Pachter, Lior

Combined 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
• Sierra, Noemie and Olsman, Noah, et el. (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
• Rich, Joseph M. and Moses, Lambda, et el. (2024) The impact of package selection and versioning on single-cell RNA-seq analysis; PMCID PMC11014608; 10.1101/2024.04.04.588111
• Booeshaghi, Ali Sina and Chen, Xi, et el. (2024) A machine-readable specification for genomics assays; Bioinformatics; Vol. 40; No. 4; btae168; PMCID PMC11009023; 10.1093/bioinformatics/btae168
• Booeshaghi, A. Sina and Galvez-Merchán, Ángel, et el. (2024) Algorithms for a Commons Cell Atlas; 10.1101/2024.03.23.586413
• Galvez-Merchán, Ángel and Booeshaghi, A. Sina, et el. (2024) A human commons cell atlas reveals cell type specificity for OAS1 isoforms; 10.1101/2024.03.23.586412
• Luebbert, Laura and Hoang, Chi, et el. (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), 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
• Booeshaghi, A. Sina and Beltrame, Eduardo da Veiga, et el. (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
• Gorin, Gennady and Vastola, John J., et el. (2023) Studying stochastic systems biology of the cell with single-cell genomics data; PMCID PMC10245677; 10.1101/2023.05.17.541250
• Xiong, Lingyun and Liu, Jing, et el. (2023) Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney; PMCID PMC10187285; 10.1101/2023.05.06.539585
• 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
• Sullivan, Delaney K. and Pachter, Lior (2023) Flexible parsing and preprocessing of technical sequences with splitcode; PMCID PMC10055216; 10.1101/2023.03.20.533521
• Booeshaghi, A. Sina and Chen, Xi, et el. (2023) A machine-readable specification for genomics assays; 10.1101/2023.03.17.533215
• Gorin, Gennady and Yoshida, Shawn, et el. (2023) Transient and delay chemical master equations; 10.1101/2022.10.17.512599
• Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph), et el. (2023) Quantifying orthogonal barcodes for sequence census assays; 10.1101/2022.10.09.511501
• Gorin, Gennady and Pachter, Lior (2023) The telegraph process is not a subordinator; 10.1101/2023.01.17.524309
• Carilli, Maria and Gorin, Gennady, et el. (2023) Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data; 10.1101/2023.01.13.523995
• Fenelon, Kelli D. and Gao, Fan, et el. (2023) Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos; 10.1101/2022.12.15.519123
• Hjorleifsson, Kristján Eldjárn and Sullivan, Delaney K., et el. (2023) Accurate quantification of single-nucleus and single-cell RNA-seq transcripts; 10.1101/2022.12.02.518832
• Hjorleifsson, Kristján Eldjárn and Pachter, Lior, et el. (2023) Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes; 10.1101/2022.12.02.518787
• 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
• Gorin, Gennady and Vastola, John J., et el. (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, et el. (2022) RNA velocity unraveled; PLOS Computational Biology; Vol. 18; No. 9; Art. No. e1010492; PMCID PMC9499228; 10.1371/journal.pcbi.1010492
• Gorin, Gennady and Carilli, Maria, et el. (2022) Spectral neural approximations for models of transcriptional dynamics; 10.1101/2022.06.16.496448
• Gorin, Gennady and Pachter, Lior (2022) Monod: mechanistic analysis of single-cell RNA sequencing count data; 10.1101/2022.06.11.495771
• Booeshaghi, A. Sina and Pachter, Lior (2022) Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads; 10.1101/2022.06.04.494845
• Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph), et el. (2022) Metadata retrieval from sequence databases with ffq; 10.1101/2022.05.18.492548
• Luebbert, Laura and Pachter, Lior (2022) Efficient querying of genomic reference databases with gget; 10.1101/2022.05.17.492392
• Booeshaghi, A. Sina and Hallgrímsdóttir, Ingileif B., et el. (2022) Depth normalization for single-cell genomics count data; 10.1101/2022.05.06.490859
• 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
• Gorin, Gennady and Fang, Meichen, et el. (2022) RNA velocity unraveled; 10.1101/2022.02.12.480214
• Gayoso, Adam and Lopez, Romain, et el. (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
• Gao, Fan and Pachter, Lior (2021) Efficient pre-processing of Single-cell ATAC-seq data; 10.1101/2021.12.08.471788
• Chari, Tara and Weissbourd, Brandon, et el. (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
• 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
• Adkins, Ricky S. and Aldridge, Andrew I., et el. (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
• Yao, Zizhen and Liu, Hanqing, et el. (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 Kil, Yeokyoung, et el. (2021) Low-cost, scalable, and automated fluid sampling for fluidics applications; HardwareX; Vol. 10; Art. No. e00201; 10.1016/j.ohx.2021.e00201
• Gorin, Gennady and Vastola, John J., et el. (2021) Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments; 10.1101/2021.09.06.459173
