. 2016 Mar;17(5).
doi: 10.1038/nrg.2016.10.

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

Sara A Byron 1 Kendall R Van Keuren-Jensen 2 David M Engelthaler 3 John D Carpten 4 David W Craig 2 
  • PMID: 26996076
  •     153 References
  •     148 citations


With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules hold expanded promise for their diagnostic, prognostic and therapeutic applicability in various diseases, including cancers and infectious diseases. Detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq represent some of the most immediate opportunities. However, it is the diversity of RNA species detected through RNA-seq that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including the potential of extracellular RNAs as non-invasive diagnostic indicators of disease. Ongoing efforts towards the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Joseph K Pickrell, John C Marioni, +7 authors, Jonathan K Pritchard.
Nature, 2010 Mar 12; 464(7289). PMID: 20220758    Free PMC article.
Highly Cited.
Integrative clinical genomics of advanced prostate cancer.
Dan Robinson, Eliezer M Van Allen, +70 authors, Arul M Chinnaiyan.
Cell, 2015 May 23; 161(5). PMID: 26000489    Free PMC article.
Highly Cited.
Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement.
Hani Goodarzi, Xuhang Liu, +3 authors, Sohail F Tavazoie.
Cell, 2015 May 11; 161(4). PMID: 25957686    Free PMC article.
Highly Cited.
Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers.
Johan Skog, Tom Würdinger, +7 authors, Xandra O Breakefield.
Nat Cell Biol, 2008 Nov 18; 10(12). PMID: 19011622    Free PMC article.
Highly Cited.
Genetic predisposition to human disease: allele-specific expression and low-penetrance regulatory loci.
A de la Chapelle.
Oncogene, 2009 Jul 15; 28(38). PMID: 19597467    Free PMC article.
Identical splicing of aberrant epidermal growth factor receptor transcripts from amplified rearranged genes in human glioblastomas.
N Sugawa, A J Ekstrand, C D James, V P Collins.
Proc Natl Acad Sci U S A, 1990 Nov 01; 87(21). PMID: 2236070    Free PMC article.
Highly Cited.
Computational methods for transcriptome annotation and quantification using RNA-seq.
Manuel Garber, Manfred G Grabherr, Mitchell Guttman, Cole Trapnell.
Nat Methods, 2011 May 31; 8(6). PMID: 21623353
Highly Cited. Review.
A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.
Soonmyung Paik, Steven Shak, +12 authors, Norman Wolmark.
N Engl J Med, 2004 Dec 14; 351(27). PMID: 15591335
Highly Cited.
Noninvasive monitoring of infection and rejection after lung transplantation.
Iwijn De Vlaminck, Lance Martin, +13 authors, Stephen R Quake.
Proc Natl Acad Sci U S A, 2015 Oct 16; 112(43). PMID: 26460048    Free PMC article.
Highly Cited.
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.
Wenqian Zhang, Ying Yu, +73 authors, Matthias Fischer.
Genome Biol, 2015 Jun 26; 16. PMID: 26109056    Free PMC article.
Highly Cited.
Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries.
Halime Ekici, Shwetha D Rao, +3 authors, Ujjwal Neogi.
J Antimicrob Chemother, 2014 Aug 03; 69(12). PMID: 25085657
Preoperative diagnosis of benign thyroid nodules with indeterminate cytology.
Erik K Alexander, Giulia C Kennedy, +15 authors, Bryan R Haugen.
N Engl J Med, 2012 Jun 27; 367(8). PMID: 22731672
Highly Cited.
Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts.
Nancy B Y Tsui, Peiyong Jiang, +5 authors, Y M Dennis Lo.
Clin Chem, 2014 Apr 18; 60(7). PMID: 24740362
Association of ERG and TMPRSS2-ERG with grade, stage, and prognosis of prostate cancer is dependent on their expression levels.
Alba Font-Tello, Núria Juanpere, +7 authors, Silvia Hernández.
Prostate, 2015 May 06; 75(11). PMID: 25939480
Detecting and correcting systematic variation in large-scale RNA sequencing data.
Sheng Li, Paweł P Łabaj, +11 authors, Christopher E Mason.
Nat Biotechnol, 2014 Aug 26; 32(9). PMID: 25150837    Free PMC article.
Highly Cited.
cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.
Christopher R Cabanski, Vincent Magrini, +12 authors, Christopher A Maher.
J Mol Diagn, 2014 May 13; 16(4). PMID: 24814956    Free PMC article.
Primary breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.
E Senkus, S Kyriakides, +6 authors, ESMO Guidelines Committee.
Ann Oncol, 2015 Sep 01; 26 Suppl 5. PMID: 26314782
Highly Cited.
design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR.
Wei Wang, Peijun Ren, +12 authors, Vincent Deubel.
J Clin Microbiol, 2008 Oct 31; 47(1). PMID: 18971359    Free PMC article.
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Eliezer M Van Allen, Diana Miao, +19 authors, Levi A Garraway.
Science, 2015 Sep 12; 350(6257). PMID: 26359337    Free PMC article.
Highly Cited.
Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types.
Julia Salzman, Charles Gawad, +2 authors, Patrick O Brown.
PLoS One, 2012 Feb 10; 7(2). PMID: 22319583    Free PMC article.
Highly Cited.
Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants.
Josep Gregori, Juan I Esteban, +8 authors, Josep Quer.
PLoS One, 2014 Jan 07; 8(12). PMID: 24391758    Free PMC article.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Gang Li, Jae Hoon Bahn, +4 authors, Xinshu Xiao.
Nucleic Acids Res, 2012 Apr 03; 40(13). PMID: 22467206    Free PMC article.
Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth.
Rajen J Mody, Yi-Mi Wu, +32 authors, Arul M Chinnaiyan.
JAMA, 2015 Sep 02; 314(9). PMID: 26325560    Free PMC article.
Highly Cited.
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Krishna R Kalari, Asha A Nair, +12 authors, Jean-Pierre A Kocher.
BMC Bioinformatics, 2014 Jun 29; 15. PMID: 24972667    Free PMC article.
Highly Cited.
Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer.
Ramon Salazar, Paul Roepman, +16 authors, Rob Tollenaar.
J Clin Oncol, 2010 Nov 26; 29(1). PMID: 21098318
Highly Cited.
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
Marc Sultan, Marcel H Schulz, +13 authors, Marie-Laure Yaspo.
Science, 2008 Jul 05; 321(5891). PMID: 18599741
Highly Cited.
miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones.
Nucleic Acids Res, 2013 Nov 28; 42(Database issue). PMID: 24275495    Free PMC article.
Highly Cited.
Tailoring therapies--improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015.
A S Coates, E P Winer, +6 authors, Panel Members.
Ann Oncol, 2015 May 06; 26(8). PMID: 25939896    Free PMC article.
Highly Cited.
Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples.
Nicole Fischer, Daniela Indenbirken, +6 authors, Adam Grundhoff.
J Clin Microbiol, 2015 May 15; 53(7). PMID: 25972420    Free PMC article.
FusionCancer: a database of cancer fusion genes derived from RNA-seq data.
Yunjin Wang, Nan Wu, +2 authors, Dong Dong.
Diagn Pathol, 2015 Jul 29; 10. PMID: 26215638    Free PMC article.
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
Yi Wang, James Lu, +2 authors, Fuli Yu.
Genome Res, 2013 Jan 09; 23(5). PMID: 23296920    Free PMC article.
Resistance to tyrosine kinase inhibition by mutant epidermal growth factor receptor variant III contributes to the neoplastic phenotype of glioblastoma multiforme.
Chris A Learn, Tristan L Hartzell, +6 authors, John H Sampson.
Clin Cancer Res, 2004 May 08; 10(9). PMID: 15131063
A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium, Gonçalo R Abecasis, +6 authors, Gil A McVean.
Nature, 2010 Oct 29; 467(7319). PMID: 20981092    Free PMC article.
Highly Cited.
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.
Stephen K Gire, Augustine Goba, +55 authors, Pardis C Sabeti.
Science, 2014 Sep 13; 345(6202). PMID: 25214632    Free PMC article.
Highly Cited.
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.
Settara C Chandrasekharappa, Francis P Lach, +11 authors, NISC Comparative Sequencing Program.
Blood, 2013 Apr 25; 121(22). PMID: 23613520    Free PMC article.
Multicenter clinical experience with the Afirma gene expression classifier.
Erik K Alexander, Melanie Schorr, +7 authors, Bryan R Haugen.
J Clin Endocrinol Metab, 2013 Oct 25; 99(1). PMID: 24152684
Noninvasive in vivo monitoring of tissue-specific global gene expression in humans.
Winston Koh, Wenying Pan, +6 authors, Stephen R Quake.
Proc Natl Acad Sci U S A, 2014 May 07; 111(20). PMID: 24799715    Free PMC article.
Highly Cited.
Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study.
Pieter Mestdagh, Nicole Hartmann, +33 authors, Jo Vandesompele.
Nat Methods, 2014 Jun 30; 11(8). PMID: 24973947
Highly Cited.
