Pachter, Lior

Article from CaltechAUTHORS

• Felce, Catherine and Liorsdóttir, Steinunn, el al. (2025) Analogies between the virial theorem and the Price equation; Physical Review E; Vol. 112; No. 5; 054139; 10.1103/r8bd-lhm3
• Gorin, Gennady and Chari, Tara, el al. (2025) Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data; Nature Methods; Vol. 22; No. 11; 2286-2300; 10.1038/s41592-025-02832-x
• Luebbert, Laura and Sullivan, Delaney K., el al. (2025) Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes; Nature Biotechnology; 10.1038/s41587-025-02614-y
• Felce, Catherine and Gorin, Gennady, el al. (2024) Biophysical model for joint analysis of chromatin and RNA sequencing data; Physical Review E; Vol. 110; No. 6; 064405; 10.1103/physreve.110.064405
• 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, el al. (2024) PSCA-CAR T cell therapy in metastatic castration-resistant prostate cancer: a phase 1 trial; Nature Medicine; 10.1038/s41591-024-02979-8
• Sierra, Noemie and Olsman, Noah, el al. (2024) A novel approach to comparative RNA-Seq does not support a conserved set of orthologs underlying animal regeneration; Genome Biology and Evolution; Vol. 16; No. 6; evae120; PMCID PMC11214158; 10.1093/gbe/evae120
• Booeshaghi, Ali Sina and Chen, Xi, el al. (2024) A machine-readable specification for genomics assays; Bioinformatics; Vol. 40; No. 4; btae168; PMCID PMC11009023; 10.1093/bioinformatics/btae168
• Luebbert, Laura and Hoang, Chi, el al. (2024) Fast and scalable querying of eukaryotic linear motifs with gget elm; Bioinformatics; Vol. 40; No. 3; btae095; PMCID PMC10927331; 10.1093/bioinformatics/btae095
• 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
• Xiong, Lingyun and Liu, Jing, el al. (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, el al. (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., el al. (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
• Booeshaghi, A. Sina and Beltrame, Eduardo da Veiga, el al. (2023) Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system; Scientific Reports; Vol. 13; 14834; PMCID PMC10491597; 10.1038/s41598-023-42035-y
• 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, el al. (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), el al. (2023) Metadata retrieval from sequence databases with ffq; Bioinformatics; Vol. 39; No. 1; Art. No. btac667; PMCID PMC9883619; 10.1093/bioinformatics/btac667
• Gorin, Gennady and Vastola, John J., el al. (2022) Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments; Nature Communications; Vol. 13; Art. No. 7620; PMCID PMC9734650; 10.1038/s41467-022-34857-7
• Gorin, Gennady and Fang, Meichen, el al. (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
• Gayoso, Adam and Lopez, Romain, el al. (2022) A Python library for probabilistic analysis of single-cell omics data; Nature Biotechnology; Vol. 40; No. 2; 163-166; 10.1038/s41587-021-01206-w
• Chari, Tara and Weissbourd, Brandon, el al. (2021) Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types; Science Advances; Vol. 7; No. 48; Art. No. eabh1683; PMCID PMC8626072; 10.1126/sciadv.abh1683
• 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
• Yao, Zizhen and Liu, Hanqing, el al. (2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex; Nature; Vol. 598; No. 7879; 103-110; PMCID PMC8494649; 10.1038/s41586-021-03500-8
• Booeshaghi, A. Sina and Yao, Zizhen, el al. (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
• Adkins, Ricky S. and Aldridge, Andrew I., el al. (2021) A multimodal cell census and atlas of the mammalian primary motor cortex; Nature; Vol. 598; No. 7879; 86-102; 10.1038/s41586-021-03950-0
• Booeshaghi, A. Sina and Kil, Yeokyoung, el al. (2021) Low-cost, scalable, and automated fluid sampling for fluidics applications; HardwareX; Vol. 10; Art. No. e00201; 10.1016/j.ohx.2021.e00201
