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
• Dorff, Tanya B. and Blanchard, M. Suzette, et el. (2024) PSCA-CAR T cell therapy in metastatic castration-resistant prostate cancer: a phase 1 trial; Nature Medicine; 10.1038/s41591-024-02979-8
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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), et el. (2024) Quantifying orthogonal barcodes for sequence census assays; Bioinformatics Advances; Vol. 4; vbad181; PMCID PMC10783946; 10.1093/bioadv/vbad181
• Xiong, Lingyun and Liu, Jing, et el. (2023) Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney; Developmental Cell; Vol. 58; No. 21; 2338-2358.e5; PMCID PMC10873092; 10.1016/j.devcel.2023.08.010
• Gorin, Gennady and Yoshida, Shawn, et el. (2023) Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing; Bulletin of Mathematical Biology; Vol. 85; No. 11; 114; 10.1007/s11538-023-01213-9
• Gorin, Gennady and Vastola, John J., et el. (2023) Studying stochastic systems biology of the cell with single-cell genomics data; Cell Systems; Vol. 14; No. 10; 822-843.e22; PMCID PMC10725240; 10.1016/j.cels.2023.08.004
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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
• Fenelon, Kelli D. and Gao, Fan, et el. (2023) Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos; Frontiers in Cell and Developmental Biology; Vol. 11; Art. No. 1126507; PMCID PMC10083704; 10.3389/fcell.2023.1126507
• 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
• Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph), et el. (2023) Metadata retrieval from sequence databases with ffq; Bioinformatics; Vol. 39; No. 1; Art. No. btac667; PMCID PMC9883619; 10.1093/bioinformatics/btac667
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• Gorin, Gennady and Fang, Meichen, et el. (2022) RNA velocity unraveled; PLOS Computational Biology; Vol. 18; No. 9; Art. No. e1010492; PMCID PMC9499228; 10.1371/journal.pcbi.1010492
• 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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• Booeshaghi, A. Sina and Yao, Zizhen, et el. (2021) Isoform cell-type specificity in the mouse primary motor cortex; Nature; Vol. 598; No. 7879; 195-199; PMCID PMC8494650; 10.1038/s41586-021-03969-3
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• Booeshaghi, A. Sina and Pachter, Lior (2021) Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*; Bioinformatics; Vol. 37; No. 15; 2223-2224; PMCID PMC7989636; 10.1093/bioinformatics/btab085
• Bloom, Joshua S. and Sathe, Laila, et el. (2021) Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples; Nature Biomedical Engineering; Vol. 5; No. 7; 657-665; PMCID PMC7480060; 10.1038/s41551-021-00754-5
• Melsted, Páll and Booeshaghi, A. Sina, et el. (2021) Modular, efficient and constant-memory single-cell RNA-seq preprocessing; Nature Biotechnology; Vol. 39; No. 7; 813-818; 10.1038/s41587-021-00870-2
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• Vastola, John J. and Gorin, Gennady, et el. (2021) Learning the Dynamics of Bursty Transcription and Splicing using Ultra-Fast Parameter Inference and New Analytical Solutions of the Chemical Master Equation; Biophysical Journal; Vol. 120; No. 3; 135A; 10.1016/j.bpj.2020.11.1018
• 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
• Booeshaghi, A. Sina and Lubock, Nathan B., et el. (2020) Reliable and accurate diagnostics from highly multiplexed sequencing assays; Scientific Reports; Vol. 10; Art. No. 21759; PMCID PMC7730459; 10.1038/s41598-020-78942-7
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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, et el. (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, et el. (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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• Melsted, Páll and Ntranos, Vasilis, et el. (2019) Barcode, UMI, Set format and BUStools; Bioinformatics; Vol. 35; No. 21; 4472-4473; 10.1093/bioinformatics/btz279
