Lior Pachter - Publications

Electrical Engineering and Computer Science University of California, Berkeley, Berkeley, CA 
Biosystems & Computational Biology (BIO); Artificial Intelligence (AI)

114 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Melsted P, Booeshaghi AS, Liu L, Gao F, Lu L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature Biotechnology. PMID 33795888 DOI: 10.1038/s41587-021-00870-2  0.772
2021 Booeshaghi AS, Pachter L. Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x). Bioinformatics (Oxford, England). PMID 33676365 DOI: 10.1093/bioinformatics/btab085  0.77
2020 Booeshaghi AS, Lubock NB, Cooper AR, Simpkins SW, Bloom JS, Gehring J, Luebbert L, Kosuri S, Pachter L. Reliable and accurate diagnostics from highly multiplexed sequencing assays. Scientific Reports. 10: 21759. PMID 33303831 DOI: 10.1038/s41598-020-78942-7  0.793
2020 Gorin G, Pachter L. Special function methods for bursty models of transcription. Physical Review. E. 102: 022409. PMID 32942485 DOI: 10.1103/Physreve.102.022409  0.301
2020 Bloom JS, Jones EM, Gasperini M, Lubock NB, Sathe L, Munugala C, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, ... ... Pachter L, et al. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. Medrxiv : the Preprint Server For Health Sciences. PMID 32909008 DOI: 10.1101/2020.08.04.20167874  0.772
2020 Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. Elife. 9. PMID 32701060 DOI: 10.7554/Elife.59610  0.322
2020 Mao S, Pachter L, Tse D, Kannan S. RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition. Plos One. 15: e0232946. PMID 32484809 DOI: 10.1371/Journal.Pone.0232946  0.424
2020 Svensson V, Gayoso A, Yosef N, Pachter L. Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinformatics (Oxford, England). PMID 32176273 DOI: 10.1093/Bioinformatics/Btaa169  0.324
2020 Gorin G, Svensson V, Pachter L. Protein velocity and acceleration from single-cell multiomics experiments. Genome Biology. 21: 39. PMID 32070398 DOI: 10.1186/S13059-020-1945-3  0.318
2019 Gehring J, Hwee Park J, Chen S, Thomson M, Pachter L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nature Biotechnology. PMID 31873215 DOI: 10.1038/S41587-019-0372-Z  0.354
2019 Booeshaghi AS, Beltrame EDV, Bannon D, Gehring J, Pachter L. Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific Reports. 9: 12385. PMID 31455877 DOI: 10.1038/S41598-019-48815-9  0.743
2019 Melsted P, Ntranos V, Pachter L. The Barcode, UMI, Set format and BUStools. Bioinformatics (Oxford, England). PMID 31073610 DOI: 10.1093/Bioinformatics/Btz279  0.325
2019 McCurdy SR, Ntranos V, Pachter L. Deterministic column subset selection for single-cell RNA-Seq. Plos One. 14: e0210571. PMID 30682053 DOI: 10.1371/Journal.Pone.0210571  0.338
2019 Ntranos V, Yi L, Melsted P, Pachter L. A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nature Methods. PMID 30664774 DOI: 10.1038/S41592-018-0303-9  0.351
2019 Tambe A, Pachter L. Barcode identification for single cell genomics. Bmc Bioinformatics. 20: 32. PMID 30654736 DOI: 10.1186/S12859-019-2612-0  0.372
2019 Melsted P, Booeshaghi AS, Liu L, Gao F, Min KH, Beltrame E, Lu L, Hjörleifsson KE, Gehring J, Pachter L. Algorithms and infrastructure for accurate pre-processing and analysis of single-cell RNA-seq F1000research. 8. DOI: 10.7490/F1000Research.1117626.1  0.768
2018 Brown BC, Bray NL, Pachter L. Expression reflects population structure. Plos Genetics. 14: e1007841. PMID 30566439 DOI: 10.1371/Journal.Pgen.1007841  0.305
2018 Tunney R, McGlincy NJ, Graham ME, Naddaf N, Pachter L, Lareau LF. Accurate design of translational output by a neural network model of ribosome distribution. Nature Structural & Molecular Biology. PMID 29967537 DOI: 10.1038/S41594-018-0080-2  0.757
2018 Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L. Association mapping from sequencing reads using -mers. Elife. 7. PMID 29897334 DOI: 10.7554/Elife.32920  0.451