Distinct phenotypes distinguish the molecular classes of Angelman syndrome.
A C Lossie, M M Whitney, +8 authors, D J Driscoll.
J Med Genet, 2001 Dec 19; 38(12). PMID: 11748306    Free PMC article.
Human papillomavirus E6/E7 mRNA testing as a predictive marker for cervical carcinoma.
A Kathrine Lie, Gunnar Kristensen.
Expert Rev Mol Diagn, 2008 Jul 05; 8(4). PMID: 18598223
Identification of miR-93 as a suitable miR for normalizing miRNA in plasma of tuberculosis patients.
Simone E Barry, Brian Chan, +6 authors, Bernadette M Saunders.
J Cell Mol Med, 2015 Mar 11; 19(7). PMID: 25753045    Free PMC article.
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
Sheng Li, Scott W Tighe, +26 authors, Christopher E Mason.
Nat Biotechnol, 2014 Aug 26; 32(9). PMID: 25150835    Free PMC article.
Highly Cited.
Personalized treatment of Sézary syndrome by targeting a novel CTLA4:CD28 fusion.
Aleksandar Sekulic, Winnie S Liang, +13 authors, Timothy K McDaniel.
Mol Genet Genomic Med, 2015 Mar 25; 3(2). PMID: 25802883    Free PMC article.
Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma.
Jason D Arroyo, John R Chevillet, +9 authors, Muneesh Tewari.
Proc Natl Acad Sci U S A, 2011 Mar 09; 108(12). PMID: 21383194    Free PMC article.
Highly Cited.
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Robert E Handsaker, Joshua M Korn, James Nemesh, Steven A McCarroll.
Nat Genet, 2011 Feb 15; 43(3). PMID: 21317889    Free PMC article.
Highly Cited.
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Jacob F Degner, John C Marioni, +4 authors, Jonathan K Pritchard.
Bioinformatics, 2009 Oct 08; 25(24). PMID: 19808877    Free PMC article.
Highly Cited.
Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.
David L A Wood, Katia Nones, +7 authors, Sean M Grimmond.
PLoS One, 2015 May 13; 10(5). PMID: 25965996    Free PMC article.
Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma.
Meabh Beatty, Jasenka Guduric-Fuchs, +4 authors, David Arthur Simpson.
BMC Genomics, 2014 Oct 27; 15. PMID: 25344700    Free PMC article.
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Justin M Zook, Brad Chapman, +4 authors, Marc Salit.
Nat Biotechnol, 2014 Feb 18; 32(3). PMID: 24531798
Highly Cited.
High-throughput characterization of Echinococcus spp. metacestode miRNomes.
Marcela Cucher, Natalia Macchiaroli, +3 authors, Mara Cecilia Rosenzvit.
Int J Parasitol, 2015 Feb 11; 45(4). PMID: 25659494
The NIH Extracellular RNA Communication Consortium.
Alexandra M Ainsztein, Philip J Brooks, +18 authors, Sundar Venkatachalam.
J Extracell Vesicles, 2015 Sep 01; 4. PMID: 26320938    Free PMC article.
Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer.
Soonmyung Paik, Gong Tang, +11 authors, Norman Wolmark.
J Clin Oncol, 2006 May 25; 24(23). PMID: 16720680
Highly Cited.
Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.
Debora Fumagalli, Alexis Blanchet-Cohen, +13 authors, Benjamin Haibe-Kains.
BMC Genomics, 2014 Nov 22; 15. PMID: 25412710    Free PMC article.
Analytical validation of the Oncotype DX prostate cancer assay - a clinical RT-PCR assay optimized for prostate needle biopsies.
Dejan Knezevic, Audrey D Goddard, +8 authors, Christopher Quale.
BMC Genomics, 2013 Oct 10; 14. PMID: 24103217    Free PMC article.
Highly Cited.
Chronic Myelogenous Leukemia, Version 1.2014.
Susan O'Brien, Jerald P Radich, +21 authors, Ntational comprehensive cancer network.
J Natl Compr Canc Netw, 2013 Nov 15; 11(11). PMID: 24225967    Free PMC article.
Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.
Mitesh J Borad, Mia D Champion, +46 authors, John D Carpten.
PLoS Genet, 2014 Feb 20; 10(2). PMID: 24550739    Free PMC article.
Highly Cited.
Breast cancer index identifies early-stage estrogen receptor-positive breast cancer patients at risk for early- and late-distant recurrence.
Yi Zhang, Catherine A Schnabel, +7 authors, Mark G Erlander.
Clin Cancer Res, 2013 Jun 13; 19(15). PMID: 23757354
Tau exon 10 alternative splicing and tauopathies.
Fei Liu, Cheng-Xin Gong.
Mol Neurodegener, 2008 Jul 12; 3. PMID: 18616804    Free PMC article.
Perspective for the development of companion diagnostics and regulatory landscape to encourage personalized medicine in Japan.
Yoshiaki Tazawa.
Breast Cancer, 2015 Jan 22; 23(1). PMID: 25605056
Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing.
Lucia Cavelier, Adam Ameur, +4 authors, Monica Hermanson.
BMC Cancer, 2015 Apr 17; 15. PMID: 25880391    Free PMC article.
Exosomes from human saliva as a source of microRNA biomarkers.
A Michael, S D Bajracharya, +4 authors, I Alevizos.
Oral Dis, 2009 Jul 25; 16(1). PMID: 19627513    Free PMC article.
Highly Cited.
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium.
Nat Biotechnol, 2014 Aug 26; 32(9). PMID: 25150838    Free PMC article.
Highly Cited.
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
Brian T Wilhelm, Samuel Marguerat, +6 authors, Jürg Bähler.
Nature, 2008 May 20; 453(7199). PMID: 18488015
Highly Cited.
Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
Shu-Jen Chen, Gian-Hung Chen, +4 authors, Hua-Chien Chen.
PLoS One, 2010 Sep 24; 5(9). PMID: 20862214    Free PMC article.
Analysis of small nucleolar RNAs in sputum for lung cancer diagnosis.
Jian Su, Jeipi Liao, +6 authors, Feng Jiang.
Oncotarget, 2015 Aug 08; 7(5). PMID: 26246471    Free PMC article.
An Oncogenic NTRK Fusion in a Patient with Soft-Tissue Sarcoma with Response to the Tropomyosin-Related Kinase Inhibitor LOXO-101.
Robert C Doebele, Lara E Davis, +13 authors, Jennifer A Low.
Cancer Discov, 2015 Jul 29; 5(10). PMID: 26216294    Free PMC article.
Highly Cited.
Altered lysosomal proteins in neural-derived plasma exosomes in preclinical Alzheimer disease.
Edward J Goetzl, Adam Boxer, +4 authors, Dimitrios Kapogiannis.
Neurology, 2015 Jun 13; 85(1). PMID: 26062630    Free PMC article.
Highly Cited.
A second-generation microRNA-based assay for diagnosing tumor tissue origin.
Eti Meiri, Wolf C Mueller, +18 authors, Ranit Aharonov.
Oncologist, 2012 May 24; 17(6). PMID: 22618571    Free PMC article.
GtRNAdb: a database of transfer RNA genes detected in genomic sequence.
Patricia P Chan, Todd M Lowe.
Nucleic Acids Res, 2008 Nov 06; 37(Database issue). PMID: 18984615    Free PMC article.
Highly Cited.
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
Peter A C 't Hoen, Marc R Friedländer, +16 authors, Tuuli Lappalainen.
Nat Biotechnol, 2013 Sep 17; 31(11). PMID: 24037425
Highly Cited.
The impact of Docker containers on the performance of genomic pipelines.
Paolo Di Tommaso, Emilio Palumbo, +3 authors, Cedric Notredame.
PeerJ, 2015 Oct 01; 3. PMID: 26421241    Free PMC article.
An international interpretation study using the ALK IHC antibody D5F3 and a sensitive detection kit demonstrates high concordance between ALK IHC and ALK FISH and between evaluators.
Murry W Wynes, Lynette M Sholl, +5 authors, Fred R Hirsch.
J Thorac Oncol, 2014 Apr 12; 9(5). PMID: 24722153    Free PMC article.
Highly Cited.
Characterization of three alternative transcripts of the BRCA1 gene in patients with breast cancer and a family history of breast and/or ovarian cancer who tested negative for pathogenic mutations.
Gaetana Gambino, Mariella Tancredi, +2 authors, Maria Adelaide Caligo.
Int J Mol Med, 2015 Feb 17; 35(4). PMID: 25683334    Free PMC article.
MicroRNA signatures from multidrug‑resistant Mycobacterium tuberculosis.
Na Ren, Guiju Gao, +5 authors, Xingwang Li.
Mol Med Rep, 2015 Sep 02; 12(5). PMID: 26324150    Free PMC article.
A comparative study of techniques for differential expression analysis on RNA-Seq data.
Zong Hong Zhang, Dhanisha J Jhaveri, +8 authors, Qiong-Yi Zhao.
PLoS One, 2014 Aug 15; 9(8). PMID: 25119138    Free PMC article.
Highly Cited.
Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.
