Pachter, Lior

Article from CaltechAUTHORS

• Sullivan, Delaney K. and Pachter, Lior (2024) Flexible parsing, interpretation, and editing of technical sequences with splitcode; Bioinformatics; Vol. 40; No. 6; btae331; PMCID PMC11193061; 10.1093/bioinformatics/btae331
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• Gorin, Gennady and Pachter, Lior (2024) New and notable: Revisiting the "two cultures" through extrinsic noise; Biophysical Journal; Vol. 123; No. 1; 1-3; 10.1016/j.bpj.2023.11.3400
• Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph), el al. (2024) Quantifying orthogonal barcodes for sequence census assays; Bioinformatics Advances; Vol. 4; vbad181; PMCID PMC10783946; 10.1093/bioadv/vbad181
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• Jackson, Kayla C. and Pachter, Lior (2023) A standard for sharing spatial transcriptomics data; Cell Genomics; Vol. 3; No. 8; 100374; PMCID PMC10435375; 10.1016/j.xgen.2023.100374
• Chari, Tara and Pachter, Lior (2023) The specious art of single-cell genomics; PLOS Computational Biology; Vol. 19; No. 8; e1011288; PMCID PMC10434946; 10.1371/journal.pcbi.1011288
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• Luebbert, Laura and Pachter, Lior (2023) Efficient querying of genomic reference databases with gget; Bioinformatics; Vol. 39; No. 1; Art. No. btac836; PMCID PMC9835474; 10.1093/bioinformatics/btac836
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• Moses, Lambda and Pachter, Lior (2022) Museum of spatial transcriptomics; Nature Methods; Vol. 19; No. 5; 534-546; 10.1038/s41592-022-01409-2
• Gorin, Gennady and Pachter, Lior (2022) Modeling bursty transcription and splicing with the chemical master equation; Biophysical Journal; Vol. 121; No. 6; 1056-1069; 10.1016/j.bpj.2022.02.004
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• Rahman, Atif and Pachter, Lior (2021) SWALO: scaffolding with assembly likelihood optimization; Nucleic Acids Research; Vol. 49; No. 20; Art. No. e117; 10.1093/nar/gkab717
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• Gorin, Gennady and Pachter, Lior (2021) Analysis of Length Biases in Single-Cell RNA Sequencing of Unspliced mRNA by Markov Modeling; Biophysical Journal; Vol. 120; No. 3; 81A; 10.1016/j.bpj.2020.11.706
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• Gorin, Gennady and Pachter, Lior (2020) Special function methods for bursty models of transcription; Physical Review E; Vol. 102; No. 2; Art. No. 022409; 10.1103/physreve.102.022409
• Koromila, Theodora and Gao, Fan, el al. (2020) Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos; eLife; Vol. 9; Art. No. e59610; PMCID PMC7417190; 10.7554/eLife.59610
• Mao, Shunfu and Pachter, Lior, el al. (2020) RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition; PLoS ONE; Vol. 15; No. 6; Art. No. e0232946; PMCID PMC7266320; 10.1371/journal.pone.0232946
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• Mihaescu, Radu and Pachter, Lior (2008) Combinatorics of least squares trees; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 36; 13206-13211; PMCID PMC2533170; 10.1073/pnas.0802089105
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• Stark, Alexander and Pachter, Lior (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures; Nature; Vol. 450; No. 7167; 219-232; PMCID PMC2474711; 10.1038/nature06340
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• Chatterji, Sourav and Pachter, Lior (2007) Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor; Genomics; Vol. 90; No. 1; 44-48; PMCID PMC2034525; 10.1016/j.ygeno.2007.03.008
• Birney, Ewan and Pachter, Lior, el al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project; Nature; Vol. 447; No. 7146; 799-816; PMCID PMC2212820; 10.1038/nature05874
• Pachter, Lior (2007) Interpreting the unculturable majority; Nature Methods; Vol. 4; No. 6; 479-480; 10.1038/nmeth0607-479
• Margulies, Elliott H. and Pachter, Lior, el al. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome; Genome Research; Vol. 17; No. 6; 760-774; PMCID PMC1891336; 10.1101/gr.6034307
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• Pachter, Lior and Sturmfels, Bernd (2007) The Mathematics of Phylogenomics; SIAM Review; Vol. 49; No. 1; 3-31; 10.1137/050632634
• Schwartz, Ariel S. and Pachter, Lior (2007) Multiple alignment by sequence annealing; Bioinformatics; Vol. 23; No. 2; e24-e29; 10.1093/bioinformatics/btl311
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• Dewey, Colin N. and Pachter, Lior (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment; Human Molecular Genetics; Vol. 15; No. Suppl. 1; R51-R56; 10.1093/hmg/ddl056