• 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, el al. (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, el al. (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
• Gustafsson, Johan and Robinson, Jonathan, el al. (2021) BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq; Genome Biology; Vol. 22; Art. No. 174; PMCID PMC8188791; 10.1186/s13059-021-02386-z
• Vastola, John J. and Gorin, Gennady, el al. (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., el al. (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
• Svensson, Valentine and da Veiga Beltrame, Eduardo, el al. (2020) A curated database reveals trends in single cell transcriptomics; Database: The Journal of Biological Databases and Curation; Vol. 2020; Art. No. baaa073; PMCID PMC7698659; 10.1093/database/baaa073
• Mehrab, Zakaria and Mobin, Jaiaid, el al. (2020) A faster implementation of association mapping from k-mers; Bio-protocol; Vol. 10; No. 21; Art. No. e3815; 10.21769/bioprotoc.3815
• 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
• Svensson, Valentine and Gayoso, Adam, el al. (2020) Interpretable factor models of single-cell RNA-seq via variational autoencoders; Bioinformatics; Vol. 36; No. 11; 3418-3421; PMCID PMC7267837; 10.1093/bioinformatics/btaa169
• Gorin, Gennady and Svensson, Valentine, el al. (2020) RNA velocity and protein acceleration from single-cell multiomics experiments; Genome Biology; Vol. 21; Art. No. 39; PMCID PMC7029606; 10.1186/s13059-020-1945-3
• Gehring, Jase and Park, Jong Hwee, el al. (2020) Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins; Nature Biotechnology; Vol. 38; No. 1; 35-38; 10.1038/s41587-019-0372-z
• Gao, Fan and da Veiga Beltrame, Eduardo, el al. (2019) The BUS Format for Single-Cell RNA-Seq Processing and Analysis; Journal of Biomolecular Techniques; Vol. 30; No. S1; S62; PMCID PMC6938108
• Melsted, Páll and Ntranos, Vasilis, el al. (2019) Barcode, UMI, Set format and BUStools; Bioinformatics; Vol. 35; No. 21; 4472-4473; 10.1093/bioinformatics/btz279
• Kim, Dong-Wook and Yao, Zizhen, el al. (2019) Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior; Cell; Vol. 179; No. 3; 713-728; PMCID PMC7534821; 10.1016/j.cell.2019.09.020
• Wright, Matthew and Goin, Dana, el al. (2019) Investigating the Post-Partum Flare in Rheumatoid Arthritis Using Transcriptome Analysis; Arthritis and Rheumatology; Vol. 71; No. S10; Art. No. 1940; 10.1002/art.41108
• Pathi, Amogh and Smed, Mette, el al. (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
• McCurdy, Shannon and Molinaro, Annette, el al. (2019) Factor analysis for survival time prediction with informative censoring and diverse covariates; Statistics in Medicine; Vol. 38; No. 20; 3719-3732; 10.1002/sim.8151
• Booeshaghi, A. Sina and da Veiga Beltrame, Eduardo, el al. (2019) Principles of open source bioinstrumentation applied to the poseidon syringe pump system; Scientific Reports; Vol. 9; 12385; PMCID PMC6711986; 10.1038/s41598-019-48815-9
• Ntranos, Vasilis and Yi, Lynn, el al. (2019) A discriminative learning approach to differential expression analysis for single-cell RNA-seq; Nature Methods; Vol. 16; No. 2; 163-166; 10.1038/s41592-018-0303-9
• McCurdy, Shannon R. and Ntranos, Vasilis, el al. (2019) Deterministic column subset selection for single-cell RNA-Seq; PLoS ONE; Vol. 14; No. 1; Art. No. e0210571; PMCID PMC6347249; 10.1371/journal.pone.0210571
• Tambe, Akshay and Pachter, Lior (2019) Barcode identification for single cell genomics; BMC Bioinformatics; Vol. 20; Art. No. 32; PMCID PMC6337828; 10.1186/s12859-019-2612-0
• Brown, Brielin C. and Bray, Nicolas L., el al. (2018) Expression reflects population structure; PLoS Genetics; Vol. 14; No. 12; Art. No. e1007841; PMCID PMC6317812; 10.1371/journal.pgen.1007841