Tim R Mercer, Michael B Clark, +6 authors, John S Mattick.
Nat Protoc, 2014 Apr 08; 9(5). PMID: 24705597
Prospective Validation of a 21-Gene Expression Assay in Breast Cancer.
Joseph A Sparano, Robert J Gray, +28 authors, George W Sledge.
N Engl J Med, 2015 Sep 29; 373(21). PMID: 26412349    Free PMC article.
Highly Cited.
Molecular testing for selection of patients with lung cancer for epidermal growth factor receptor and anaplastic lymphoma kinase tyrosine kinase inhibitors: American Society of Clinical Oncology endorsement of the College of American Pathologists/International Association for the study of lung cancer/association for molecular pathology guideline.
Natasha B Leighl, Natasha Rekhtman, +6 authors, Mark R Somerfield.
J Clin Oncol, 2014 Oct 15; 32(32). PMID: 25311215    Free PMC article.
Highly Cited.
Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes.
Yan Guo, Amma Bosompem, +11 authors, Annette S Kim.
BMC Genomics, 2015 Sep 25; 16. PMID: 26400237    Free PMC article.
Germline allele-specific expression of TGFBR1 confers an increased risk of colorectal cancer.
Laura Valle, Tarsicio Serena-Acedo, +10 authors, Albert de la Chapelle.
Science, 2008 Aug 16; 321(5894). PMID: 18703712    Free PMC article.
Validation of a cell-cycle progression gene panel to improve risk stratification in a contemporary prostatectomy cohort.
Matthew R Cooperberg, Jeffry P Simko, +8 authors, Peter R Carroll.
J Clin Oncol, 2013 Mar 06; 31(11). PMID: 23460710
Highly Cited.
The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.
Anna K Andersson, Jing Ma, +48 authors, St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project.
Nat Genet, 2015 Mar 03; 47(4). PMID: 25730765    Free PMC article.
Highly Cited.
The microRNA Transcriptome of Human Cytomegalovirus (HCMV).
Mesfin K Meshesha, Isana Veksler-Lublinsky, +6 authors, Yonat Shemer Avni.
Open Virol J, 2012 Jun 21; 6. PMID: 22715351    Free PMC article.
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.
Waibhav D Tembe, Stephanie J K Pond, +8 authors, John D Carpten.
BMC Genomics, 2014 Oct 01; 15. PMID: 25266161    Free PMC article.
Using circular RNA as a novel type of biomarker in the screening of gastric cancer.
Peifei Li, Shengcan Chen, +5 authors, Junming Guo.
Clin Chim Acta, 2015 Feb 18; 444. PMID: 25689795
Highly Cited.
Molecular profiling diagnosis in unknown primary cancer: accuracy and ability to complement standard pathology.
F Anthony Greco, Wayne J Lennington, David R Spigel, John D Hainsworth.
J Natl Cancer Inst, 2013 May 04; 105(11). PMID: 23641043
Differential and limited expression of mutant alleles in multiple myeloma.
Naim U Rashid, Adam S Sperling, +15 authors, Nikhil C Munshi.
Blood, 2014 Sep 23; 124(20). PMID: 25237203    Free PMC article.
A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, +15 authors, Mark J Daly.
Nat Genet, 2011 Apr 12; 43(5). PMID: 21478889    Free PMC article.
Highly Cited.
Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression.
Nicholas B Larson, Shannon McDonnell, +9 authors, Stephen N Thibodeau.
Am J Hum Genet, 2015 May 20; 96(6). PMID: 25983244    Free PMC article.
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.
Charles Wang, Binsheng Gong, +43 authors, Weida Tong.
Nat Biotechnol, 2014 Aug 26; 32(9). PMID: 25150839    Free PMC article.
Highly Cited.
HCV genotype 3 is associated with an increased risk of cirrhosis and hepatocellular cancer in a national sample of U.S. Veterans with HCV.
Fasiha Kanwal, Jennifer R Kramer, +2 authors, Hashem B El-Serag.
Hepatology, 2014 Mar 13; 60(1). PMID: 24615981    Free PMC article.
Highly Cited.
Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection.
Iwijn De Vlaminck, Hannah A Valantine, +9 authors, Kiran K Khush.
Sci Transl Med, 2014 Jun 20; 6(241). PMID: 24944192    Free PMC article.
Highly Cited.
Splicing: is there an alternative contribution to Parkinson's disease?
Valentina La Cognata, Velia D'Agata, Francesca Cavalcanti, Sebastiano Cavallaro.
Neurogenetics, 2015 May 20; 16(4). PMID: 25980689    Free PMC article.
An integrated framework for reporting clinically relevant biomarkers from paired tumor/normal genomic and transcriptomic sequencing data in support of clinical trials in personalized medicine.
Sara Nasser, Ahmet A Kurdolgu, +14 authors, David W Craig.
Pac Symp Biocomput, 2015 Jan 17;. PMID: 25592568
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.
Zhou Du, Teng Fei, +5 authors, X Shirley Liu.
Nat Struct Mol Biol, 2013 Jun 04; 20(7). PMID: 23728290    Free PMC article.
Highly Cited.
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
John C Marioni, Christopher E Mason, +2 authors, Yoav Gilad.
Genome Res, 2008 Jun 14; 18(9). PMID: 18550803    Free PMC article.
Highly Cited.
The extracellular RNA complement of Escherichia coli.
Anubrata Ghosal, Bimal Babu Upadhyaya, +8 authors, Paul Wilmes.
Microbiologyopen, 2015 Jan 23; 4(2). PMID: 25611733    Free PMC article.
Transmitted/founder hepatitis C viruses induce cell-type- and genotype-specific differences in innate signaling within the liver.
Angela M Mitchell, Amy E L Stone, +8 authors, Hugo R Rosen.
mBio, 2015 Feb 26; 6(2). PMID: 25714713    Free PMC article.
Serial analysis of gene expression.
V E Velculescu, L Zhang, B Vogelstein, K W Kinzler.
Science, 1995 Oct 20; 270(5235). PMID: 7570003
Highly Cited.
Development and verification of the PAM50-based Prosigna breast cancer gene signature assay.
Brett Wallden, James Storhoff, +16 authors, Joel S Parker.
BMC Med Genomics, 2015 Aug 25; 8. PMID: 26297356    Free PMC article.
Highly Cited.
Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells.
Hadi Valadi, Karin Ekström, +3 authors, Jan O Lötvall.
Nat Cell Biol, 2007 May 09; 9(6). PMID: 17486113
Highly Cited.
RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder.
Nat Rev Genet, 2008 Nov 19; 10(1). PMID: 19015660    Free PMC article.
Highly Cited. Review.
Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.
Neal I Lindeman, Philip T Cagle, +9 authors, Marc Ladanyi.
Arch Pathol Lab Med, 2013 Apr 05; 137(6). PMID: 23551194    Free PMC article.
Highly Cited.
Translating tumor biology into personalized treatment planning: analytical performance characteristics of the Oncotype DX Colon Cancer Assay.
Kim M Clark-Langone, Chithra Sangli, Jayadevi Krishnakumar, Drew Watson.
BMC Cancer, 2010 Dec 24; 10. PMID: 21176237    Free PMC article.
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.
Marcin Cieslik, Rashmi Chugh, +11 authors, Dan Robinson.
Genome Res, 2015 Aug 09; 25(9). PMID: 26253700    Free PMC article.
Highly Cited.
Clinical and molecular characterization of a cohort of patients with novel nucleotide alterations of the Dystrophin gene detected by direct sequencing.
Francesca Magri, Roberto Del Bo, +14 authors, Giacomo P Comi.
BMC Med Genet, 2011 Mar 15; 12. PMID: 21396098    Free PMC article.
Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood.
Sebastian Memczak, Panagiotis Papavasileiou, Oliver Peters, Nikolaus Rajewsky.
PLoS One, 2015 Oct 21; 10(10). PMID: 26485708    Free PMC article.
Highly Cited.
ACMG clinical laboratory standards for next-generation sequencing.
Heidi L Rehm, Sherri J Bale, +8 authors, Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee.
Genet Med, 2013 Jul 28; 15(9). PMID: 23887774    Free PMC article.
Highly Cited.
Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling.
M C Deng, H J Eisen, +17 authors, CARGO Investigators.
Am J Transplant, 2006 Jan 26; 6(1). PMID: 16433769
Highly Cited.
Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium.
Louise C Laurent, Asim B Abdel-Mageed, +47 authors, Stephen Gould.
J Extracell Vesicles, 2015 Sep 01; 4. PMID: 26320937    Free PMC article.
Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Manuel A Rivas, Matti Pirinen, +36 authors, Daniel G MacArthur.
Science, 2015 May 09; 348(6235). PMID: 25954003    Free PMC article.
Highly Cited.
Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs.
Helena Kelly, Tim Downing, +6 authors, Kate Reddington.
PLoS One, 2015 Sep 12; 10(9). PMID: 26355751    Free PMC article.
Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection.
Lawrence Shih-Hsin Wu, Shih-Wei Lee, +3 authors, Julia Tzu-Ya Weng.
