serine 105 is associated with good prognosis in breast cancer.
Werbena Hamilton-Burke, Louise Coleman, +9 authors, Valerie Speirs.
Am J Pathol, 2010 Aug 11; 177(3). PMID: 20696772    Free PMC article.
Genomic index of sensitivity to endocrine therapy for breast cancer.
W Fraser Symmans, Christos Hatzis, +13 authors, Lajos Pusztai.
J Clin Oncol, 2010 Aug 11; 28(27). PMID: 20697068    Free PMC article.
Highly Cited.
The Expression Patterns of ER, PR, HER2, CK5/6, EGFR, Ki-67 and AR by Immunohistochemical Analysis in Breast Cancer Cell Lines.
Kristina Subik, Jin-Feng Lee, +8 authors, Ping Tang.
Breast Cancer (Auckl), 2010 Aug 11; 4. PMID: 20697531    Free PMC article.
Highly Cited.
Overexpression of POLQ confers a poor prognosis in early breast cancer patients.
Geoff S Higgins, Adrian L Harris, +3 authors, Francesca M Buffa.
Oncotarget, 2010 Aug 12; 1(3). PMID: 20700469    Free PMC article.
Rough set soft computing cancer classification and network: one stone, two birds.
Yue Zhang.
Cancer Inform, 2010 Aug 14; 9. PMID: 20706619    Free PMC article.
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Alexander Lachmann, Huilei Xu, +3 authors, Avi Ma'ayan.
Bioinformatics, 2010 Aug 17; 26(19). PMID: 20709693    Free PMC article.
Highly Cited.
Defining breast cancer prognosis based on molecular phenotypes: results from a large cohort study.
Shaheenah Dawood, Rong Hu, +5 authors, Rulla M Tamimi.
Breast Cancer Res Treat, 2010 Aug 17; 126(1). PMID: 20711652    Free PMC article.
Molecular apocrine differentiation is a common feature of breast cancer in patients with germline PTEN mutations.
Guillaume Banneau, Mickaël Guedj, +15 authors, Michel Longy.
Breast Cancer Res, 2010 Aug 18; 12(4). PMID: 20712882    Free PMC article.
Module-based prediction approach for robust inter-study predictions in microarray data.
Zhibao Mi, Kui Shen, +4 authors, George C Tseng.
Bioinformatics, 2010 Aug 20; 26(20). PMID: 20719761    Free PMC article.
Antibody-based proteomics: fast-tracking molecular diagnostics in oncology.
Donal J Brennan, Darran P O'Connor, +2 authors, William M Gallagher.
Nat Rev Cancer, 2010 Aug 20; 10(9). PMID: 20720569
Review.
The APC/C recruits cyclin B1-Cdk1-Cks in prometaphase before D box recognition to control mitotic exit.
Wouter van Zon, Janneke Ogink, +3 authors, Rob M F Wolthuis.
J Cell Biol, 2010 Aug 25; 190(4). PMID: 20733055    Free PMC article.
In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology.
Sangwon Cha, Marcin B Imielinski, +4 authors, Barry L Karger.
Mol Cell Proteomics, 2010 Aug 27; 9(11). PMID: 20739354    Free PMC article.
Hybrid models identified a 12-gene signature for lung cancer prognosis and chemoresponse prediction.
Ying-Wooi Wan, Ebrahim Sabbagh, +6 authors, Nancy Lan Guo.
PLoS One, 2010 Sep 03; 5(8). PMID: 20808922    Free PMC article.
An algorithm to discover gene signatures with predictive potential.
Robin M Hallett, Anna Dvorkin, Christine M Gabardo, John A Hassell.
J Exp Clin Cancer Res, 2010 Sep 04; 29. PMID: 20813028    Free PMC article.
Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer.
Aleix Prat, Joel S Parker, +5 authors, Charles M Perou.
Breast Cancer Res, 2010 Sep 04; 12(5). PMID: 20813035    Free PMC article.