• Svensson, Valentine and Pachter, Lior (2018) RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq; Molecular Cell; Vol. 72; No. 1; 7-9; 10.1016/j.molcel.2018.09.026
• Tunney, Robert and McGlincy, Nicholas J., el al. (2018) Accurate design of translational output by a neural network model of ribosome distribution; Nature Structural & Molecular Biology; Vol. 25; No. 7; 577-582; PMCID PMC6457438; 10.1038/s41594-018-0080-2
• Rahman, Atif and Hallgrímsdóttir, Ingileif, el al. (2018) Association mapping from sequencing reads using k-mers; eLife; Vol. 7; Art. No. e32920; PMCID PMC6044908; 10.7554/elife.32920
• Yi, Lynn and Pimentel, Harold, el al. (2018) Gene-level differential analysis at transcript-level resolution; Genome Biology; Vol. 19; Art. No. 53; PMCID PMC5896116; 10.1186/s13059-018-1419-z
• Goin, Dana E. and Smed, Mette, el al. (2017) Transcriptome Analysis in Women with Rheumatoid Arthritis Who Improve or Worsen during Pregnancy; Arthritis and Rheumatology; Vol. 69; No. S10; Art. No. 2433; 10.1002/art.40321
• Goin, Dana E. and Smed, Mette, el al. (2017) Longitudinal Changes in Gene Expression Associated with Disease Activity during Pregnancy and Post-Partum Among Women with Rheumatoid Arthritis; Arthritis and Rheumatology; Vol. 69; No. S10; Art. No. 2432; 10.1002/art.40321
• Schaeffer, L. and Pimentel, H., el al. (2017) Pseudoalignment for metagenomic read assignment; Bioinformatics; Vol. 33; No. 14; 2082-2088; PMCID PMC5870846; 10.1093/bioinformatics/btx106
• Pimentel, Harold and Bray, Nicolas L., el al. (2017) Differential analysis of RNA-seq incorporating quantification uncertainty; Nature Methods; Vol. 14; No. 7; 687-690; 10.1038/nmeth.4324
• Goin, Dana E. and Smed, Mette Kiel, el al. (2017) Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study; Arthritis Research and Therapy; Vol. 19; No. 1; Art. No. 104; PMCID PMC5445464; 10.1186/s13075-017-1312-2
• Li, Bo and Tambe, Akshay, el al. (2017) PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays; Cell Systems; Vol. 4; No. 5; 568-574; PMCID PMC5758053; 10.1016/j.cels.2017.04.007
• Yi, Lynn and Pimentel, Harold, el al. (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways; PLoS ONE; Vol. 12; No. 4; Art. No. e0175744; PMCID PMC5407828; 10.1371/journal.pone.0175744
• Pimentel, Harold and Sturmfels, Pascal, el al. (2016) The Lair: a resource for exploratory analysis of published RNA-Seq data; BMC Bioinformatics; Vol. 17; No. 1; Art. No. 490; PMCID PMC5131447; 10.1186/s12859-016-1357-2
• Fu, Audrey Qiuyan and Pachter, Lior (2016) Estimating intrinsic and extrinsic noise from single-cell gene expression measurements; Statistical Applications in Genetics and Molecular Biology; Vol. 15; No. 6; 447-471; PMCID PMC5518956; 10.1515/sagmb-2016-0002
• Chen, Xi and Love, J. Christopher, el al. (2016) Single-cell analysis at the threshold; Nature Biotechnology; Vol. 34; No. 11; 1111-1118; 10.1038/nbt.3721
• Hateley, Shannon and Hosamani, Ravikumar, el al. (2016) Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity; Genomics; Vol. 108; No. 3-4; 158-167; 10.1016/j.ygeno.2016.09.002
• Ntranos, Vasilis and Kamath, Govinda M., el al. (2016) Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts; Genome Biology; Vol. 17; No. 1; Art. No. 112; PMCID PMC4881296; 10.1186/s13059-016-0970-8
• Bray, Nicolas L. and Pimentel, Harold, el al. (2016) Near-optimal probabilistic RNA-seq quantification; Nature Biotechnology; Vol. 34; No. 5; 525-527; 10.1038/nbt.3519
• Pimentel, Harold and Parra, Marilyn, el al. (2016) A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis; Nucleic Acids Research; Vol. 44; No. 2; 838-851; PMCID PMC4737145; 10.1093/nar/gkv1168