Biomed Res Int, 2014 Oct 03; 2014. PMID: 25276827    Free PMC article.
Tools and best practices for data processing in allelic expression analysis.
Stephane E Castel, Ami Levy-Moonshine, +2 authors, Tuuli Lappalainen.
Genome Biol, 2015 Sep 19; 16. PMID: 26381377    Free PMC article.
Highly Cited.
AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer.
Emmanuel S Antonarakis, Changxue Lu, +18 authors, Jun Luo.
N Engl J Med, 2014 Sep 04; 371(11). PMID: 25184630    Free PMC article.
Highly Cited.
Molecular testing in the management of cardiac transplant recipients: initial clinical experience.
Randall C Starling, Michael Pham, +12 authors, Working Group on Molecular Testing in Cardiac Transplantation.
J Heart Lung Transplant, 2006 Dec 21; 25(12). PMID: 17178330
Expression of the stem cell self-renewal gene Hiwi and risk of tumour-related death in patients with soft-tissue sarcoma.
H Taubert, T Greither, +12 authors, S Hauptmann.
Oncogene, 2006 Sep 06; 26(7). PMID: 16953229
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
Sarah A Munro, Steven P Lund, +30 authors, Marc Salit.
Nat Commun, 2014 Sep 26; 5. PMID: 25254650
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, +2 authors, Barbara Wold.
Nat Methods, 2008 Jun 03; 5(7). PMID: 18516045
Highly Cited.
Real time quantitative PCR.
C A Heid, J Stevens, K J Livak, P M Williams.
Genome Res, 1996 Oct 01; 6(10). PMID: 8908518
Highly Cited.
Individualization of therapy using Mammaprint: from development to the MINDACT Trial.
Stella Mook, Laura J Van't Veer, +2 authors, Fatima Cardoso.
Cancer Genomics Proteomics, 2007 Sep 20; 4(3). PMID: 17878518
Epigenetic events regulating monoallelic gene expression.
Shabnam Massah, Timothy V Beischlag, Gratien G Prefontaine.
Crit Rev Biochem Mol Biol, 2015 Jul 15; 50(4). PMID: 26155735
Synthetic spike-in standards for RNA-seq experiments.
Lichun Jiang, Felix Schlesinger, +5 authors, Brian Oliver.
Genome Res, 2011 Aug 06; 21(9). PMID: 21816910    Free PMC article.
Highly Cited.
Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus.
Gilberto A Santiago, Edgardo Vergne, +7 authors, Jorge L Muñoz-Jordán.
PLoS Negl Trop Dis, 2013 Jul 23; 7(7). PMID: 23875046    Free PMC article.
Highly Cited.
A novel whole-blood miRNA signature for a rapid diagnosis of pulmonary tuberculosis.
Irene Latorre, Petra Leidinger, +12 authors, Andreas Meyerhans.
Eur Respir J, 2015 Feb 07; 45(4). PMID: 25657026
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.
Alexander J Westermann, Konrad U Förstner, +7 authors, Jörg Vogel.
Nature, 2016 Jan 21; 529(7587). PMID: 26789254
Highly Cited.
Splicing of a novel androgen receptor exon generates a constitutively active androgen receptor that mediates prostate cancer therapy resistance.
Scott M Dehm, Lucy J Schmidt, +2 authors, Donald J Tindall.
Cancer Res, 2008 Jul 03; 68(13). PMID: 18593950    Free PMC article.
Highly Cited.
The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes.
James W Vardiman, Jüergen Thiele, +8 authors, Clara D Bloomfield.
Blood, 2009 Apr 10; 114(5). PMID: 19357394
Highly Cited. Review.
The noncoding RNA revolution-trashing old rules to forge new ones.
Thomas R Cech, Joan A Steitz.
Cell, 2014 Apr 01; 157(1). PMID: 24679528
Highly Cited. Review.
Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy.
Nicholas Erho, Anamaria Crisan, +16 authors, Robert B Jenkins.
PLoS One, 2013 Jul 05; 8(6). PMID: 23826159    Free PMC article.
Highly Cited.
Alternative splicing in cancer: implications for biology and therapy.
J Chen, W A Weiss.
Oncogene, 2014 Jan 21; 34(1). PMID: 24441040
Highly Cited. Review.
The complex exogenous RNA spectra in human plasma: an interface with human gut biota?
Kai Wang, Hong Li, +5 authors, David Galas.
PLoS One, 2012 Dec 20; 7(12). PMID: 23251414    Free PMC article.
Highly Cited.
Cancer drug development and the evolving regulatory framework for companion diagnostics in the European union.
Francesco Pignatti, Falk Ehmann, +5 authors, Guido Rasi.
Clin Cancer Res, 2014 Mar 19; 20(6). PMID: 24634469
Extracellular RNAs: development as biomarkers of human disease.
Joseph F Quinn, Tushar Patel, +16 authors, Julie A Saugstad.
J Extracell Vesicles, 2015 Sep 01; 4. PMID: 26320940    Free PMC article.
Expression monitoring by hybridization to high-density oligonucleotide arrays.
D J Lockhart, H Dong, +8 authors, E L Brown.
Nat Biotechnol, 1996 Dec 01; 14(13). PMID: 9634850
Highly Cited.
Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.
David W Craig, Joyce A O'Shaughnessy, +25 authors, John D Carpten.
Mol Cancer Ther, 2012 Nov 23; 12(1). PMID: 23171949
Highly Cited.
Plasma exosomal α-synuclein is likely CNS-derived and increased in Parkinson's disease.
Min Shi, Changqin Liu, +15 authors, Jing Zhang.
Acta Neuropathol, 2014 Jul 07; 128(5). PMID: 24997849    Free PMC article.
Highly Cited.
The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, +7 authors, 1000 Genome Project Data Processing Subgroup.
Bioinformatics, 2009 Jun 10; 25(16). PMID: 19505943    Free PMC article.
Highly Cited.
Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial.
Kathy S Albain, William E Barlow, +20 authors, Breast Cancer Intergroup of North America.
Lancet Oncol, 2009 Dec 17; 11(1). PMID: 20005174    Free PMC article.
Highly Cited.
Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia.
B J Druker, M Talpaz, +8 authors, C L Sawyers.
N Engl J Med, 2001 Apr 05; 344(14). PMID: 11287972
Highly Cited.
Performance of five FDA-approved rapid antigen tests in the detection of 2009 H1N1 influenza A virus.
Deena E Sutter, Sue A Worthy, +4 authors, Luke T Daum.
J Med Virol, 2012 Sep 22; 84(11). PMID: 22997071
Normalization of RNA-seq data using factor analysis of control genes or samples.
Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit.
Nat Biotechnol, 2014 Aug 26; 32(9). PMID: 25150836    Free PMC article.
Highly Cited.
Biogenesis, delivery, and function of extracellular RNA.
James G Patton, Jeffrey L Franklin, +16 authors, Michael T McManus.
J Extracell Vesicles, 2015 Sep 01; 4. PMID: 26320939    Free PMC article.
Global transcriptome analysis reveals small RNAs affecting Neisseria meningitidis bacteremia.
Luca Fagnocchi, Silvia Bottini, +10 authors, Isabel Delany.
PLoS One, 2015 May 08; 10(5). PMID: 25951061    Free PMC article.
Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.
Szabolcs Szelinger, Ivana Malenica, +8 authors, David W Craig.
PLoS One, 2014 Dec 17; 9(12). PMID: 25503791    Free PMC article.
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
Wei Zhao, Xiaping He, +3 authors, Charles M Perou.
BMC Genomics, 2014 Jun 04; 15. PMID: 24888378    Free PMC article.
Highly Cited.
Guidelines for diagnostic next-generation sequencing.
Gert Matthijs, Erika Souche, +13 authors, European Society of Human Genetics.
Eur J Hum Genet, 2015 Oct 29; 24(1). PMID: 26508566    Free PMC article.
Highly Cited.
Optimal Molecular Methods in Detecting p190 (BCR-ABL) Fusion Variants in Hematologic Malignancies: A Case Report and Review of the Literature.
Rebecca J Sonu, Brian A Jonas, +2 authors, Hooman H Rashidi.
Case Rep Hematol, 2015 May 08; 2015. PMID: 25949834    Free PMC article.
The FDA and genomic tests--getting regulation right.
Barbara J Evans, Wylie Burke, Gail P Jarvik.
N Engl J Med, 2015 May 28; 372(23). PMID: 26014592    Free PMC article.
Validation and clinical use of a sensitive HIV-2 viral load assay that uses a whole virus internal control.
Linda M Styer, Thomas T Miller, Monica M Parker.
J Clin Virol, 2013 Dec 18; 58 Suppl 1. PMID: 24342472
Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus.
Benjamin A Pinsky, Malaya K Sahoo, +18 authors, David H Persing.
PLoS One, 2015 Nov 13; 10(11). PMID: 26562786    Free PMC article.
Evaluating the effect of spastin splice mutations by quantitative allele-specific expression assay.
S Klimpe, A Zibat, +5 authors, A U Mannan.