2018 Yi L, Pimentel H, Bray NL, Pachter L. Gene-level differential analysis at transcript-level resolution. Genome Biology. 19: 53. PMID 29650040 DOI: 10.1186/S13059-018-1419-Z  0.351
2018 Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment. Bioinformatics (Oxford, England). 33: 2082-2088. PMID 28334086 DOI: 10.1093/Bioinformatics/Btx106  0.366
2017 Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods. PMID 28581496 DOI: 10.1038/Nmeth.4324  0.334
2017 Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems. PMID 28501650 DOI: 10.1016/J.Cels.2017.04.007  0.51
2016 Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. The Lair: a resource for exploratory analysis of published RNA-Seq data. Bmc Bioinformatics. 17: 490. PMID 27905880 DOI: 10.1186/S12859-016-1357-2  0.368
2016 Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biology. 17: 112. PMID 27230763 DOI: 10.1186/S13059-016-0970-8  0.36
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. PMID 27043002 DOI: 10.1038/Nbt.3519  0.34
2015 Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Research. PMID 26531823 DOI: 10.1093/Nar/Gkv1168  0.324
2015 Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047  0.377
2015 Singer M, Pachter L. Controlling for conservation in genome-wide DNA methylation studies. Bmc Genomics. 16: 420. PMID 26024968 DOI: 10.1186/S12864-015-1604-3  0.544
2015 Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y. A diverse epigenetic landscape at human exons with implication for expression. Nucleic Acids Research. 43: 3498-508. PMID 25765649 DOI: 10.1093/Nar/Gkv153  0.541
2015 Joseph I, McCurdy S, Costello JF, Pachter L. Method for combining multiple genomic and clinical datatypes to predict recurrence grade in gliomas F1000research. 6. DOI: 10.7490/F1000Research.1097884.1  0.342
2015 Pimentel H, Parra M, Gee S, Mohandas N, Pachter L, Conboy JG. The Erythroid Intron Retention Program Encompasses Developmentally Stable and Dynamic Networks and Regulates Diverse Gene Classes Blood. 126: 3331-3331. DOI: 10.1182/Blood.V126.23.3331.3331  0.362
2014 Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. Rna (New York, N.Y.). 20: 1864-77. PMID 25332375 DOI: 10.1261/Rna.043844.113  0.414
2014 Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D. Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Research. 24: 821-30. PMID 24558263 DOI: 10.1101/Gr.162412.113  0.362
2014 Pimentel H, Parra M, Gee S, Mohandas N, Pachter L, Conboy JG. An Erythroid-Specific Intron Retention Program Regulates Expression of Selected Genes during Terminal Erythropoiesis Blood. 124: 449-449. DOI: 10.1182/Blood.V124.21.449.449  0.354
2013 Roberts A, Feng H, Pachter L. Fragment assignment in the cloud with eXpress-D. Bmc Bioinformatics. 14: 358. PMID 24314033 DOI: 10.1186/1471-2105-14-358  0.401
2013 Roberts A, Schaeffer L, Pachter L. Updating RNA-Seq analyses after re-annotation. Bioinformatics (Oxford, England). 29: 1631-7. PMID 23677943 DOI: 10.1093/Bioinformatics/Btt197  0.398
2013 Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biology. 14: R8. PMID 23360652 DOI: 10.1186/Gb-2013-14-1-R8  0.343
2013 Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 31: 46-53. PMID 23222703 DOI: 10.1038/Nbt.2450  0.347
2013 Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods. 10: 71-3. PMID 23160280 DOI: 10.1038/Nmeth.2251  0.417
2013 Pimentel H, Parra M, Li J, Gee S, Ghanem D, Hu J, An X, Narla M, Pachter L, Conboy JG. A Dynamic Alternative Splicing Program Regulates Gene Expression In A Differentiation Stage-Specific Manner During Terminal Erythropoiesis Blood. 122: 3413-3413. DOI: 10.1182/Blood.V122.21.3413.3413  0.362
2013 Kleinman A, Harel M, Pachter L. Affine and Projective Tree Metric Theorems Annals of Combinatorics. 17: 205-228. DOI: 10.1007/S00026-012-0173-2  0.759