• Chatterji, Sourav and Pachter, Lior (2006) Reference based annotation with GeneMapper; Genome Biology; Vol. 7; No. 4; Art. No. R29; PMCID PMC1557983; 10.1186/gb-2006-7-4-r29
• Lall, Sabbi and Grün, Dominic, el al. (2006) A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans; Current Biology; Vol. 16; No. 5; 460-471; 10.1016/j.cub.2006.01.050
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• Caspi, Anat and Pachter, Lior (2006) Identification of transposable elements using multiple alignments of related genomes; Genome Research; Vol. 16; No. 2; 260-270; PMCID PMC1361722; 10.1101/gr.4361206
• Chatterji, Sourav and Pachter, Lior (2005) Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling; Journal of Computational Biology; Vol. 12; No. 6; 599-608; 10.1089/cmb.2005.12.599
• Chen, Kevin and Pachter, Lior (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities; PLoS Computational Biology; Vol. 1; No. 2; Art. No. e24; PMCID PMC1185649; 10.1371/journal.pcbi.0010024
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• Hillier, LaDeana W. and Pachter, Lior, el al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution; Nature; Vol. 432; No. 7018; 695-716; 10.1038/nature03154
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• Pachter, Lior and Sturmfels, Bernd (2004) Tropical Geometry of Statistical Models; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16132-16137; PMCID PMC528960; 10.1073/pnas.0406010101
• Feingold, E. A. and Pachter, L., el al. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project; Science; Vol. 306; No. 5696; 636-640; 10.1126/science.1105136
• McAuliffe, Jon D. and Pachter, Lior, el al. (2004) Multiple-sequence functional annotation and the generalized hidden Markov phylogeny; Bioinformatics; Vol. 20; No. 12; 1850-1860; 10.1093/bioinformatics/bth153
• Frazer, Kelly A. and Pachter, Lior, el al. (2004) VISTA: computational tools for comparative genomics; Nucleic Acids Research; Vol. 32; No. Suppl. 2; W273-W279; PMCID PMC441596; 10.1093/nar/gkh458
• Pachter, L. and Speyer, D. (2004) Reconstructing Trees from Subtree Weights; Applied Mathematics Letters; Vol. 17; No. 6; 615-621; 10.1016/S0893-9659(04)90095-X
• Gibbs, Richard A. and Pachter, Lior, el al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution; Nature; Vol. 428; No. 6982; 493-521; 10.1038/nature02426
• Chakrabarti, Kushal and Pachter, Lior (2004) Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER; Genome Research; Vol. 14; No. 4; 716-720; PMCID PMC383318; 10.1101/gr.1957004
• Dewey, Colin and Wu, Jia Qian, el al. (2004) Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat; Genome Research; Vol. 14; No. 4; 661-664; PMCID PMC383310; 10.1101/gr.1939804
• Yap, Von Bing and Pachter, Lior (2004) Identification of Evolutionary Hotspots in the Rodent Genomes; Genome Research; Vol. 14; No. 4; 574-579; PMCID PMC383301; 10.1101/gr.1967904
• Bray, Nicolas and Pachter, Lior (2004) MAVID: Constrained ancestral alignment of multiple sequences; Genome Research; Vol. 14; No. 4; 693-699; PMCID PMC383315; 10.1101/gr.1960404
• Cawley, Simon L. and Pachter, Lior (2003) HMM sampling and applications to gene finding and alternative splicing; Bioinformatics; Vol. 19; No. Suppl 2; ii36-ii41; 10.1093/bioinformatics/btg1057
• Lam, Fumei and Pachter, Lior (2003) Forcing numbers of stop signs; Theoretical Computer Science; Vol. 303; No. 2-3; 409-416; 10.1016/S0304-3975(02)00499-1
• Bray, Nicolas and Pachter, Lior (2003) MAVID multiple alignment server; Nucleic Acids Research; Vol. 31; No. 13; 3525-3526; PMCID PMC169029; 10.1093/nar/gkg623
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• Benos, Panayiotis and Pachter, Lior (2002) From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies; Genome Research; Vol. 11; No. 5; 710-730; PMCID PMC311117; 10.1101/gr.173801
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• Peter, Annette and Pachter, Lior (2002) Mapping and identification of essential gene functions on the X chromosome of Drosophila; EMBO Reports; Vol. 3; No. 1; 34-38; PMCID PMC1083931; 10.1093/embo-reports/kvf012
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• Kleitman, D. and Pachter, L. (1998) Finding Convex Sets Among Points in the Plane; Discrete and Computational Geometry; Vol. 19; No. 3; 405-410; 10.1007/PL00009358
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• Pachter, Lior (1997) Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes; Electronic Journal of Combinatorics; Vol. 4; No. 1; Art. No. R29