• Mittal, Anuradha and Pachter, Lior, el al. (2015) Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis; PLOS ONE; Vol. 10; No. 12; Art. No. e0145204; PMCID PMC4684291; 10.1371/journal.pone.0145204
• Hanchate, Naresh K. and Kondoh, Kunio, el al. (2015) Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis; Science; Vol. 350; No. 6265; 1251-1255; PMCID PMC5642900; 10.1126/science.aad2456
• Paten, Benedict and Diekhans, Mark, el al. (2015) The NIH BD2K center for big data in translational genomics; Journal of the American Medical Informatics Association; Vol. 22; No. 6; 1143-1147; PMCID PMC5009913; 10.1093/jamia/ocv047
• Brat, Daniel J. and Pachter, Lior, el al. (2015) Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas; New England Journal of Medicine; Vol. 372; No. 26; 2481-2498; PMCID PMC4530011; 10.1056/NEJMoa1402121
• Singer, Meromit and Pachter, Lior (2015) Controlling for conservation in genome-wide DNA methylation studies; BMC Genomics; Vol. 16; Art. No. 420; PMCID PMC4448855; 10.1186/s12864-015-1604-3
• Singer, Meromit and Kosti, Idit, el al. (2015) A diverse epigenetic landscape at human exons with implication for expression; Nucleic Acids Research; Vol. 43; No. 7; 3498-3508; PMCID PMC4402514; 10.1093/nar/gkv153
• Aviran, Sharon and Pachter, Lior (2014) Rational experiment design for sequencing-based RNA structure mapping; RNA; Vol. 20; No. 12; 1864-1877; PMCID PMC4238353; 10.1261/rna.043844.113
• Forster, Ryan and Chiba, Kunitoshi, el al. (2014) Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells; Stem Cell Reports; Vol. 2; No. 6; 838-852; PMCID PMC4050346; 10.1016/j.stemcr.2014.05.001
• Wong, Valerie L. and Ellison, Christopher E., el al. (2014) Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum; PLoS ONE; Vol. 9; No. 5; Art. No. e96784; PMCID PMC4019546; 10.1371/journal.pone.0096784
• Takayama, Sachiko and Dhahbi, Joseph, el al. (2014) Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity; Genome Research; Vol. 24; No. 5; 821-830; PMCID PMC4009611; 10.1101/gr.162412.113
• Pimentel, Harold and Parra, Marilynn, el al. (2014) A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis; Nucleic Acids Research; Vol. 42; No. 6; 4031-4042; PMCID PMC3973340; 10.1093/nar/gkt1388
• Roberts, Adam and Feng, Harvey, el al. (2013) Fragment assignment in the cloud with eXpress-D; BMC Bioinformatics; Vol. 14; Art. No. 358; PMCID PMC3881492; 10.1186/1471-2105-14-358
• Roberts, Adam and Schaeffer, Lorian, el al. (2013) Updating RNA-Seq analyses after re-annotation; Bioinformatics; Vol. 29; No. 13; 1631-1637; PMCID PMC3694665; 10.1093/bioinformatics/btt197
• Kleinman, Aaron and Harel, Matan, el al. (2013) Affine and Projective Tree Metric Theorems; Annals of Combinatorics; Vol. 17; No. 1; 205-228; 10.1007/s00026-012-0173-2
• Rahman, Atif and Pachter, Lior (2013) CGAL: computing genome assembly likelihoods; Genome Biology; Vol. 14; No. 1; Art. No. R8; PMCID PMC3663106; 10.1186/gb-2013-14-1-r8
• Trapnell, Cole and Hendrickson, David G., el al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq; Nature Biotechnology; Vol. 31; No. 1; 46-53; PMCID PMC3869392; 10.1038/nbt.2450
• Roberts, Adam and Pachter, Lior (2013) Streaming fragment assignment for real-time analysis of sequencing experiments; Nature Methods; Vol. 10; No. 1; 71-73; PMCID PMC3880119; 10.1038/nmeth.2251
• Hower, Valerie and Starfield, Richard, el al. (2012) Quantifying uniformity of mapped reads; Bioinformatics; Vol. 28; No. 20; 2680-2682; PMCID PMC3467739; 10.1093/bioinformatics/bts451
• Trapnell, Cole and Roberts, Adam, el al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks; Nature Protocols; Vol. 7; No. 3; 562-578; PMCID PMC3334321; 10.1038/nprot.2012.016
• Pachter, Lior (2012) A closer look at RNA editing; Nature Biotechnology; Vol. 30; No. 3; 246-247; 10.1038/nbt.2156