2012 Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4: 275-97. PMID 23788555 DOI: 10.1002/9780470559277.Ch120019  0.344
2012 Pachter L. A closer look at RNA editing. Nature Biotechnology. 30: 246-7. PMID 22398619 DOI: 10.1038/Nbt.2156  0.407
2012 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/Nprot.2012.016  0.422
2012 Pimentel H, Li J, Parra M, Ghanem D, Gee S, Hu J, An X, Mohandas N, Pachter L, Conboy JG. Abundance of Alternative Splicing Events and Differentiation Stage-Specific Changes in Splicing Suggest A Major Role in Regulation of Gene Expression During Late Erythropoiesis Blood. 120: 978-978. DOI: 10.1182/Blood.V120.21.978.978  0.356
2011 Singer M, Engström A, Schönhuth A, Pachter L. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains. Statistical Applications in Genetics and Molecular Biology. 10. PMID 23089814 DOI: 10.2202/1544-6115.1677  0.609
2011 Roberts A, Pachter L. RNA-Seq and find: entering the RNA deep field. Genome Medicine. 3: 74. PMID 22113004 DOI: 10.1186/Gm290  0.349
2011 Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. Bmc Bioinformatics. 12: 451. PMID 22099972 DOI: 10.1186/1471-2105-12-451  0.534
2011 Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research. 21: 2049-57. PMID 21908772 DOI: 10.1101/Gr.122721.111  0.546
2011 Snir S, Pachter L. Tracing the most parsimonious indel history. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 967-86. PMID 21728862 DOI: 10.1089/Cmb.2010.0325  0.429
2011 Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (Oxford, England). 27: 2325-9. PMID 21697122 DOI: 10.1093/Bioinformatics/Btr355  0.4
2011 Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108  0.432
2011 Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. 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. 108: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108  0.389
2011 Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 12: R22. PMID 21410973 DOI: 10.1186/Gb-2011-12-3-R22  0.344
2010 Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. Plos One. 5: e13564. PMID 21042592 DOI: 10.1371/Journal.Pone.0013564  0.351
2010 Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L. MetMap enables genome-scale Methyltyping for determining methylation states in populations. Plos Computational Biology. 6: e1000888. PMID 20856582 DOI: 10.1371/Journal.Pcbi.1000888  0.637
2010 Levin TC, Glazer AM, Pachter L, Brem RB, Eisen MB. Exploring the genetic basis of variation in gene predictions with a synthetic association study. Plos One. 5: e11645. PMID 20686598 DOI: 10.1371/Journal.Pone.0011645  0.399
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/Nbt.1621  0.44
2010 Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biology. 8: e1000343. PMID 20351773 DOI: 10.1371/Journal.Pbio.1000343  0.313
2009 Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. Plos Computational Biology. 5: e1000392. PMID 19478997 DOI: 10.1371/Journal.Pcbi.1000392  0.784
2009 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England). 25: 1105-11. PMID 19289445 DOI: 10.1093/Bioinformatics/Btp120  0.404
2009 Mihaescu R, Levy D, Pachter L. Why neighbor-joining works Algorithmica (New York). 54: 1-24. DOI: 10.1007/S00453-007-9116-4  0.761
2008 Bradley RK, Pachter L, Holmes I. Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (Oxford, England). 24: 2677-83. PMID 18796475 DOI: 10.1093/Bioinformatics/Btn495  0.486
2008 Mihaescu R, Pachter L. Combinatorics of least-squares trees. Proceedings of the National Academy of Sciences of the United States of America. 105: 13206-11. PMID 18779558 DOI: 10.1073/Pnas.0802089105  0.767
2008 Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O. Comparison of pattern detection methods in microarray time series of the segmentation clock. Plos One. 3: e2856. PMID 18682743 DOI: 10.1371/Journal.Pone.0002856  0.351