Eur J Neurol, 2010 May 25; 18(1). PMID: 20491894
Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma.
Alexander Baraniskin, Stefanie Nöpel-Dünnebacke, +22 authors, Stephan A Hahn.
Int J Cancer, 2012 Aug 22; 132(2). PMID: 22907602
FGFR3-TACC3 fusion in solid tumors: mini review.
Ricardo Costa, Benedito A Carneiro, +5 authors, Francis J Giles.
Oncotarget, 2016 Jul 14; 7(34). PMID: 27409839    Free PMC article.
A sensitive DNA capacitive biosensor using interdigitated electrodes.
Lei Wang, Milena Veselinovic, +3 authors, Tom Chen.
Biosens Bioelectron, 2016 Sep 14; 87. PMID: 27619528    Free PMC article.
Impact of RNA degradation on fusion detection by RNA-seq.
Jaime I Davila, Numrah M Fadra, +12 authors, Kevin C Halling.
BMC Genomics, 2016 Oct 22; 17(1). PMID: 27765019    Free PMC article.
Emerging technologies for salivaomics in cancer detection.
Karolina Elżbieta Kaczor-Urbanowicz, Carmen Martín Carreras-Presas, +4 authors, David T W Wong.
J Cell Mol Med, 2016 Nov 20; 21(4). PMID: 27862926    Free PMC article.
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences.
Claudia Manzoni, Demis A Kia, +4 authors, Raffaele Ferrari.
Brief Bioinform, 2016 Nov 25; 19(2). PMID: 27881428    Free PMC article.
Highly Cited. Review.
Plasma vesicle miRNAs for therapy response monitoring in Hodgkin lymphoma patients.
Monique Aj van Eijndhoven, Josée M Zijlstra, +14 authors, D Michiel Pegtel.
JCI Insight, 2016 Nov 25; 1(19). PMID: 27882350    Free PMC article.
Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls.
Peter Horak, Stefan Fröhling, Hanno Glimm.
ESMO Open, 2016 Dec 10; 1(5). PMID: 27933214    Free PMC article.
Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts.
Wenjing Kang, Claus Heiner Bang-Berthelsen, +6 authors, Marc R Friedländer.
RNA, 2017 Jan 08; 23(4). PMID: 28062594    Free PMC article.
The PeptideAtlas of the Domestic Laying Hen.
James McCord, Zhi Sun, +2 authors, David C Muddiman.
J Proteome Res, 2017 Feb 09; 16(3). PMID: 28166638    Free PMC article.
Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy.
Till S M Mathan, Johannes Textor, +7 authors, I Jolanda M de Vries.
Oncotarget, 2017 Feb 12; 8(12). PMID: 28186996    Free PMC article.
Comparative RNA-Seq transcriptome analyses reveal distinct metabolic pathways in diabetic nerve and kidney disease.
Lucy M Hinder, Meeyoung Park, +6 authors, Eva L Feldman.
J Cell Mol Med, 2017 Mar 09; 21(9). PMID: 28272773    Free PMC article.
Potential Use of MicroRNA for Monitoring Therapeutic Response to Antidepressants.
Raoul Belzeaux, Rixing Lin, Gustavo Turecki.
CNS Drugs, 2017 Mar 16; 31(4). PMID: 28290081
Effect of method of deduplication on estimation of differential gene expression using RNA-seq.
Anna V Klepikova, Artem S Kasianov, +3 authors, Maria Logacheva.
PeerJ, 2017 Mar 23; 5. PMID: 28321364    Free PMC article.
Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era.
Sixto M Leal, Margaret L Gulley.
J Mol Diagn, 2017 Mar 23; 19(3). PMID: 28325688    Free PMC article.
Modeling bias and variation in the stochastic processes of small RNA sequencing.
Christos Argyropoulos, Alton Etheridge, Nikita Sakhanenko, David Galas.
Nucleic Acids Res, 2017 Apr 04; 45(11). PMID: 28369495    Free PMC article.
Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, +3 authors, Cedric Notredame.
Nat Biotechnol, 2017 Apr 12; 35(4). PMID: 28398311
Highly Cited.
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.
Beryl B Cummings, Jamie L Marshall, +36 authors, Daniel G MacArthur.
Sci Transl Med, 2017 Apr 21; 9(386). PMID: 28424332    Free PMC article.
Highly Cited.
Fluorescence in situ hybridization in surgical pathology: principles and applications.
Liang Cheng, Shaobo Zhang, +2 authors, Darrell D Davidson.
J Pathol Clin Res, 2017 Apr 30; 3(2). PMID: 28451457    Free PMC article.
Transcriptomics technologies.
Rohan Lowe, Neil Shirley, +2 authors, Thomas Shafee.
PLoS Comput Biol, 2017 May 26; 13(5). PMID: 28545146    Free PMC article.
Highly Cited.
Analysis of in vivo Interaction between RNA Binding Proteins and Their RNA Targets by UV Cross-linking and Immunoprecipitation (CLIP) Method.
Pamela Bielli, Claudio Sette.
Bio Protoc, 2017 Jun 03; 7(10). PMID: 28573168    Free PMC article.
A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.
Sven Schuierer, Walter Carbone, +4 authors, Guglielmo Roma.
BMC Genomics, 2017 Jun 07; 18(1). PMID: 28583074    Free PMC article.
Reference standards for next-generation sequencing.
Simon A Hardwick, Ira W Deveson, Tim R Mercer.
Nat Rev Genet, 2017 Jun 20; 18(8). PMID: 28626224
Highly Cited. Review.
Managing the genomic revolution in cancer diagnostics.
Doreen Nguyen, Christopher D Gocke.
Virchows Arch, 2017 Jun 24; 471(2). PMID: 28639053
Integrating personalized gene expression profiles into predictive disease-associated gene pools.
Jörg Menche, Emre Guney, +5 authors, Albert-László Barabási.
NPJ Syst Biol Appl, 2017 Jun 27; 3. PMID: 28649437    Free PMC article.
Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.
Mu Zhou, Ann Leung, +8 authors, Olivier Gevaert.
Radiology, 2017 Jul 21; 286(1). PMID: 28727543    Free PMC article.
'Lnc'-ing Wnt in female reproductive cancers: therapeutic potential of long non-coding RNAs in Wnt signalling.
Mei S Ong, Wanpei Cai, +14 authors, Alan P Kumar.
Br J Pharmacol, 2017 Jul 25; 174(24). PMID: 28736855    Free PMC article.
Transcriptome Analysis of Canine Cutaneous Melanoma and Melanocytoma Reveals a Modulation of Genes Regulating Extracellular Matrix Metabolism and Cell Cycle.
Chiara Brachelente, Katia Cappelli, +7 authors, Monica Sforna.
Sci Rep, 2017 Jul 27; 7(1). PMID: 28743863    Free PMC article.
Integrating RNA sequencing into neuro-oncology practice.
David S Rogawski, Nicholas A Vitanza, +2 authors, Carl Koschmann.
Transl Res, 2017 Jul 27; 189. PMID: 28746860    Free PMC article.
Transcriptome Profiling in Human Diseases: New Advances and Perspectives.
Amelia Casamassimi, Antonio Federico, +2 authors, Alfredo Ciccodicola.
Int J Mol Sci, 2017 Aug 02; 18(8). PMID: 28758927    Free PMC article.
Highly Cited. Review.
Integrative clinical genomics of metastatic cancer.
Dan R Robinson, Yi-Mi Wu, +30 authors, Arul M Chinnaiyan.
Nature, 2017 Aug 08; 548(7667). PMID: 28783718    Free PMC article.
Highly Cited.
A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.
Nicholas F Lahens, Emanuela Ricciotti, +7 authors, Gregory R Grant.
BMC Genomics, 2017 Aug 12; 18(1). PMID: 28797240    Free PMC article.
The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.
Ashwini Kumar, Matti Kankainen, +3 authors, Caroline A Heckman.
BMC Genomics, 2017 Aug 19; 18(1). PMID: 28818039    Free PMC article.
3D brain Organoids derived from pluripotent stem cells: promising experimental models for brain development and neurodegenerative disorders.
Chun-Ting Lee, Raphael M Bendriem, Wells W Wu, Rong-Fong Shen.
J Biomed Sci, 2017 Aug 22; 24(1). PMID: 28822354    Free PMC article.
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.
Jérôme Audoux, Mikaël Salson, +4 authors, Nicolas Philippe.
BMC Bioinformatics, 2017 Oct 04; 18(1). PMID: 28969586    Free PMC article.
Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.
Anna M Kietrys, Willem A Velema, Eric T Kool.
J Am Chem Soc, 2017 Nov 08; 139(47). PMID: 29111692    Free PMC article.
A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries.
Yuguang Xiong, Magali Soumillon, +20 authors, Marc R Birtwistle.
Sci Rep, 2017 Nov 09; 7(1). PMID: 29116112    Free PMC article.
Oestrogen receptor beta isoform expression in sporadic colorectal cancer, familial adenomatous polyposis and progressive stages of colorectal cancer.
Paulo Roberto Stevanato Filho, Samuel Aguiar Júnior, +9 authors, Ademar Lopes.
