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TopHat: discovering splice junctions with RNA-Seq C Trapnell, L Pachter, SL Salzberg Bioinformatics 25 (9), 1105-1111, 2009 | 13520 | 2009 |
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ... Nature protocols 7 (3), 562-578, 2012 | 13214 | 2012 |
Near-optimal probabilistic RNA-seq quantification NL Bray, H Pimentel, P Melsted, L Pachter Nature biotechnology 34 (5), 525-527, 2016 | 9012 | 2016 |
Initial sequencing and comparative analysis of the mouse genome European Bioinformatics Institute: Birney Ewan 3 Goldman Nick 3 Kasprzyk ... Nature 420 (6915), 520-562, 2002 | 8714 | 2002 |
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project EP Consortium Nature 447 (7146), 799, 2007 | 6043 | 2007 |
Differential analysis of gene regulation at transcript resolution with RNA-seq C Trapnell*, DG Hendrickson*, M Sauvageau, L Goff, JL Rinn, L Pachter Nature biotechnology 31 (1), 46-53, *co-first author, 2013 | 3909 | 2013 |
Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas Cancer Genome Atlas Research Network New England Journal of Medicine 372 (26), 2481-2498, 2015 | 3052 | 2015 |
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution LDW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, ... Nature 432 (7018), 695-716, 2004 | 2957 | 2004 |
VISTA: computational tools for comparative genomics KA Frazer, L Pachter, A Poliakov, EM Rubin, I Dubchak Nucleic acids research 32 (suppl_2), W273-W279, 2004 | 2573 | 2004 |
Genome sequence of the Brown Norway rat yields insights into mammalian evolution RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, ... Nature 428 (6982), 493-521, 2004 | 2567 | 2004 |
The ENCODE (ENCyclopedia of DNA elements) project EP Consortium Science 306 (5696), 636-640, 2004 | 2442* | 2004 |
Evolution of genes and genomes on the Drosophila phylogeny DG Consortium Nature 450 (7167), 203-218, 2007 | 2276* | 2007 |
Disordered microbial communities in asthmatic airways M Hilty, C Burke, H Pedro, P Cardenas, A Bush, C Bossley, J Davies, ... PloS one 5 (1), e8578, 2010 | 2051 | 2010 |
Improving RNA-Seq expression estimates by correcting for fragment bias A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter Genome biology 12, 1-14, 2011 | 1612 | 2011 |
Differential analysis of RNA-seq incorporating quantification uncertainty H Pimentel, NL Bray, S Puente, P Melsted, L Pachter Nature methods 14 (7), 687-690, 2017 | 1516 | 2017 |
Identification of novel transcripts in annotated genomes using RNA-Seq A Roberts, H Pimentel, C Trapnell, L Pachter Bioinformatics 27 (17), 2325-2329, 2011 | 1235 | 2011 |
VISTA : visualizing global DNA sequence alignments of arbitrary length C Mayor, M Brudno, JR Schwartz, A Poliakov, EM Rubin, KA Frazer, ... Bioinformatics 16 (11), 1046-1047, 2000 | 1174 | 2000 |
Streaming fragment assignment for real-time analysis of sequencing experiments A Roberts, L Pachter Nature methods 10 (1), 71-73, 2013 | 1115 | 2013 |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans DJ Begun, AK Holloway, K Stevens, LDW Hillier, YP Poh, MW Hahn, ... PLoS biology 5 (11), e310, 2007 | 734 | 2007 |