Highly Cited.
EGFR signaling in breast cancer: bad to the bone.
John Foley, Nicole K Nickerson, +4 authors, David J Riese.
Semin Cell Dev Biol, 2010 Sep 04; 21(9). PMID: 20813200    Free PMC article.
Review.
Aberrant expression of LMO4 induces centrosome amplification and mitotic spindle abnormalities in breast cancer cells.
Marjorie E Montañez-Wiscovich, Melissa D Shelton, +6 authors, Ruth A Keri.
J Pathol, 2010 Sep 04; 222(3). PMID: 20814902    Free PMC article.
Poly (ADP-ribose) polymerase as a novel therapeutic target in cancer.
Christina M Annunziata, Joyce O'Shaughnessy.
Clin Cancer Res, 2010 Sep 09; 16(18). PMID: 20823142    Free PMC article.
Review.
Perspectives on Breast Cancer Management: Tailoring Treatment to the Individual Patient.
Christoph Thomssen.
Breast Care (Basel), 2008 Jan 01; 3(s1). PMID: 20824005    Free PMC article.
Array-based DNA methylation profiling for breast cancer subtype discrimination.
Ilse Van der Auwera, Wayne Yu, +7 authors, Steven J Van Laere.
PLoS One, 2010 Sep 11; 5(9). PMID: 20830311    Free PMC article.
Analyzing the regulation of metabolic pathways in human breast cancer.
Gunnar Schramm, Eva-Maria Surmann, +4 authors, Rainer König.
BMC Med Genomics, 2010 Sep 14; 3. PMID: 20831783    Free PMC article.
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes.
Devin C Koestler, Carmen J Marsit, +5 authors, E Andres Houseman.
Bioinformatics, 2010 Sep 14; 26(20). PMID: 20834038    Free PMC article.
A systems biology approach to defining metastatic biomarkers and signaling pathways.
Natalie E Goldberger, Kent W Hunter.
Wiley Interdiscip Rev Syst Biol Med, 2009 Jul 01; 1(1). PMID: 20835983    Free PMC article.
Review.
Transmembrane BAX inhibitor motif containing (TMBIM) family proteins perturbs a trans-Golgi network enzyme, Gb3 synthase, and reduces Gb3 biosynthesis.
Toshiyuki Yamaji, Kiyotaka Nishikawa, Kentaro Hanada.
J Biol Chem, 2010 Sep 15; 285(46). PMID: 20837469    Free PMC article.
A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer.
Torsten O Nielsen, Joel S Parker, +12 authors, Matthew J Ellis.
Clin Cancer Res, 2010 Sep 15; 16(21). PMID: 20837693    Free PMC article.
Highly Cited.
Should we abandon the t-test in the analysis of gene expression microarray data: a comparison of variance modeling strategies.
Marine Jeanmougin, Aurelien de Reynies, +3 authors, Mickael Guedj.
PLoS One, 2010 Sep 15; 5(9). PMID: 20838429    Free PMC article.
Transcriptional profiling of ErbB signalling in mammary luminal epithelial cells--interplay of ErbB and IGF1 signalling through IGFBP3 regulation.
Jenny Worthington, Mariana Bertani, +2 authors, John F Timms.
BMC Cancer, 2010 Sep 16; 10. PMID: 20840765    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.
Lactic acidosis triggers starvation response with paradoxical induction of TXNIP through MondoA.
Julia Ling-Yu Chen, Daniel Merl, +7 authors, Jen-Tsan Chi.
PLoS Genet, 2010 Sep 17; 6(9). PMID: 20844768    Free PMC article.
ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research--an update.
Joshua Xu, Reagan Kelly, Hong Fang, Weida Tong.
Hum Genomics, 2010 Sep 18; 4(6). PMID: 20846933    Free PMC article.
Review.
Targeted Therapy in Breast Cancer.
Andreas Schneeweiss.
Breast Care (Basel), 2010 Sep 18; 5(3). PMID: 20847825    Free PMC article.