BMC Cancer, 2017 Nov 15; 17(1). PMID: 29132333    Free PMC article.
RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy.
Candice P Chu, Jessica A Hokamp, +4 authors, Mary B Nabity.
Sci Rep, 2017 Dec 03; 7(1). PMID: 29196624    Free PMC article.
Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis.
Zhongqing Qian, Hui Liu, +15 authors, Wanjun Gu.
EBioMedicine, 2017 Dec 19; 27. PMID: 29248507    Free PMC article.
Cancer transcriptome profiling at the juncture of clinical translation.
Marcin Cieślik, Arul M Chinnaiyan.
Nat Rev Genet, 2017 Dec 28; 19(2). PMID: 29279605
The Expanding Landscape of Alternative Splicing Variation in Human Populations.
Eddie Park, Zhicheng Pan, +2 authors, Yi Xing.
Am J Hum Genet, 2018 Jan 06; 102(1). PMID: 29304370    Free PMC article.
Highly Cited. Review.
Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals.
Stephen Y Chan, Jonathan W Snow.
Genes Nutr, 2018 Jan 09; 12. PMID: 29308096    Free PMC article.
"Transcriptomics": molecular diagnosis of inborn errors of metabolism via RNA-sequencing.
Laura S Kremer, Saskia B Wortmann, Holger Prokisch.
J Inherit Metab Dis, 2018 Jan 27; 41(3). PMID: 29372369    Free PMC article.
Combining asymmetric PCR-based enzymatic amplification with silicon photonic microring resonators for the detection of lncRNAs from low input human RNA samples.
Maria C Cardenosa-Rubio, Richard M Graybill, Ryan C Bailey.
Analyst, 2018 Feb 13; 143(5). PMID: 29431756    Free PMC article.
Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
Tetsutaro Hayashi, Haruka Ozaki, +3 authors, Itoshi Nikaido.
Nat Commun, 2018 Feb 13; 9(1). PMID: 29434199    Free PMC article.
Highly Cited.
Control of Infectious Diseases in the Era of European Clinical Microbiology Laboratory Consolidation: New Challenges and Opportunities for the Patient and for Public Health Surveillance.
Olivier Vandenberg, Zisis Kozlakidis, +2 authors, Judith Breuer.
Front Med (Lausanne), 2018 Feb 20; 5. PMID: 29457001    Free PMC article.
Platforms for Single-Cell Collection and Analysis.
Lukas Valihrach, Peter Androvic, Mikael Kubista.
Int J Mol Sci, 2018 Mar 15; 19(3). PMID: 29534489    Free PMC article.
Lung cancer health disparities.
Bríd M Ryan.
Carcinogenesis, 2018 Mar 17; 39(6). PMID: 29547922    Free PMC article.
Circular noncoding RNAs as potential therapies and circulating biomarkers for cardiovascular diseases.
Ahmed S Bayoumi, Tatsuya Aonuma, +2 authors, Il-Man Kim.
Acta Pharmacol Sin, 2018 Mar 23; 39(7). PMID: 29565037    Free PMC article.
Developing a genetic signature to predict drug response in ovarian cancer.
Stephen Hyter, Jeff Hirst, +5 authors, Andrew K Godwin.
Oncotarget, 2018 Mar 31; 9(19). PMID: 29599910    Free PMC article.
Small non-coding RNAs are altered by short-term sprint interval training in men.
Joshua Denham, Adrian J Gray, +2 authors, Aron J Murphy.
Physiol Rep, 2018 Apr 04; 6(7). PMID: 29611322    Free PMC article.
New chimeric RNAs in acute myeloid leukemia.
Florence Rufflé, Jerome Audoux, +14 authors, Therese Commes.
F1000Res, 2018 Apr 10; 6. PMID: 29623188    Free PMC article.
Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation.
Leila Taher, Julia Beck, +13 authors, Hugo Murua Escobar.
Sci Rep, 2018 Apr 21; 8(1). PMID: 29674676    Free PMC article.
Profiling of 179 miRNA Expression in Blood Plasma of Lung Cancer Patients and Cancer-Free Individuals.
Ivan A Zaporozhchenko, Evgeny S Morozkin, +7 authors, Pavel P Laktionov.
Sci Rep, 2018 Apr 22; 8(1). PMID: 29679068    Free PMC article.
Evaluation of commercially available small RNASeq library preparation kits using low input RNA.
Ashish Yeri, Amanda Courtright, +10 authors, Kendall Van Keuren-Jensen.
BMC Genomics, 2018 May 08; 19(1). PMID: 29728066    Free PMC article.
Diversity and signature of small RNA in different bodily fluids using next generation sequencing.
Mohamed El-Mogy, Bernard Lam, +6 authors, Yousef Haj-Ahmad.
BMC Genomics, 2018 May 31; 19(1). PMID: 29843592    Free PMC article.
Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.
Jialu Li, Chunxiao Fu, +2 authors, W Fraser Symmans.
JCO Precis Oncol, 2018 Jun 05; 2018. PMID: 29862382    Free PMC article.
Co-fuse: a new class discovery analysis tool to identify and prioritize recurrent fusion genes from RNA-sequencing data.
Sakrapee Paisitkriangkrai, Kelly Quek, +3 authors, Chung Hoow Kok.
Mol Genet Genomics, 2018 Jun 09; 293(5). PMID: 29882166
viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors.
Krithika Bhuvaneshwar, Lei Song, Subha Madhavan, Yuriy Gusev.
Front Microbiol, 2018 Jun 21; 9. PMID: 29922260    Free PMC article.
Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers?
Nathan T Johnson, Andi Dhroso, Katelyn J Hughes, Dmitry Korkin.
RNA, 2018 Jun 27; 24(9). PMID: 29941426    Free PMC article.
RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue.
Kobe Reynders, Els Wauters, +10 authors, Dirk De Ruysscher.
Radiat Oncol, 2018 Jul 19; 13(1). PMID: 30016964    Free PMC article.
Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope?
Hetty Helsmoortel, Celine Everaert, +2 authors, Jo Vandesompele.
Noncoding RNA Res, 2018 Aug 31; 3(2). PMID: 30159441    Free PMC article.
TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.
Readman Chiu, Ka Ming Nip, Justin Chu, Inanc Birol.
BMC Med Genomics, 2018 Sep 12; 11(1). PMID: 30200994    Free PMC article.
Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine.
Naresh Prodduturi, Aditya Bhagwate, Jean-Pierre A Kocher, Zhifu Sun.
BMC Med Genomics, 2018 Sep 27; 11(Suppl 3). PMID: 30255803    Free PMC article.
Quantitative and synthetic biology approaches to combat bacterial pathogens.
Feilun Wu, Jonathan H Bethke, Meidi Wang, Lingchong You.
Curr Opin Biomed Eng, 2018 Sep 29; 4. PMID: 30263975    Free PMC article.
Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens.
T L Masters, C A Hilker, +9 authors, R Patel.
J Microbiol Methods, 2018 Oct 18; 154. PMID: 30332617    Free PMC article.
TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.
Pedro Seoane, Marina Espigares, +8 authors, M Gonzalo Claros.
BMC Bioinformatics, 2018 Nov 21; 19(Suppl 14). PMID: 30453874    Free PMC article.
Exploring the effect of library preparation on RNA sequencing experiments.
Lei Wang, Sara J Felts, +2 authors, Yuji Zhang.
Genomics, 2018 Dec 12; 111(6). PMID: 30529531    Free PMC article.
Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis.
Marielle H van den Esker, Ad P Koets.
Vet Sci, 2019 Jun 30; 6(3). PMID: 31247942    Free PMC article.
A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease.
Gavin R Oliver, Xiaojia Tang, +10 authors, Eric W Klee.
PLoS One, 2019 Oct 03; 14(10). PMID: 31577830    Free PMC article.
RNA-Seq Perspectives to Improve Clinical Diagnosis.
Guillermo Marco-Puche, Sergio Lois, Javier Benítez, Juan Carlos Trivino.
Front Genet, 2019 Nov 30; 10. PMID: 31781178    Free PMC article.
The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues.
Michal Marczyk, Chunxiao Fu, +7 authors, W Fraser Symmans.
BMC Cancer, 2019 Dec 07; 19(1). PMID: 31805884    Free PMC article.
Current and emerging biomarkers in metastatic colorectal cancer.
M K C Lee, J M Loree.
Curr Oncol, 2019 Dec 11; 26(Suppl 1). PMID: 31819705    Free PMC article.
QuantSeq. 3' Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis.
Susan M Corley, Niamh M Troy, Anthony Bosco, Marc R Wilkins.
Sci Rep, 2019 Dec 13; 9(1). PMID: 31827207    Free PMC article.
HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data.
Lydia Mok, Yongkang Kim, +4 authors, Taesung Park.
Genes (Basel), 2019 Nov 20; 10(11). PMID: 31739607    Free PMC article.
Intracerebral Hemorrhage Induces Inflammatory Gene Expression in Peripheral Blood: Global Transcriptional Profiling in Intracerebral Hemorrhage Patients.
