Lior Pachter
Lior Pachter
Bren Professor of Computational Biology, Caltech
Verified email at caltech.edu - Homepage
TitleCited byYear
TopHat: discovering splice junctions with RNA-Seq
C Trapnell, L Pachter, SL Salzberg
Bioinformatics 25 (9), 1105-1111, 2009
93542009
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, 2010
92192010
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, 2012
74742012
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium
Nature 420 (6915), 520, 2002
67592002
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium
Nature 447 (7146), 799, 2007
48872007
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, 2013
23742013
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
22332004
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
20552004
Near-optimal probabilistic RNA-seq quantification
NL Bray, H Pimentel, P Melsted, L Pachter
Nature biotechnology 34 (5), 525, 2016
19202016
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium
Nature 450 (7167), 203, 2007
18162007
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
13682004
Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas
Cancer Genome Atlas Research Network
New England Journal of Medicine 372 (26), 2481-2498, 2015
11992015
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
11142010
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
9032000
Improving RNA-Seq expression estimates by correcting for fragment bias
A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter
Genome biology 12 (3), R22, 2011
8202011
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 2011
8112011
Algebraic statistics for computational biology
L Pachter, B Sturmfels
Cambridge University Press, 2005
6752005
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, 2007
6302007
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
D Boffelli, J McAuliffe, D Ovcharenko, KD Lewis, I Ovcharenko, L Pachter, ...
Science 299 (5611), 1391-1394, 2003
6222003
Streaming fragment assignment for real-time analysis of sequencing experiments
A Roberts, L Pachter
Nature methods 10 (1), 71, 2013
6172013
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