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Lior Pachter

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TOP 3
Adam Roberts; Lior Pachter
Streaming fragment assignment for real-time analysis of sequencing experiments.
Valerie Hower; Adam Roberts; Richard Starfield; Lior Pachter
Quantifying uniformity of mapped reads.
Lior Pachter
A closer look at RNA editing.

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All Publications

2013: Adam Roberts; Lior Pachter
Streaming fragment assignment for real-time analysis of sequencing experiments.
Nature methods 2013;10(1):71-3.
2012: Valerie Hower; Adam Roberts; Richard Starfield; Lior Pachter
Quantifying uniformity of mapped reads.
Bioinformatics (Oxford, England) 2012;28(20):2680-2.
2012: Lior Pachter
A closer look at RNA editing.
Nature biotechnology 2012;30(3):246-7.
2012: Cole Trapnell; Loyal Goff; David R Kelley; Daehwan Kim; Geo Pertea; Harold Pimentel; John L Rinn; Adam Roberts; Steven L Salzberg; Lior Pachter
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Nature protocols 2012;7(3):562-78.
2011: David I K Martin; Lior Pachter; Gary P Schroth; Meromit Singer; Lu Zhang; Joseph M Dhahbi; Guanxiong Mao; Dario Boffelli
Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states.
Genome research 2011;21(12):2049-57.
2011: Sharon Aviran; Jennifer A Doudna; Julius B Lucks; Shujun Luo; Stefanie A Mortimer; Gary P Schroth; Cole Trapnell; Adam P Arkin; Lior Pachter
Modeling and automation of sequencing-based characterization of RNA structure.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(27):11069-74.
2011: Julius B Lucks; Shujun Luo; Stefanie A Mortimer; Lior Pachter; Gary P Schroth; Cole Trapnell; Sharon Aviran; Jennifer A Doudna; Adam P Arkin
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
Proceedings of the National Academy of Sciences of the United States of America 2011;108(27):11063-8.
2011: Meromit Singer; Alexander Schönhuth; Alexander Engström; Lior Pachter
Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.
Statistical applications in genetics and molecular biology 2011;10(1):.
2011: Frazer Meacham; Dario Boffelli; Joseph Dhahbi; David I K Martin; Meromit Singer; Lior Pachter
Identification and correction of systematic error in high-throughput sequence data.
BMC bioinformatics 2011;12():451.
2011: Valerie Hower; Steven N Evans; Lior Pachter
Shape-based peak identification for ChIP-Seq.
BMC bioinformatics 2011;12():15.
2010: Anna Lapuk; Henry Marr; Lakshmi Jakkula; Helder Pedro; Sanchita Bhattacharya; Elizabeth Purdom; Zhi Hu; Ken Simpson; Lior Pachter; Steffen Durinck; Nicholas Wang; Bahram Parvin; Gerald Fontenay; Terence P Speed; James Garbe; Martha Stampfer; Hovig Bayandorian; Shannon Dorton; Tyson A Clark; Anthony Schweitzer; Andrew Wyrobek; Heidi Feiler; Paul Spellman; John G Conboy; Joe Gray
Exon-level microarray analyses identify alternative splicing programs in breast cancer.
Molecular cancer research : MCR 2010;8(7):961-74.
2010: Cole Trapnell; Brian A Williams; Geo Pertea; Ali Mortazavi; Gordon Kwan; Marijke J van Baren; Steven L Salzberg; Barbara J Wold; Lior Pachter
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Nature biotechnology 2010;28(5):511-5.
2010: Robert K Bradley; Xiao-Yong Li; Cole Trapnell; Stuart Davidson; Lior Pachter; Hou Cheng Chu; Leath A Tonkin; Mark D Biggin; Michael B Eisen
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.
PLoS biology 2010;8(3):e1000343.
2010: Stephanie M Willerth; Hélder A M Pedro; Lior Pachter; Laurent M Humeau; Adam P Arkin; David V Schaffer
Development of a low bias method for characterizing viral populations using next generation sequencing technology.
PloS one 2010;5(10):e13564.
2010: Meromit Singer; Dario Boffelli; Joseph Dhahbi; Alexander Schönhuth; Gary P Schroth; David I K Martin; Lior Pachter
MetMap enables genome-scale Methyltyping for determining methylation states in populations.
PLoS computational biology 2010;6(8):e1000888.
2010: Steven N Evans; Valerie Hower; Lior Pachter
Coverage statistics for sequence census methods.