Kyle B Walsh, Xiang Zhang, +4 authors, Opeolu Adeoye.
DNA Cell Biol, 2019 May 24; 38(7). PMID: 31120332    Free PMC article.
Biomarker potential of repetitive-element transcriptome in lung cancer.
Macarena Arroyo, Rocío Bautista, +2 authors, M Gonzalo Claros.
PeerJ, 2019 Dec 26; 7. PMID: 31875158    Free PMC article.
HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression data.
Lydia Mok, Taesung Park.
Genomics Inform, 2020 Jan 04; 17(4). PMID: 31896245    Free PMC article.
Whole Exome and Transcriptome RNA-Sequencing Model for the Diagnosis of Prostate Cancer.
Jason B Nikas, Nikos T Mitanis, Emily G Nikas.
ACS Omega, 2020 Jan 21; 5(1). PMID: 31956794    Free PMC article.
Modeling the effect of prolonged ethanol exposure on global gene expression and chromatin accessibility in normal 3D colon organoids.
Matthew Devall, Lucas T Jennelle, +4 authors, Graham Casey.
PLoS One, 2020 Jan 18; 15(1). PMID: 31951625    Free PMC article.
An Optimised Protocol Harnessing Laser Capture Microdissection for Transcriptomic Analysis on Matched Primary and Metastatic Colorectal Tumours.
Chin-Ann J Ong, Qiu Xuan Tan, +17 authors, Melissa C C Teo.
Sci Rep, 2020 Jan 22; 10(1). PMID: 31959771    Free PMC article.
Integrated profiling identifies SLC5A6 and MFAP2 as novel diagnostic and prognostic biomarkers in gastric cancer patients.
Tao Sun, Danhua Wang, +7 authors, Weiwei Liu.
Int J Oncol, 2020 Jan 03; 56(2). PMID: 31894266    Free PMC article.
Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies.
Xiaohong Li, Nigel G F Cooper, Timothy E O'Toole, Eric C Rouchka.
BMC Genomics, 2020 Jan 30; 21(1). PMID: 31992223    Free PMC article.
Circulating molecular biomarkers for screening or early diagnosis of colorectal cancer: which is ready for prime time?
Elisa Danese, Martina Montagnana, Giuseppe Lippi.
Ann Transl Med, 2020 Feb 13; 7(21). PMID: 32047771    Free PMC article.
A Novel Gene Signature-Based Model Predicts Biochemical Recurrence-Free Survival in Prostate Cancer Patients after Radical Prostatectomy.
Run Shi, Xuanwen Bao, +11 authors, Minglun Li.
Cancers (Basel), 2019 Dec 22; 12(1). PMID: 31861273    Free PMC article.
Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers.
Zhao Zhang, Youqiong Ye, +9 authors, Leng Han.
Commun Biol, 2018 Dec 28; 1. PMID: 30588513    Free PMC article.
Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples.
Marie-Ange Palomares, Cyril Dalmasso, +6 authors, Robert Olaso.
Sci Rep, 2019 May 19; 9(1). PMID: 31101892    Free PMC article.
Proteomics and phosphoproteomics in precision medicine: applications and challenges.
Girolamo Giudice, Evangelia Petsalaki.
Brief Bioinform, 2017 Oct 28; 20(3). PMID: 29077858    Free PMC article.
RNA sequencing data from neutrophils of patients with cystic fibrosis reveals potential for developing biomarkers for pulmonary exacerbations.
Kaiyu Jiang, Kerry E Poppenberg, +8 authors, James N Jarvis.
J Cyst Fibros, 2018 Jun 27; 18(2). PMID: 29941318    Free PMC article.
Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response.
Isabel Carrascoso, José Alcalde, +2 authors, José M Izquierdo.
PLoS One, 2018 Dec 12; 13(12). PMID: 30533021    Free PMC article.
Diagnosing rare diseases after the exome.
Laure Frésard, Stephen B Montgomery.
Cold Spring Harb Mol Case Stud, 2018 Dec 19; 4(6). PMID: 30559314    Free PMC article.
Nucleoside analogs in the study of the epitranscriptome.
Cody M Palumbo, Peter A Beal.
Methods, 2019 Mar 05; 156. PMID: 30827466    Free PMC article.
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.
Hernan D Gonorazky, Sergey Naumenko, +15 authors, James J Dowling.
Am J Hum Genet, 2019 Mar 05; 104(3). PMID: 30827497    Free PMC article.
Highly Cited.
Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees.
Thomas J Colgan, Isabel K Fletcher, +5 authors, Yannick Wurm.
Mol Ecol, 2019 Mar 08; 28(8). PMID: 30843300    Free PMC article.
Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.
Jerome Bouquet, Tony Li, +18 authors, Charles Y Chiu.
PLoS One, 2019 Mar 22; 14(3). PMID: 30897114    Free PMC article.
Catalyzing Transcriptomics Research in Cardiovascular Disease: The CardioRNA COST Action CA17129.
Clarissa Pedrosa da C Gomes, Bence Ágg, +52 authors, on behalf of the EU-CardioRNA COST Action (CA17129).
Noncoding RNA, 2019 Apr 03; 5(2). PMID: 30934986    Free PMC article.
Insights into rheumatic diseases from next-generation sequencing.
Laura T Donlin, Sung-Ho Park, +4 authors, Lionel B Ivashkiv.
Nat Rev Rheumatol, 2019 Apr 20; 15(6). PMID: 31000790    Free PMC article.
Bridging the gap between reference and real transcriptomes.
Antonin Morillon, Daniel Gautheret.
Genome Biol, 2019 Jun 05; 20(1). PMID: 31159855    Free PMC article.
RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB.
William C Reinhold, Sudhir Varma, +7 authors, Yves Pommier.
Cancer Res, 2019 May 23; 79(13). PMID: 31113817    Free PMC article.
exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.
Joel Rozowsky, Robert R Kitchen, +7 authors, Mark Gerstein.
Cell Syst, 2019 Apr 09; 8(4). PMID: 30956140    Free PMC article.
Feasibility of primary human cell cultures as a model for adamantinomatous craniopharyngioma research: Evidence from RNA-Seq analysis.
Pei-Dong Zhang, Chao-Hu Wang, +4 authors, Yi Liu.
Oncol Lett, 2020 Mar 21; 19(3). PMID: 32194734    Free PMC article.
Elevated TOP2A and UBE2C expressions correlate with poor prognosis in patients with surgically resected lung adenocarcinoma: a study based on immunohistochemical analysis and bioinformatics.
Wei Guo, Sijin Sun, +11 authors, Jie He.
J Cancer Res Clin Oncol, 2020 Feb 28; 146(4). PMID: 32103339
Pan-cancer systematic identification of lncRNAs associated with cancer prognosis.
Matthew Ung, Evelien Schaafsma, +2 authors, Chao Cheng.
PeerJ, 2020 Apr 02; 8. PMID: 32231885    Free PMC article.
Colorectal cancer screening: Assessment of CEACAM6, LGALS4, TSPAN8 and COL1A2 as blood markers in faecal immunochemical test negative subjects.
Enea Ferlizza, Rossella Solmi, +4 authors, Mattia Lauriola.
J Adv Res, 2020 Apr 08; 24. PMID: 32257432    Free PMC article.
The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine.
Sophia Doll, Florian Gnad, Matthias Mann.
Proteomics Clin Appl, 2019 Feb 23; 13(2). PMID: 30790462    Free PMC article.
Human papillomavirus 16E6/E7 activates autophagy via Atg9B and LAMP1 in cervical cancer cells.
Chen Tingting, Yang Shizhou, +4 authors, Xie Xing.
Cancer Med, 2019 Jun 20; 8(9). PMID: 31215164    Free PMC article.
Human in vitro models for understanding mechanisms of autism spectrum disorder.
Aaron Gordon, Daniel H Geschwind.
Mol Autism, 2020 Apr 18; 11(1). PMID: 32299488    Free PMC article.
Metatranscriptome of human faecal microbial communities in a cohort of adult men.
Galeb S Abu-Ali, Raaj S Mehta, +9 authors, Curtis Huttenhower.
Nat Microbiol, 2018 Jan 18; 3(3). PMID: 29335555    Free PMC article.
Highly Cited.
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.
Gloria M Sheynkman, Katharine S Tuttle, +11 authors, Marc Vidal.
Nat Commun, 2020 May 13; 11(1). PMID: 32393825    Free PMC article.
RNA-Seq Data-Mining Allows the Discovery of Two Long Non-Coding RNA Biomarkers of Viral Infection in Humans.
Ruth Barral-Arca, Alberto Gómez-Carballa, +6 authors, Antonio Salas.
Int J Mol Sci, 2020 Apr 25; 21(8). PMID: 32326627    Free PMC article.
Identification of the Potential Prognostic Markers from the miRNA-lncRNA-mRNA Interactions for Metastatic Renal Cancer via Next-Generation Sequencing and Bioinformatics.
I-Jeng Yeh, Kuan-Ting Liu, +4 authors, Po-Lin Kuo.