2008 Eickmeyer K, Huggins P, Pachter L, Yoshida R. On the optimality of the neighbor-joining algorithm. Algorithms For Molecular Biology : Amb. 3: 5. PMID 18447942 DOI: 10.1186/1748-7188-3-5  0.717
2008 Satija R, Pachter L, Hein J. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics (Oxford, England). 24: 1236-42. PMID 18353788 DOI: 10.1093/Bioinformatics/Btn104  0.438
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Pachter L, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  0.81
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Pachter L, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.778
2007 Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Plos Biology. 5: e310. PMID 17988176 DOI: 10.1371/Journal.Pbio.0050310  0.798
2007 Huggins P, Pachter L, Sturmfels B. Toward the human genotope. Bulletin of Mathematical Biology. 69: 2723-35. PMID 17874271 DOI: 10.1007/S11538-007-9244-7  0.705
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Pachter L, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.811
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Pachter L, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.815
2007 Chatterji S, Pachter L. Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics. 90: 44-8. PMID 17499477 DOI: 10.1016/J.Ygeno.2007.03.008  0.599
2007 Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, Lenski RE. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. Bmc Evolutionary Biology. 7: 60. PMID 17433106 DOI: 10.1186/1471-2148-7-60  0.514
2007 Schwartz AS, Pachter L. Multiple alignment by sequence annealing. Bioinformatics (Oxford, England). 23: e24-9. PMID 17237099 DOI: 10.1093/Bioinformatics/Btl311  0.708
2007 Pachter L, Sturmsfels B. The mathematics of phylogenomics Siam Review. 49: 3-31. DOI: 10.1137/050632634  0.414
2006 Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. Plos Computational Biology. 2: e73. PMID 16789815 DOI: 10.1371/Journal.Pcbi.0020073  0.802
2006 Dewey CN, Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics. 15: R51-6. PMID 16651369 DOI: 10.1093/Hmg/Ddl056  0.807
2006 Chatterji S, Pachter L. Reference based annotation with GeneMapper. Genome Biology. 7: R29. PMID 16600017 DOI: 10.1186/Gb-2006-7-4-R29  0.66
2006 Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Current Biology : Cb. 16: 460-71. PMID 16458514 DOI: 10.1016/J.Cub.2006.01.050  0.759
2006 Caspi A, Pachter L. Identification of transposable elements using multiple alignments of related genomes. Genome Research. 16: 260-70. PMID 16354754 DOI: 10.1101/Gr.4361206  0.452
2006 Levy D, Yoshida R, Pachter L. Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Molecular Biology and Evolution. 23: 491-8. PMID 16280538 DOI: 10.1093/Molbev/Msj059  0.328
2005 Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. Plos Computational Biology. 1: 106-12. PMID 16110337 DOI: 10.1371/Journal.Pcbi.0010024  0.375
2005 Chatterji S, Pachter L. Large multiple organism gene finding by collapsed Gibbs sampling. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 599-608. PMID 16108706 DOI: 10.1089/Cmb.2005.12.599  0.677
2005 McAuliffe JD, Jordan MI, Pachter L. Subtree power analysis and species selection for comparative genomics. Proceedings of the National Academy of Sciences of the United States of America. 102: 7900-5. PMID 15911755 DOI: 10.1073/Pnas.0502790102  0.397
2004 Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, Rubin EM. Intraspecies sequence comparisons for annotating genomes. Genome Research. 14: 2406-11. PMID 15545499 DOI: 10.1101/Gr.3199704  0.475
2004 Pachter L, Sturmfels B. Parametric inference for biological sequence analysis. Proceedings of the National Academy of Sciences of the United States of America. 101: 16138-43. PMID 15534223 DOI: 10.1073/Pnas.0406011101  0.346
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Pachter L, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.794