BMC bioinformatics 2010;11():430.
2010: Tera C Levin; Andrew M Glazer; Lior Pachter; Rachel B Brem; Michael B Eisen
Exploring the genetic basis of variation in gene predictions with a synthetic association study.
PloS one 2010;5(7):e11645.
2009: Robert K Bradley; Adam Roberts; Michael Smoot; Sudeep Juvekar; Jaeyoung Do; Colin Dewey; Ian Holmes; Lior Pachter
Fast statistical alignment.
PLoS computational biology 2009;5(5):e1000392.
2008: Robert K Bradley; Lior Pachter; Ian Holmes
Specific alignment of structured RNA: stochastic grammars and sequence annealing.
Bioinformatics (Oxford, England) 2008;24(23):2677-83.
2008: Radu Mihaescu; Lior Pachter
Combinatorics of least-squares trees.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(36):13206-11.
2008: Kord Eickmeyer; Peter Huggins; Lior Pachter; Ruriko Yoshida
On the optimality of the neighbor-joining algorithm.
Algorithms for molecular biology : AMB 2008;3():5.
2007: David J Begun; Alisha K Holloway; Kristian Stevens; LaDeana W Hillier; Yu-Ping Poh; Matthew W Hahn; Phillip M Nista; Corbin D Jones; Andrew D Kern; Colin N Dewey; Lior Pachter; Eugene Myers; Charles H Langley
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
PLoS biology 2007;5(11):e310.
2007: Peter Huggins; Lior Pachter; Bernd Sturmfels
Toward the human genotope.
Bulletin of mathematical biology 2007;69(8):2723-35.
2007: Sourav Chatterji; Lior Pachter
Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor.
Genomics 2007;90(1):44-8.
2007: Lior Pachter
Interpreting the unculturable majority.
Nature methods 2007;4(6):479-80.
2007: Ariel S Schwartz; Lior Pachter
Multiple alignment by sequence annealing.
Bioinformatics (Oxford, England) 2007;23(2):e24-9.
2007: Jason Morton; Lior Pachter; Anne Shiu; Bernd Sturmfels
The cyclohedron test for finding periodic genes in time course expression studies.
Statistical applications in genetics and molecular biology 2007;6():Article 21.
2007: Niko Beerenwinkel; Lior Pachter; Bernd Sturmfels; Santiago F Elena; Richard E Lenski
Analysis of epistatic interactions and fitness landscapes using a new geometric approach.
BMC evolutionary biology 2007;7():60.
2006: Colin N Dewey; Peter M Huggins; Kevin Woods; Bernd Sturmfels; Lior Pachter
Parametric alignment of Drosophila genomes.
PLoS computational biology 2006;2(6):e73.
2006: Colin N Dewey; Lior Pachter
Evolution at the nucleotide level: the problem of multiple whole-genome alignment.
Human molecular genetics 2006;15 Spec No 1():R51-6.
2006: Sabbi Lall; Dominic Grün; Azra Krek; Kevin Chen; Yi-Lu Wang; Colin N Dewey; Pranidhi Sood; Teresa Colombo; Nicolas Bray; Philip MacMenamin; Huey-Ling Kao; Kristin C Gunsalus; Lior Pachter; Fabio Piano; Nikolaus Rajewsky
A genome-wide map of conserved microRNA targets in C. elegans.
Current biology : CB 2006;16(5):460-71.
2006: Dan Levy; Ruriko Yoshida; Lior Pachter
Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.
Molecular biology and evolution 2006;23(3):491-8.
2006: Anat Caspi; Lior Pachter
Identification of transposable elements using multiple alignments of related genomes.
Genome research 2006;16(2):260-70.
2006: Sourav Chatterji; Lior Pachter
Reference based annotation with GeneMapper.
Genome biology 2006;7(4):R29.
2005: Kevin Chen; Lior Pachter
Bioinformatics for whole-genome shotgun sequencing of microbial communities.
PLoS computational biology 2005;1(2):106-12.
2005: Sourav Chatterji; Lior Pachter
Large multiple organism gene finding by collapsed Gibbs sampling.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(6):599-608.
2005: Jon McAuliffe; Michael I Jordan; Lior Pachter
Subtree power analysis and species selection for comparative genomics.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(22):7900-5.
2004: Dario Boffelli; Claire V Weer; Li Weng; Keith D Lewis; Malak Shoukry; Lior Pachter; David N Keys; Edward M Rubin
Intraspecies sequence comparisons for annotating genomes.