CSPG4 protein as a new target for the antibody-based immunotherapy of triple-negative breast cancer.
Xinhui Wang, Takuya Osada, +12 authors, Soldano Ferrone.
J Natl Cancer Inst, 2010 Sep 21; 102(19). PMID: 20852124    Free PMC article.
Triple-negative, basal-like, and quintuple-negative breast cancers: better prediction model for survival.
Yoon-La Choi, Ensel Oh, +12 authors, Young Kee Shin.
BMC Cancer, 2010 Sep 24; 10. PMID: 20860845    Free PMC article.
ANCCA/ATAD2 overexpression identifies breast cancer patients with poor prognosis, acting to drive proliferation and survival of triple-negative cells through control of B-Myb and EZH2.
Ekaterina V Kalashnikova, Alexey S Revenko, +6 authors, Hong-Wu Chen.
Cancer Res, 2010 Sep 25; 70(22). PMID: 20864510    Free PMC article.
DNA repair and personalized breast cancer therapy.
Shu-Xia Li, Ashley Sjolund, Lyndsay Harris, Joann B Sweasy.
Environ Mol Mutagen, 2010 Sep 28; 51(8-9). PMID: 20872853    Free PMC article.
Review.
Triple-negative breast cancer: disease entity or title of convenience?
Lisa Carey, Eric Winer, +2 authors, Luca Gianni.
Nat Rev Clin Oncol, 2010 Sep 30; 7(12). PMID: 20877296
Highly Cited. Review.
Tumor gene expression profiling in women with breast cancer. Test category: prognostic.
Cecelia Bellcross, W David Dotson.
PLoS Curr, 2010 Sep 30; 2. PMID: 20877449    Free PMC article.
Int6 regulates both proteasomal degradation and translation initiation and is critical for proper formation of acini by human mammary epithelium.
J Suo, S J Snider, +5 authors, E C Chang.
Oncogene, 2010 Oct 05; 30(6). PMID: 20890303    Free PMC article.
Maximum growth and survival of estrogen receptor-alpha positive breast cancer cells requires the Sin3A transcriptional repressor.
Stephanie J Ellison-Zelski, Elaine T Alarid.
Mol Cancer, 2010 Oct 06; 9. PMID: 20920219    Free PMC article.
Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data.
Yijun Sun, Yunpeng Cai, +4 authors, Steve Goodison.
Nucleic Acids Res, 2010 Oct 12; 38(22). PMID: 20929878    Free PMC article.
Nuclear receptor coregulators as a new paradigm for therapeutic targeting.
Elaine Y Hsia, Michael L Goodson, +2 authors, Hong-Wu Chen.
Adv Drug Deliv Rev, 2010 Oct 12; 62(13). PMID: 20933027    Free PMC article.
Review.
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays.
Hong Fang, Joshua Xu, +14 authors, Weida Tong.
BMC Bioinformatics, 2010 Oct 22; 11 Suppl 6. PMID: 20946615    Free PMC article.
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network.
Junjie Su, Byung-Jun Yoon, Edward R Dougherty.
BMC Bioinformatics, 2010 Oct 22; 11 Suppl 6. PMID: 20946619    Free PMC article.
A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancer.
Christina Yau, Laura Esserman, +3 authors, Christopher C Benz.
Breast Cancer Res, 2010 Oct 16; 12(5). PMID: 20946665    Free PMC article.
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs.
Jonghwan Kim, Andrew J Woo, +5 authors, Stuart H Orkin.
Cell, 2010 Oct 16; 143(2). PMID: 20946988    Free PMC article.
Highly Cited.
Integration of biological knowledge and gene expression data for biomarker selection: FN1 as a potential predictor of radiation resistance in head and neck cancer.
Sally A Amundson, Lubomir B Smilenov.
Cancer Biol Ther, 2010 Oct 16; 10(12). PMID: 20948301    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.
