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Nature Biotechnology|May 4, 2010
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationCole Trapnell, Brian A Williams, Geo Pertea, et al.Proceedings of the National Academy of Sciences of the United States of America|June 7, 2011
Modeling and automation of sequencing-based characterization of RNA structureSharon Aviran, Cole Trapnell, Julius B Lucks, et al.Proceedings of the National Academy of Sciences of the United States of America|June 7, 2011
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)Julius B Lucks, Stefanie A Mortimer, Cole Trapnell, et al.Nature Protocols|March 3, 2012
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksCole Trapnell, Adam Roberts, Loyal Goff, et al.Plos Biology|March 31, 2010
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila speciesRobert K Bradley, Xiao-Yong Li, Cole Trapnell, et al.Biorxiv : the Preprint Server for Biology|June 9, 2023
Resilience of A Learned Motor Behavior After Chronic Disruption of Inhibitory CircuitsZsofia Torok, Laura Luebbert, Jordan Feldman, et al.Arthritis Research & Therapy|May 27, 2017
Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot studyDana E Goin, Mette Kiel Smed, Lior Pachter, et al.Science Advances|November 26, 2021
Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across <i>Clytia</i> medusa cell typesTara Chari, Brandon Weissbourd, Jase Gehring, et al.Cell Systems|March 28, 2026
The impact of package selection and versioning on single-cell RNA-seq analysisJoseph M Rich, Lambda Moses, Pétur Helgi Einarsson, et al.Biorxiv : the Preprint Server for Biology|April 15, 2024
The impact of package selection and versioning on single-cell RNA-seq analysisJoseph M Rich, Lambda Moses, Pétur Helgi Einarsson, et al.Pageof 20