Genome research 2004;14(12):2406-11.
2004: Lior Pachter; Bernd Sturmfels
Tropical geometry of statistical models.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(46):16132-7.
2004: Lior Pachter; Bernd Sturmfels
Parametric inference for biological sequence analysis.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(46):16138-43.
2004: Jon McAuliffe; Lior Pachter; Michael I Jordan
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
Bioinformatics (Oxford, England) 2004;20(12):1850-60.
2004: Kelly A Frazer; Lior Pachter; Alexander Poliakov; Edward M Rubin; Inna Dubchak
VISTA: computational tools for comparative genomics.
Nucleic acids research 2004;32(Web Server issue):W273-9.
2004: Kushal Chakrabarti; Lior Pachter
Visualization of multiple genome annotations and alignments with the K-BROWSER.
Genome research 2004;14(4):716-20.
2004: Nicolas Bray; Lior Pachter
MAVID: constrained ancestral alignment of multiple sequences.
Genome research 2004;14(4):693-9.
2004: Colin Dewey; Jia Qian Wu; Simon Cawley; Marina Alexandersson; Richard Gibbs; Lior Pachter
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.
Genome research 2004;14(4):661-4.
2004: Von Bing Yap; Lior Pachter
Identification of evolutionary hotspots in the rodent genomes.
Genome research 2004;14(4):574-9.
2003: Simon Cawley; Lior Pachter
HMM sampling and applications to gene finding and alternative splicing.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii36-41.
2003: Nicolas Bray; Lior Pachter
MAVID multiple alignment server.
Nucleic acids research 2003;31(13):3525-6.
2003: Simon Cawley; Lior Pachter; Marina Alexandersson
SLAM web server for comparative gene finding and alignment.
Nucleic acids research 2003;31(13):3507-9.
2003: Marina Alexandersson; Simon Cawley; Lior Pachter
SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.
Genome research 2003;13(3):496-502.
2003: Dario Boffelli; Jon McAuliffe; Dmitriy Ovcharenko; Keith D Lewis; Ivan Ovcharenko; Lior Pachter; Edward M Rubin
Phylogenetic shadowing of primate sequences to find functional regions of the human genome.
Science (New York, N.Y.) 2003;299(5611):1391-4.
2003: Fumei Lam; Marina Alexandersson; Lior Pachter
Picking alignments from (Steiner) trees.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):509-20.
2003: Nicolas Bray; Inna Dubchak; Lior Pachter
AVID: A global alignment program.
Genome research 2003;13(1):97-102.
2003: Olivier Couronne; Alexander Poliakov; Nicolas Bray; Tigran Ishkhanov; Dmitriy Ryaboy; Edward Rubin; Lior Pachter; Inna Dubchak
Strategies and tools for whole-genome alignments.
Genome research 2003;13(1):73-80.
2002: Gabriela G Loots; Ivan Ovcharenko; Lior Pachter; Inna Dubchak; Edward M Rubin
rVista for comparative sequence-based discovery of functional transcription factor binding sites.
Genome research 2002;12(5):832-9.
2002: Inna Dubchak; Lior Pachter
The computational challenges of applying comparative-based computational methods to whole genomes.
Briefings in bioinformatics 2002;3(1):18-22.
2002: Lior Pachter; Marina Alexandersson; Simon Cawley
Applications of generalized pair hidden Markov models to alignment and gene finding problems.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(2):389-99.
2000: C Mayor; Michael Brudno; J R Schwartz; Alexander Poliakov; Edward M Rubin; Kelly A Frazer; Lior Pachter; Inna Dubchak
VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinformatics (Oxford, England) 2000;16(11):1046-7.
2000: Inna Dubchak; Michael Brudno; Gabriela G Loots; Lior Pachter; C Mayor; Edward M Rubin; Kelly A Frazer
Active conservation of noncoding sequences revealed by three-way species comparisons.
Genome research 2000;10(9):1304-6.
2000: Serafim Batzoglou; Lior Pachter; Jill P Mesirov; Bonnie Berger; Eric S Lander
Human and mouse gene structure: comparative analysis and application to exon prediction.
Genome research 2000;10(7):950-8.
1999: Lior Pachter; Serafim Batzoglou; V I Spitkovsky; E Banks; Eric S Lander; D J Kleitman; Bonnie Berger
A dictionary-based approach for gene annotation.
Journal of computational biology : a journal of computational molecular cell biology 1999;6(3-4):419-30.