Mapping the cellular and molecular heterogeneity of normal and malignant breast tissues and cultured cell lines.
Patrica J Keller, Amy F Lin, +10 authors, Charlotte Kuperwasser.
Breast Cancer Res, 2010 Oct 23; 12(5). PMID: 20964822    Free PMC article.
Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways.
Jeffrey C Miecznikowski, Dan Wang, +2 authors, David Gold.
BMC Cancer, 2010 Oct 23; 10. PMID: 20964848    Free PMC article.
Down-regulation of the oncogene cyclin D1 increases migratory capacity in breast cancer and is linked to unfavorable prognostic features.
Sophie Lehn, Nicholas P Tobin, +6 authors, Göran Landberg.
Am J Pathol, 2010 Oct 26; 177(6). PMID: 20971731    Free PMC article.
Identification of high-quality cancer prognostic markers and metastasis network modules.
Jie Li, Anne E G Lenferink, +5 authors, Edwin Wang.
Nat Commun, 2010 Oct 27; 1. PMID: 20975711    Free PMC article.
Highly Cited.
Breast cancer assessment tools and optimizing adjuvant therapy.
Catherine Oakman, Libero Santarpia, Angelo Di Leo.
Nat Rev Clin Oncol, 2010 Oct 27; 7(12). PMID: 20975745
Review.
Genetics: How to validate a breast cancer prognostic signature.
Paul D Pharoah, Carlos Caldas.
Nat Rev Clin Oncol, 2010 Oct 29; 7(11). PMID: 20981123
Breast cancer in the personal genomics era.
Rachel E Ellsworth, David J Decewicz, Craig D Shriver, Darrell L Ellsworth.
Curr Genomics, 2010 Nov 03; 11(3). PMID: 21037853    Free PMC article.
Biological impact of missing-value imputation on downstream analyses of gene expression profiles.
Sunghee Oh, Dongwan D Kang, Guy N Brock, George C Tseng.
Bioinformatics, 2010 Nov 04; 27(1). PMID: 21045072    Free PMC article.
Systems biology and genomics of breast cancer.
Charles M Perou, Anne-Lise Børresen-Dale.
Cold Spring Harb Perspect Biol, 2010 Nov 05; 3(2). PMID: 21047916    Free PMC article.
Review.
Adjuvant Systemic Therapy, Quo Vadis? Patient Selection, Prognostic and Predictive Factors.
Fatima Cardoso.
Breast Care (Basel), 2008 Jan 01; 3(6). PMID: 21048908    Free PMC article.
The UCSC Cancer Genomics Browser: update 2011.
J Zachary Sanborn, Stephen C Benz, +12 authors, Jingchun Zhu.
Nucleic Acids Res, 2010 Nov 10; 39(Database issue). PMID: 21059681    Free PMC article.
Gene expression profiles of estrogen receptor-positive and estrogen receptor-negative breast cancers are detectable in histologically normal breast epithelium.
Kelly Graham, Xijin Ge, +2 authors, Carol L Rosenberg.
Clin Cancer Res, 2010 Nov 10; 17(2). PMID: 21059815    Free PMC article.
Metastatic canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human breast cancer profiles.
Robert Klopfleisch, Dido Lenze, Michael Hummel, Achim D Gruber.
BMC Cancer, 2010 Nov 11; 10. PMID: 21062462    Free PMC article.
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.
Discovering hidden relationships between renal diseases and regulated genes through 3D network visualizations.
Suresh K Bhavnani, Arunkumaar Ganesan, +6 authors, Matthias Kretzler.
BMC Res Notes, 2010 Nov 13; 3. PMID: 21070623    Free PMC article.
Metastasis: tumor cells becoming MENAcing.
Frank Gertler, John Condeelis.
Trends Cell Biol, 2010 Nov 13; 21(2). PMID: 21071226    Free PMC article.
Review.
Node-Negative Breast Cancer: Which Patients Should Be Treated?
Marcus Schmidt.
