Lior Pachter
Lior Pachter
Bren Professor of Computational Biology, Caltech
Verified email at caltech.edu - Homepage
Title
Cited by
Cited by
Year
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Van Baren, ...
Nature biotechnology 28 (5), 511-515, 2010
124052010
TopHat: discovering splice junctions with RNA-Seq
C Trapnell, L Pachter, SL Salzberg
Bioinformatics 25 (9), 1105-1111, 2009
117692009
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
105262012
Initial sequencing and comparative analysis of the mouse genome
RH Waterston, L Pachter
Nature 420 (6915), 520-562, 2002
74032002
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
EP Consortium
Nature 447 (7146), 799, 2007
54442007
Near-optimal probabilistic RNA-seq quantification
NL Bray, H Pimentel, P Melsted, L Pachter
Nature biotechnology 34 (5), 525-527, 2016
45212016
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
31842013
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
25142004
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
22962004
Evolution of genes and genomes on the Drosophila phylogeny
AG Clark, MB Eisen, DR Smith, CM Bergman, B Oliver, TA Markow, ...
Nature 450 (7167), 203-218, 2007
20532007
Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas
Cancer Genome Atlas Research Network
New England Journal of Medicine 372 (26), 2481-2498, 2015
19712015
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
17432004
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
15092010
Improving RNA-Seq expression estimates by correcting for fragment bias
A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter
Genome biology 12 (3), 1-14, 2011
10932011
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
10202000
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 2011
10082011
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
8642017
Streaming fragment assignment for real-time analysis of sequencing experiments
A Roberts, L Pachter
Nature methods 10 (1), 71-73, 2013
8362013
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
A Stark, MF Lin, P Kheradpour, JS Pedersen, L Parts, JW Carlson, ...
Nature 450 (7167), 219-232, 2007
6772007
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
6652007
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