PubRank

Lior Pachter

Author PubWeight™ 594.58‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Initial sequencing and comparative analysis of the mouse genome. Nature 2002 96.15
2 TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009 81.13
3 Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010 75.21
4 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
5 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012 35.75
6 Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004 24.40
7 Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007 18.01
8 Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 2012 14.01
9 VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004 13.52
10 Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007 11.66
11 Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011 10.63
12 A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 2006 10.14
13 AVID: A global alignment program. Genome Res 2003 10.06
14 Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003 9.93
15 Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011 8.05
16 rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002 7.33
17 Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007 7.05
18 Disordered microbial communities in asthmatic airways. PLoS One 2010 6.35
19 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol 2007 6.18
20 Fast statistical alignment. PLoS Comput Biol 2009 5.92
21 Viral population estimation using pyrosequencing. PLoS Comput Biol 2008 5.89
22 MAVID: constrained ancestral alignment of multiple sequences. Genome Res 2004 5.83
23 Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015 5.71
24 Strategies and tools for whole-genome alignments. Genome Res 2003 4.86
25 Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 2012 4.43
26 SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 2003 4.17
27 MAVID multiple alignment server. Nucleic Acids Res 2003 3.53
28 Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 2005 3.39
29 Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A 2011 3.30
30 Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011 2.98
31 Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol 2010 2.32
32 Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 2010 1.84
33 Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep 2001 1.83
34 Subtree power analysis and species selection for comparative genomics. Proc Natl Acad Sci U S A 2005 1.69
35 Multiple alignment by sequence annealing. Bioinformatics 2007 1.63
36 CGAL: computing genome assembly likelihoods. Genome Biol 2013 1.53
37 HMM sampling and applications to gene finding and alternative splicing. Bioinformatics 2003 1.49
38 Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A 2011 1.49
39 Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics 2004 1.46
40 Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum Mol Genet 2006 1.43
41 Shape-based peak identification for ChIP-Seq. BMC Bioinformatics 2011 1.38
42 Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol 2007 1.30
43 Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One 2010 1.25
44 Reference based annotation with GeneMapper. Genome Biol 2006 1.24
45 Identification of evolutionary hotspots in the rodent genomes. Genome Res 2004 1.21
46 Identification of transposable elements using multiple alignments of related genomes. Genome Res 2005 1.17
47 The computational challenges of applying comparative-based computational methods to whole genomes. Brief Bioinform 2002 1.17
48 Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 2008 1.16
49 Intraspecies sequence comparisons for annotating genomes. Genome Res 2004 1.15
50 SLAM web server for comparative gene finding and alignment. Nucleic Acids Res 2003 1.15
51 A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Res 2014 1.13
52 Parametric alignment of Drosophila genomes. PLoS Comput Biol 2006 1.12
53 Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Res 2014 1.12
54 Coverage statistics for sequence census methods. BMC Bioinformatics 2010 1.07
55 SHAPE-Seq: High-Throughput RNA Structure Analysis. Curr Protoc Chem Biol 2012 1.06
56 Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Res 2004 1.05
57 Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res 2004 1.03
58 Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One 2008 0.99
59 Interpreting the unculturable majority. Nat Methods 2007 0.95
60 On the optimality of the neighbor-joining algorithm. Algorithms Mol Biol 2008 0.92
61 Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res 2011 0.91
62 Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 2008 0.90
63 Large multiple organism gene finding by collapsed Gibbs sampling. J Comput Biol 2005 0.89
64 MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol 2010 0.89
65 RNA-Seq and find: entering the RNA deep field. Genome Med 2011 0.87
66 Updating RNA-Seq analyses after re-annotation. Bioinformatics 2013 0.84
67 Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Mol Biol Evol 2005 0.84
68 Combinatorics of least-squares trees. Proc Natl Acad Sci U S A 2008 0.83
69 A closer look at RNA editing. Nat Biotechnol 2012 0.80
70 Toward the human genotope. Bull Math Biol 2007 0.78
71 The cyclohedron test for finding periodic genes in time course expression studies. Stat Appl Genet Mol Biol 2007 0.78
72 Erratum: Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 2016 0.77
73 Tracing the most parsimonious indel history. J Comput Biol 2011 0.76
74 Quantifying uniformity of mapped reads. Bioinformatics 2012 0.76
75 Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Stat Appl Genet Mol Biol 2016 0.76
76 Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics 2007 0.75
77 Exploring the genetic basis of variation in gene predictions with a synthetic association study. PLoS One 2010 0.75
78 Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains. Stat Appl Genet Mol Biol 2011 0.75
79 Picking alignments from (Steiner) trees. J Comput Biol 2003 0.75