• Martin, David I. K. and Singer, Meromit, el al. (2011) Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states; Genome Research; Vol. 21; No. 12; 2049-2057; PMCID PMC3227095; 10.1101/gr.122721.111
• Roberts, Adam and Pachter, Lior (2011) RNA-Seq and find: entering the RNA deep field; Genome Medicine; Vol. 3; No. 11; Art. No. 74; PMCID PMC3308029; 10.1186/gm290
• Meacham, Frazer and Boffelli, Dario, el al. (2011) Identification and correction of systematic error in high-throughput sequence data; BMC Bioinformatics; Vol. 12; Art. No. 451; PMCID PMC3295828; 10.1186/1471-2105-12-451
• Singer, Meromit and Engström, Alexander, el al. (2011) Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains; Statistical Applications in Genetics and Molecular Biology; Vol. 10; No. 1; Art. No. 43; 10.2202/1544-6115.1677
• Roberts, Adam and Pimentel, Harold, el al. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq; Bioinformatics; Vol. 27; No. 17; 2325-2329; 10.1093/bioinformatics/btr355
• Levy, Dan and Pachter, Lior (2011) The neighbor-net algorithm; Advances in Applied Mathematics; Vol. 47; No. 2; 240-258; 10.1016/j.aam.2010.09.002
• Snir, Sagi and Pachter, Lior (2011) Tracing the Most Parsimonious Indel History; Journal of Computational Biology; Vol. 18; No. 8; 967-986; 10.1089/cmb.2010.0325
• Lucks, Julius B. and Mortimer, Stefanie A., el al. (2011) 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; Vol. 108; No. 27; 11063-11068; PMCID PMC3131332; 10.1073/pnas.1106501108
• Aviran, Sharon and Trapnell, Cole, el al. (2011) Modeling and automation of sequencing-based characterization of RNA structure; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 27; 11069-11074; PMCID PMC3131376; 10.1073/pnas.1106541108
• Roberts, Adam and Trapnell, Cole, el al. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias; Genome Biology; Vol. 12; No. 3; Art. No. R22; PMCID PMC3129672; 10.1186/gb-2011-12-3-r22
• Hower, Valerie and Evans, Steven N., el al. (2011) Shape-based peak identification for ChIP-Seq; BMC Bioinformatics; Vol. 12; Art. No. 15; PMCID PMC3032669; 10.1186/1471-2105-12-15
• Willerth, Stephanie M. and Pedro, Hélder A. M., el al. (2010) Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology; PLOS ONE; Vol. 5; No. 10; Art. No. e13564; PMCID PMC2962647; 10.1371/journal.pone.0013564
• Evans, Steven N. and Hower, Valerie, el al. (2010) Coverage statistics for sequence census methods; BMC Bioinformatics; Vol. 11; Art. No. 430; PMCID PMC2940910; 10.1186/1471-2105-11-430
• Singer, Meromit and Boffelli, Dario, el al. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations; PLOS Computational Biology; Vol. 6; No. 8; Art. No. e1000888; PMCID PMC2924245; 10.1371/journal.pcbi.1000888
• Levin, Tera C. and Glazer, Andrew M., el al. (2010) Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study; PLOS ONE; Vol. 5; No. 7; Art. No. e11645; PMCID PMC2912228; 10.1371/journal.pone.0011645
• Lapuk, Anna and Marr, Henry, el al. (2010) Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer; Molecular Cancer Research; Vol. 8; No. 7; 961-974; PMCID PMC2911965; 10.1158/1541-7786.MCR-09-0528
• Trapnell, Cole and Williams, Brian A., el al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation; Nature Biotechnology; Vol. 28; No. 5; 511-515; PMCID PMC3146043; 10.1038/nbt.1621
• Bradley, Robert K. and Li, Xiao-Yong, el al. (2010) Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species; PLoS Biology; Vol. 8; No. 3; Art. No. e1000343; PMCID PMC2843597; 10.1371/journal.pbio.1000343
• Hilty, Markus and Burke, Conor, el al. (2010) Disordered Microbial Communities in Asthmatic Airways; PLOS ONE; Vol. 5; No. 1; Art. No. e8578; PMCID PMC2798952; 10.1371/journal.pone.0008578