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• Pathi, Amogh and Smed, Mette, et el. (2019) The Pre-pregnancy Rheumatoid Arthritis Gene Expression Signature Correlates with Improvement or Worsening of Disease Activity During Pregnancy: A Pilot Study; Arthritis and Rheumatology; Vol. 71; No. S10; Art. No. 1938; 10.1002/art.41108
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• Trapnell, Cole and Pachter, Lior, et el. (2009) TopHat: discovering splice junctions with RNA-Seq; Bioinformatics; Vol. 25; No. 9; 1105-1111; PMCID PMC2672628; 10.1093/bioinformatics/btp120
• Bradley, Robert K. and Roberts, Adam, et el. (2009) Fast Statistical Alignment; PLOS Computational Biology; Vol. 5; No. 5; Art. No. e1000392; PMCID PMC2684580; 10.1371/journal.pcbi.1000392
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• Bradley, Robert K. and Pachter, Lior, et el. (2008) Specific alignment of structured RNA: stochastic grammars and sequence annealing; Bioinformatics; Vol. 24; No. 23; 2677-2683; PMCID PMC2732270; 10.1093/bioinformatics/btn495
• 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
• Dequéant, Mary-Lee and Ahnert, Sebastian, et el. (2008) Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock; PLOS ONE; Vol. 3; No. 8; Art. No. e2856; PMCID PMC2481401; 10.1371/journal.pone.0002856
• Satija, Rahul and Pachter, Lior, et el. (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements; Bioinformatics; Vol. 24; No. 10; 1236-1242; 10.1093/bioinformatics/btn104
• Tesler, Glenn and Eriksson, Nicholas, et el. (2008) Viral Population Estimation Using Pyrosequencing; PLoS Computational Biology; Vol. 4; No. 5; Art. No. e1000074; PMCID PMC2323617; 10.1371/journal.pcbi.1000074
• Eickmeyer, Kord and Huggins, Peter, et el. (2008) On the optimality of the neighbor-joining algorithm; Algorithms for Molecular Biology; Vol. 3; Art. No. 5; PMCID PMC2430562; 10.1186/1748-7188-3-5
• Clark, Andrew G. and Pachter, Lior, et el. (2007) Evolution of genes and genomes on the Drosophila phylogeny; Nature; Vol. 450; No. 7167; 203-218; 10.1038/nature06341
• 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
• Begun, David J. and Holloway, Alisha K., et el. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans; PLoS Biology; Vol. 5; No. 11; Art. No. e310; PMCID PMC2062478; 10.1371/journal.pbio.0050310
• Huggins, Peter and Pachter, Lior, et el. (2007) Towards the Human Genotope; Bulletin of Mathematical Biology; Vol. 69; No. 8; 2723-2735; 10.1007/s11538-007-9244-7
• Beerenwinkel, Niko and Pachter, Lior, et el. (2007) Epistasis and Shapes of Fitness Landscapes; Statistica Sinica; Vol. 17; No. 4; 1317-1342; 10.48550/arXiv.0603034
• Morton, Jason and Pachter, Lior, et el. (2007) The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies; Statistical Applications in Genetics and Molecular Biology; Vol. 6; Art. No. 21; 10.2202/1544-6115.1286
• 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, et el. (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
• Margulies, Elliott H. and Pachter, Lior, et el. (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
• Pachter, Lior (2007) Interpreting the unculturable majority; Nature Methods; Vol. 4; No. 6; 479-480; 10.1038/nmeth0607-479
• Beerenwinkel, Niko and Pachter, Lior, et el. (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach; BMC Evolutionary Biology; Vol. 7; Art. No. 60; PMCID PMC1865543; 10.1186/1471-2148-7-60
• 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
• Dewey, Colin N. and Huggins, Peter M., et el. (2006) Parametric Alignment of Drosophila Genomes; PLoS Computational Biology; Vol. 2; No. 6; Art. No. e73; PMCID PMC1480539; 10.1371/journal.pcbi.0020073
• 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, et el. (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
• Levy, Dan and Yoshida, Ruriko, et el. (2006) Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates; Molecular Biology and Evolution; Vol. 23; No. 3; 491-498; 10.1093/molbev/msj059
• 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
• McAuliffe, Jon D. and Jordan, Michael I., et el. (2005) Subtree power analysis and species selection for comparative genomics; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 22; 7900-7905; PMCID PMC1142384; 10.1073/pnas.0502790102
• Hillier, LaDeana W. and Pachter, Lior, et el. (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