2004 Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Research. 32: W273-9. PMID 15215394 DOI: 10.1093/Nar/Gkh458  0.465
2004 Chakrabarti K, Pachter L. Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Research. 14: 716-20. PMID 15060015 DOI: 10.1101/Gr.1957004  0.395
2004 Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Research. 14: 693-9. PMID 15060012 DOI: 10.1101/Gr.1960404  0.476
2004 Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research. 14: 661-4. PMID 15060007 DOI: 10.1101/Gr.1939804  0.777
2004 Yap VB, Pachter L. Identification of evolutionary hotspots in the rodent genomes. Genome Research. 14: 574-9. PMID 15059998 DOI: 10.1101/Gr.1967904  0.429
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Pachter L, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.81
2004 McAuliffe JD, Pachter L, Jordan MI. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics (Oxford, England). 20: 1850-60. PMID 14988105 DOI: 10.1093/Bioinformatics/Bth153  0.449
2004 Chatterji S, Pachter L. Multiple organism gene finding by collapsed Gibbs sampling Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 187-193.  0.492
2003 Lam F, Alexandersson M, Pachter L. Picking alignments from (Steiner) trees. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 509-20. PMID 12935341 DOI: 10.1089/10665270360688156  0.393
2003 Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Research. 31: 3525-6. PMID 12824358 DOI: 10.1093/Nar/Gkg623  0.451
2003 Cawley S, Pachter L, Alexandersson M. SLAM web server for comparative gene finding and alignment. Nucleic Acids Research. 31: 3507-9. PMID 12824355 DOI: 10.1093/Nar/Gkg583  0.428
2003 Alexandersson M, Cawley S, Pachter L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Research. 13: 496-502. PMID 12618381 DOI: 10.1101/Gr.424203  0.439
2003 Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (New York, N.Y.). 299: 1391-4. PMID 12610304 DOI: 10.1126/Science.1081331  0.483
2003 Bray N, Dubchak I, Pachter L. AVID: A global alignment program. Genome Research. 13: 97-102. PMID 12529311 DOI: 10.1101/Gr.789803  0.415
2003 Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Strategies and tools for whole-genome alignments. Genome Research. 13: 73-80. PMID 12529308 DOI: 10.1101/Gr.762503  0.449
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Pachter L, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.813
2002 Dubchak I, Pachter L. The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics. 3: 18-22. PMID 12002220 DOI: 10.1093/Bib/3.1.18  0.432
2002 Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Research. 12: 832-9. PMID 11997350 DOI: 10.1101/Gr.225502  0.35
2002 Peter A, Schöttler P, Werner M, Beinert N, Dowe G, Burkert P, Mourkioti F, Dentzer L, He Y, Deak P, Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, ... ... Pachter L, et al. Mapping and identification of essential gene functions on the X chromosome of Drosophila. Embo Reports. 3: 34-8. PMID 11751581 DOI: 10.1093/Embo-Reports/Kvf012  0.395
2001 Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, ... ... Pachter L, et al. From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies. Genome Research. 11: 710-30. PMID 11337470 DOI: 10.1101/Gr.173801  0.449
2000 Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Research. 10: 1304-6. PMID 10984448 DOI: 10.1101/Gr.142200  0.449
2000 Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research. 10: 950-8. PMID 10899144 DOI: 10.1101/Gr.10.7.950  0.62
1999 Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary-based approach for gene annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 419-30. PMID 10582576 DOI: 10.1089/106652799318364  0.693
1998 Kleitman D, Pachter L. Finding Convex Sets Among Points in the Plane Discrete & Computational Geometry. 19: 405-410. DOI: 10.1007/Pl00009358  0.446
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