• Morton, Jason and Pachter, Lior, el al. (2009) Convex Rank Tests and Semigraphoids; SIAM Journal on Discrete Mathematics; Vol. 23; No. 3; 1117-1134; 10.1137/080715822
• Trapnell, Cole and Pachter, Lior, el al. (2009) TopHat: discovering splice junctions with RNA-Seq; Bioinformatics; Vol. 25; No. 9; 1105-1111; PMCID PMC2672628; 10.1093/bioinformatics/btp120
• Mihaescu, Radu and Levy, Dan, el al. (2009) Why neighbor-joining works; Algorithmica; Vol. 54; No. 1; 1-24; 10.1007/s00453-007-9116-4
• Bradley, Robert K. and Roberts, Adam, el al. (2009) Fast Statistical Alignment; PLOS Computational Biology; Vol. 5; No. 5; Art. No. e1000392; PMCID PMC2684580; 10.1371/journal.pcbi.1000392
• Bradley, Robert K. and Pachter, Lior, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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
• Huggins, Peter and Pachter, Lior, el al. (2007) Towards the Human Genotope; Bulletin of Mathematical Biology; Vol. 69; No. 8; 2723-2735; 10.1007/s11538-007-9244-7
• Begun, David J. and Holloway, Alisha K., el al. (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
• Beerenwinkel, Niko and Pachter, Lior, el al. (2007) Epistasis and Shapes of Fitness Landscapes; Statistica Sinica; Vol. 17; No. 4; 1317-1342; 10.48550/arXiv.0603034
• Morton, Jason and Pachter, Lior, el al. (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, 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
• 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
• Pachter, Lior (2007) Interpreting the unculturable majority; Nature Methods; Vol. 4; No. 6; 479-480; 10.1038/nmeth0607-479
• Beerenwinkel, Niko and Pachter, Lior, el al. (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., el al. (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, 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
• Levy, Dan and Yoshida, Ruriko, el al. (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
• 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
• 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
• McAuliffe, Jon D. and Jordan, Michael I., el al. (2005) Subtree power analysis finds optimal species 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
• McAuliffe, Jon D. and Jordan, Michael I., el al. (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, 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
• Boffelli, Dario and Weer, Claire V., el al. (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) 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
• 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
• 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
• 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
• 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
• 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
• Cawley, Simon and Pachter, Lior, el al. (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
• Lam, Fumei and Alexandersson, Marina, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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
• 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
• Loots, Gabriela G. and Ovcharenko, Ivan, el al. (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
• 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, el al. (2000) VISTA : visualizing global DNA sequence alignments of arbitrary length; Bioinformatics; Vol. 16; No. 11; 1046-1047; 10.1093/bioinformatics/16.11.1046
• Dubchak, Inna and Brudno, Michael, el al. (2000) Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons; Genome Research; Vol. 10; No. 9; 1304-1306; PMCID PMC310906; 10.1101/gr.142200
• Batzoglou, Serafim and Pachter, Lior, el al. (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, el al. (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, el al. (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