• Boffelli, Dario and Weer, Claire V., et el. (2004) Intraspecies sequence comparisons for annotating genomes; Genome Research; Vol. 14; No. 12; 2406-2411; PMCID PMC534664; 10.1101/gr.3199704
• Pachter, Lior and Sturmfels, Bernd (2004) Parametric Inference for Biological Sequence Analysis; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16138-16143; PMCID PMC528961; 10.1073/pnas.0406011101
• 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., et el. (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, et el. (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, et el. (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, et el. (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
• 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
• Dewey, Colin and Wu, Jia Qian, et el. (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
• 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
• Cawley, Simon and Pachter, Lior, et el. (2003) SLAM web server for comparative gene finding and alignment; Nucleic Acids Research; Vol. 31; No. 13; 3507-3509; PMCID PMC168989; 10.1093/nar/gkg583
• 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
• Lam, Fumei and Alexandersson, Marina, et el. (2003) Picking Alignments from (Steiner) Trees; Journal of Computational Biology; Vol. 10; No. 3-4; 509-520; 10.1089/10665270360688156
• Alexandersson, Marina and Cawley, Simon, et el. (2003) SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model; Genome Research; Vol. 13; No. 3; 496-502; PMCID PMC430255; 10.1101/gr.424203
• Boffelli, Dario and McAuliffe, Jon, et el. (2003) Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome; Science; Vol. 299; No. 5611; 1391-1394; 10.1126/science.1081331
• Bray, Nick and Dubchak, Inna, et el. (2003) AVID: A Global Alignment Program; Genome Research; Vol. 13; No. 1; 97-102; PMCID PMC430967; 10.1101/gr.789803
• Couronne, Olivier and Poliakov, Alexander, et el. (2003) Strategies and Tools for Whole-Genome Alignments; Genome Research; Vol. 13; No. 1; 73-80; PMCID PMC430965; 10.1101/gr.762503
• Waterston, Robert H. and Pachter, Lior, et el. (2002) Initial sequencing and comparative analysis of the mouse genome; Nature; Vol. 420; No. 6915; 520-562; 10.1038/nature01262
• Pachter, Lior and Alexandersson, Marina, et el. (2002) Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems; Journal of Computational Biology; Vol. 9; No. 2; 389-399; 10.1089/10665270252935520
• Loots, Gabriela G. and Ovcharenko, Ivan, et el. (2002) rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites; Genome Research; Vol. 12; No. 5; 832-839; PMCID PMC186580; 10.1101/gr.225502
• 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
• Dubchak, Inna and Pachter, Lior (2002) The computational challenges of applying comparative-based computational methods to whole genomes; Briefings in Bioinformatics; Vol. 3; No. 1; 18-22; 10.1093/bib/3.1.18
• 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
• Mayor, Chris and Brudno, Michael, et el. (2000) VISTA : visualizing global DNA sequence alignments of arbitrary length; Bioinformatics; Vol. 16; No. 11; 1046-1047; 10.1093/bioinformatics/16.11.1046
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• Batzoglou, Serafim and Pachter, Lior, et el. (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction; Genome Research; Vol. 10; No. 7; 950-958; PMCID PMC310911; 10.1101/gr.10.7.950
• Pachter, Lior and Batzoglou, Serafim, et el. (1999) A Dictionary-Based Approach for Gene Annotation; Journal of Computational Biology; Vol. 6; No. 3-4; 419-430; 10.1089/106652799318364
• Pachter, Lior and Kim, Peter (1998) Forcing matchings on square grids; Discrete Mathematics; Vol. 190; No. 1-3; 287-294; 10.1016/S0012-365X(97)00266-5
• 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
• Batzoglou, Serafim and Berger, Bonnie, et el. (1998) Recent Developments in Computational Gene Recognition; Documenta Mathematica; Vol. ICM I; 649-658
• Pachter, Lior (1997) Constructing status injective graphs; Discrete Applied Mathematics; Vol. 80; No. 1; 107-113; 10.1016/S0166-218X(97)00073-5
• 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