Breast Care (Basel), 2008 Jan 01; 3(4). PMID: 21076603    Free PMC article.
Higher levels of GATA3 predict better survival in women with breast cancer.
Nam K Yoon, Erin L Maresh, +8 authors, Lee Goodglick.
Hum Pathol, 2010 Nov 17; 41(12). PMID: 21078439    Free PMC article.
Identification of a low-risk subgroup of HER-2-positive breast cancer by the 70-gene prognosis signature.
M Knauer, F Cardoso, +4 authors, L J van 't Veer.
Br J Cancer, 2010 Nov 18; 103(12). PMID: 21081926    Free PMC article.
Breast cancer biomarker discovery in the functional genomic age: a systematic review of 42 gene expression signatures.
M C Abba, E Lacunza, M Butti, C M Aldaz.
Biomark Insights, 2010 Nov 18; 5. PMID: 21082037    Free PMC article.
Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2.
Juha K Rantala, Henrik Edgren, +9 authors, Olli Kallioniemi.
Neoplasia, 2010 Nov 18; 12(11). PMID: 21082043    Free PMC article.
Derivation of cancer diagnostic and prognostic signatures from gene expression data.
Steve Goodison, Yijun Sun, Virginia Urquidi.
Bioanalysis, 2010 Nov 19; 2(5). PMID: 21083217    Free PMC article.
Review.
Pre-clinical drug prioritization via prognosis-guided genetic interaction networks.
Jianghui Xiong, Juan Liu, +3 authors, Shanguang Chen.
PLoS One, 2010 Nov 19; 5(11). PMID: 21085674    Free PMC article.
Ranking prognosis markers in cancer genomic studies.
Shuangge Ma, Xiao Song.
Brief Bioinform, 2010 Nov 20; 12(1). PMID: 21087949    Free PMC article.
BRCA1 modulates the expression of hnRNPA2B1 and KHSRP.
Manuela Santarosa, Laura Del Col, +5 authors, Roberta Maestro.
Cell Cycle, 2010 Nov 26; 9(23). PMID: 21099359    Free PMC article.
Regulation patterns in signaling networks of cancer.
Gunnar Schramm, Nandakumar Kannabiran, Rainer König.
BMC Syst Biol, 2010 Nov 30; 4. PMID: 21110851    Free PMC article.
Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer.
Jean J Latimer, Jennifer M Johnson, +8 authors, Stephen G Grant.
Proc Natl Acad Sci U S A, 2010 Dec 02; 107(50). PMID: 21118987    Free PMC article.
Cytosolic phospholipase A2-α expression in breast cancer is associated with EGFR expression and correlates with an adverse prognosis in luminal tumours.
F Caiazza, N S McCarthy, +3 authors, W Thomas.
Br J Cancer, 2010 Dec 02; 104(2). PMID: 21119660    Free PMC article.
Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment.
Yujin Hoshida.
PLoS One, 2010 Dec 03; 5(11). PMID: 21124904    Free PMC article.
Exploring the link between germline and somatic genetic alterations in breast carcinogenesis.
Núria Bonifaci, Bohdan Górski, +12 authors, Miguel Angel Pujana.
PLoS One, 2010 Dec 03; 5(11). PMID: 21124932    Free PMC article.
In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome.
Simen Myhre, Hayat Mohammed, +7 authors, Therese Sørlie.
PLoS One, 2010 Dec 03; 5(11). PMID: 21124964    Free PMC article.
The molecular pathology of breast cancer progression.
Alessandro Bombonati, Dennis C Sgroi.
J Pathol, 2010 Dec 03; 223(2). PMID: 21125683    Free PMC article.
Review.
Biomarkers in Barrett's esophagus and esophageal adenocarcinoma: predictors of progression and prognosis.
Chin-Ann J Ong, Pierre Lao-Sirieix, Rebecca C Fitzgerald.
World J Gastroenterol, 2010 Dec 04; 16(45). PMID: 21128316    Free PMC article.