Diagnostics (Basel), 2020 Apr 23; 10(4). PMID: 32316228    Free PMC article.
Whole blood transcriptome profile at hospital admission discriminates between patients with ST-segment elevation and non-ST-segment elevation acute myocardial infarction.
Mattia Chiesa, Luca Piacentini, +4 authors, Gualtiero I Colombo.
Sci Rep, 2020 May 28; 10(1). PMID: 32457432    Free PMC article.
Profiling Extracellular Long RNA Transcriptome in Human Plasma and Extracellular Vesicles for Biomarker Discovery.
Rodosthenis S Rodosthenous, Elizabeth Hutchins, +8 authors, Saumya Das.
iScience, 2020 Jun 09; 23(6). PMID: 32512385    Free PMC article.
Brain Transcriptome Analysis Links Deficiencies of Stress-Responsive Proteins to the Pathomechanism of Kii ALS/PDC.
Satoru Morimoto, Mitsuru Ishikawa, +8 authors, Yasumasa Kokubo.
Antioxidants (Basel), 2020 May 20; 9(5). PMID: 32422904    Free PMC article.
Establishment and Validation of an Individualized Cell Cycle Process-Related Gene Signature to Predict Cancer-Specific Survival in Patients with Bladder Cancer.
Run Shi, Xuanwen Bao, +9 authors, Minglun Li.
Cancers (Basel), 2020 May 07; 12(5). PMID: 32370292    Free PMC article.
The missing heritability of familial colorectal cancer.
Stephanie A Schubert, Hans Morreau, Noel F C C de Miranda, Tom van Wezel.
Mutagenesis, 2019 Oct 13; 35(3). PMID: 31605533    Free PMC article.
An optimized workflow to improve reliability of detection of KIAA1549:BRAF fusions from RNA sequencing data.
Alexander C Sommerkamp, Sebastian Uhrig, +11 authors, David T W Jones.
Acta Neuropathol, 2020 Jun 02; 140(2). PMID: 32476062    Free PMC article.
A vaccine-induced gene expression signature correlates with protection against SIV and HIV in multiple trials.
Philip K Ehrenberg, Shida Shangguan, +17 authors, Rasmi Thomas.
Sci Transl Med, 2019 Aug 30; 11(507). PMID: 31462510    Free PMC article.
Genomic data imputation with variational auto-encoders.
Yeping Lina Qiu, Hong Zheng, Olivier Gevaert.
Gigascience, 2020 Aug 08; 9(8). PMID: 32761097    Free PMC article.
RNA-Sequencing of Umbilical Cord Blood to Investigate Spontaneous Preterm Birth: A Pilot Study.
Neeta L Vora, Joel S Parker, +3 authors, Kim A Boggess.
AJP Rep, 2019 Mar 12; 9(1). PMID: 30854245    Free PMC article.
Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research.
Isaac D Raplee, Alexei V Evsikov, Caralina Marín de Evsikova.
J Pers Med, 2019 Apr 17; 9(2). PMID: 30987214    Free PMC article.
Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis.
Cintia C Palu, Marcelo Ribeiro-Alves, +4 authors, Paul Walsh.
Front Genet, 2019 May 30; 10. PMID: 31139204    Free PMC article.
Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data.
Sadia Akter, Dong Xu, +4 authors, Trupti Joshi.
Front Genet, 2019 Sep 26; 10. PMID: 31552087    Free PMC article.
Genome-Wide Profiling of Prognostic Alternative Splicing Pattern in Pancreatic Cancer.
Min Yu, Weifeng Hong, +7 authors, Haosheng Jin.
Front Oncol, 2019 Sep 26; 9. PMID: 31552163    Free PMC article.
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.
Christian Brueffer, Sergii Gladchuk, +12 authors, Lao H Saal.
EMBO Mol Med, 2020 Sep 15; 12(10). PMID: 32926574    Free PMC article.
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients.
Shaoke Lou, Tianxiao Li, +3 authors, Mark Gerstein.
BMC Bioinformatics, 2020 Oct 17; 21(1). PMID: 33059594    Free PMC article.
Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection.
Silvia Pineda, Swastika Sur, +8 authors, Minnie M Sarwal.
Kidney Int Rep, 2020 Oct 27; 5(10). PMID: 33102963    Free PMC article.
The Problem of Microbial Dark Matter in Neonatal Sepsis.
Shamim A Sinnar, Steven J Schiff.
Emerg Infect Dis, 2020 Oct 21; 26(11). PMID: 33080169    Free PMC article.
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data.
Rui Li, Kai Hu, +2 authors, Lihua Julie Zhu.
Genes (Basel), 2020 Oct 08; 11(10). PMID: 33023248    Free PMC article.
Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients.
In Seok Yang, Sangwoo Kim.
BMC Bioinformatics, 2018 Mar 06; 19(Suppl 1). PMID: 29504894    Free PMC article.
Mechanisms and Measurement of Changes in Gene Expression.
Komal P Singh, Christine Miaskowski, +2 authors, Kord M Kober.
Biol Res Nurs, 2018 May 01; 20(4). PMID: 29706088    Free PMC article.
Novel insights into the disease transcriptome of human diabetic glomeruli and tubulointerstitium.
Anna Levin, Anna Reznichenko, +14 authors, Annika Wernerson.
Nephrol Dial Transplant, 2020 Aug 28; 35(12). PMID: 32853351    Free PMC article.
RNA sequence analysis of dermal papilla cells' regeneration in 3D culture.
Guanyu Lin, Guoqian Yin, +3 authors, Bojie Lin.
J Cell Mol Med, 2020 Oct 11; 24(22). PMID: 33038058    Free PMC article.
Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics.
Cláudia Bessa, Paulo Matos, Peter Jordan, Vânia Gonçalves.
Int J Mol Sci, 2020 Dec 03; 21(23). PMID: 33261131    Free PMC article.
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.
Siwen Hu-Lieskovan, Srabani Bhaumik, +14 authors, Holden T Maecker.
J Immunother Cancer, 2020 Dec 04; 8(2). PMID: 33268350    Free PMC article.
Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis.
Sara Rahmati, Darren D O'Rielly, +7 authors, Proton Rahman.
Sci Rep, 2020 Dec 12; 10(1). PMID: 33303908    Free PMC article.
Alzheimer's, Parkinson's Disease and Amyotrophic Lateral Sclerosis Gene Expression Patterns Divergence Reveals Different Grade of RNA Metabolism Involvement.
Maria Garofalo, Cecilia Pandini, +9 authors, Stella Gagliardi.
Int J Mol Sci, 2020 Dec 18; 21(24). PMID: 33327559    Free PMC article.
Regulation of Astrocyte Functions in Multiple Sclerosis.
Michael A Wheeler, Francisco J Quintana.
Cold Spring Harb Perspect Med, 2018 Jan 24; 9(1). PMID: 29358321    Free PMC article.
Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer.
Yumin Zhu, Siqi Wang, +16 authors, Zhi John Lu.
Theranostics, 2021 Jan 05; 11(1). PMID: 33391469    Free PMC article.
Unique bioinformatic approach and comprehensive reanalysis improve diagnostic yield of clinical exomes.
Klaus Schmitz-Abe, Qifei Li, +13 authors, Pankaj B Agrawal.
Eur J Hum Genet, 2019 Apr 14; 27(9). PMID: 30979967    Free PMC article.
A transcriptomic model to predict increase in fibrous cap thickness in response to high-dose statin treatment: Validation by serial intracoronary OCT imaging.
Kipp W Johnson, Benjamin S Glicksberg, +7 authors, Annapoorna S Kini.
EBioMedicine, 2019 May 28; 44. PMID: 31126891    Free PMC article.
Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches.
Paula Quintero-Ronderos, Paul Laissue.
Reprod Sci, 2020 May 21; 27(8). PMID: 32430708
Current status of use of high throughput nucleotide sequencing in rheumatology.
Sebastian Boegel, John C Castle, Andreas Schwarting.
RMD Open, 2021 Jan 08; 7(1). PMID: 33408124    Free PMC article.
Data structures based on k-mers for querying large collections of sequencing data sets.
Camille Marchet, Christina Boucher, +3 authors, Rayan Chikhi.
Genome Res, 2020 Dec 18; 31(1). PMID: 33328168    Free PMC article.
Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples.
Chunxiao Fu, Michal Marczyk, +10 authors, W Fraser Symmans.
BMC Cancer, 2021 Feb 06; 21(1). PMID: 33541297    Free PMC article.
Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine.
Stanislaw Supplitt, Pawel Karpinski, Maria Sasiadek, Izabela Laczmanska.
Int J Mol Sci, 2021 Feb 13; 22(3). PMID: 33572595    Free PMC article.
Cross-species RNA-seq for deciphering host-microbe interactions.
Alexander J Westermann, Jörg Vogel.
Nat Rev Genet, 2021 Feb 19;. PMID: 33597744
Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing.
Abdul Rezzak Hamzeh, T Daniel Andrews, Matt A Field.
Methods Mol Biol, 2021 Feb 20; 2243. PMID: 33606250