Review.
Interactions with fibroblasts are distinct in Basal-like and luminal breast cancers.
J Terese Camp, Fathi Elloumi, +5 authors, Melissa A Troester.
Mol Cancer Res, 2010 Dec 07; 9(1). PMID: 21131600    Free PMC article.
The α₂β₁ integrin is a metastasis suppressor in mouse models and human cancer.
Norma E Ramirez, Zhonghua Zhang, +7 authors, Mary M Zutter.
J Clin Invest, 2010 Dec 08; 121(1). PMID: 21135504    Free PMC article.
Deconstructing the molecular portraits of breast cancer.
Aleix Prat, Charles M Perou.
Mol Oncol, 2010 Dec 15; 5(1). PMID: 21147047    Free PMC article.
Highly Cited. Review.
Moving forward in human cancer risk assessment.
Richard S Paules, Jiri Aubrecht, +2 authors, Jos C Kleinjans.
Environ Health Perspect, 2010 Dec 15; 119(6). PMID: 21147607    Free PMC article.
Angiocrine factors modulate tumor proliferation and motility through EphA2 repression of Slit2 tumor suppressor function in endothelium.
Dana M Brantley-Sieders, Charlene M Dunaway, +8 authors, Jin Chen.
Cancer Res, 2010 Dec 15; 71(3). PMID: 21148069    Free PMC article.
Bayesian ensemble methods for survival prediction in gene expression data.
Vinicius Bonato, Veerabhadran Baladandayuthapani, +3 authors, Kim-Anh Do.
Bioinformatics, 2010 Dec 15; 27(3). PMID: 21148161    Free PMC article.
Biological functions of the genes in the mammaprint breast cancer profile reflect the hallmarks of cancer.
Sun Tian, Paul Roepman, +3 authors, Annuska M Glas.
Biomark Insights, 2010 Dec 15; 5. PMID: 21151591    Free PMC article.
Invasive Lobular Carcinomas Do Not Express Basal Cytokeratin Markers CK5/6, CK14 and CK17.
Natalya Khilko, Jianmin Wang, +2 authors, Ping Tang.
Breast Cancer (Auckl), 2010 Dec 15; 4. PMID: 21151863    Free PMC article.
Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status.
Qiyuan Li, Aron C Eklund, +5 authors, Charles Swanton.
PLoS One, 2010 Dec 15; 5(12). PMID: 21152022    Free PMC article.
Clinicopathlogic and immunohistochemical characteristics of triple negative invasive lobular carcinoma.
Ja Seung Koo, Woohee Jung.
Yonsei Med J, 2010 Dec 15; 52(1). PMID: 21155040    Free PMC article.
TSPYL5 suppresses p53 levels and function by physical interaction with USP7.
Mirjam T Epping, Lars A T Meijer, +3 authors, René Bernards.
Nat Cell Biol, 2010 Dec 21; 13(1). PMID: 21170034
A scalable approach for discovering conserved active subnetworks across species.
Raamesh Deshpande, Shikha Sharma, +2 authors, Chad L Myers.
PLoS Comput Biol, 2010 Dec 21; 6(12). PMID: 21170309    Free PMC article.
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform.
Monica M Reinholz, Jeanette E Eckel-Passow, +14 authors, Wilma L Lingle.
BMC Med Genomics, 2010 Dec 22; 3. PMID: 21172013    Free PMC article.
Molecular profiling currently offers no more than tumour morphology and basic immunohistochemistry.
Britta Weigelt, Jorge S Reis-Filho.
Breast Cancer Res, 2011 Jan 05; 12 Suppl 4. PMID: 21172089    Free PMC article.
Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer.
Armelle Corpet, Leanne De Koning, +9 authors, Geneviève Almouzni.
EMBO J, 2010 Dec 24; 30(3). PMID: 21179005    Free PMC article.
A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas.
Antti Ylipää, Olli Yli-Harja, Wei Zhang, Matti Nykter.