• Chari, Tara and Banerjee, Joeyta, et el. (2021) The Specious Art of Single-Cell Genomics; 10.1101/2021.08.25.457696
• Gorin, Gennady and Pachter, Lior (2021) Length Biases in Single-Cell RNA Sequencing of pre-mRNA; 10.1101/2021.07.30.454514
• 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
• Gustafsson, Johan and Robinson, Jonathan, et el. (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
• Sierra, Noemie and Olsman, Noah, et el. (2021) A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration; 10.1101/2021.03.22.434850
• 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
• 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
• Booeshaghi, A. Sina and Pachter, Lior (2021) Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing; 10.1101/2021.01.25.428188
• Gorin, Gennady and Pachter, Lior (2021) Direct simulation of a stochastically driven multi-step birth-death process; 10.1101/2021.01.20.427480
• 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
• Svensson, Valentine and da Veiga Beltrame, Eduardo, et el. (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, et el. (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) Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production; 10.1101/2020.09.25.312868
• Booeshaghi, A. Sina and Tan, Fayth, et el. (2020) Markedly heterogeneous COVID-19 testing plans among US colleges and universities; 10.1101/2020.08.09.20171223
• 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
• Svensson, Valentine and Gayoso, Adam, et el. (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
• Booeshaghi, A. Sina and Pachter, Lior (2020) Decrease in ACE2 mRNA expression in aged mouse lung; 10.1101/2020.04.02.021451
• Gorin, Gennady and Svensson, Valentine, et el. (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, et el. (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, et el. (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, et el. (2019) Barcode, UMI, Set format and BUStools; Bioinformatics; Vol. 35; No. 21; 4472-4473; 10.1093/bioinformatics/btz279
• Kim, Dong-Wook and Yao, Zizhen, et el. (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
• 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
• Wright, Matthew and Goin, Dana, et el. (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
• McCurdy, Shannon and Molinaro, Annette, et el. (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
• Svensson, Valentine and da Veiga Beltrame, Eduardo, et el. (2019) Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq; 10.1101/762773
• Booeshaghi, A. Sina and da Veiga Beltrame, Eduardo, et el. (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
• Melsted, Páll and Booeshaghi, A. Sina, et el. (2019) Modular and efficient pre-processing of single-cell RNA-seq; 10.1101/673285
• McGee, Warren A. and Pimentel, Harold, et el. (2019) Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data; 10.1101/564955
• Ntranos, Vasilis and Yi, Lynn, et el. (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, et el. (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., et el. (2018) Expression reflects population structure; PLoS Genetics; Vol. 14; No. 12; Art. No. e1007841; PMCID PMC6317812; 10.1371/journal.pgen.1007841
• Ntranos, Vasilis and Yi, Lynn, et el. (2018) Identification of transcriptional signatures for cell types from single-cell RNA-Seq; 10.1101/258566
• Yi, Lynn and Liu, Lauren, et el. (2018) A direct comparison of genome alignment and transcriptome pseudoalignment; 10.1101/444620
• Melsted, Páll and Hateley, Shannon, et el. (2018) Fusion detection and quantification by pseudoalignment; 10.1101/166322
• 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., et el. (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, et el. (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, et el. (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, et el. (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, et el. (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., et el. (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., et el. (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, et el. (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, et el. (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, et el. (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
• Schwartz, Ariel S. and Myers, Eugene W., et el. (2017) Alignment Metric Accuracy; 10.48550/arXiv.0510052
• Guigó, Roderic and Birney, Ewan, et el. (2017) Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models; 10.48550/arXiv.0410008
• Tambe, Akshay and Doudna, Jennifer, et el. (2017) Identifying RNA contacts from SHAPE-MaP by partial correlation analysis; 10.48550/arXiv.1412.3800
• McAuliffe, Jon D. and Jordan, Michael I., et el. (2017) 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
• Huggins, Peter and Pachter, Lior (2017) Selecting universities: personal preference and rankings; 10.48550/arXiv.0805.1026
• Bray, Nicolas and Pachter, Lior (2017) Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions"; 10.48550/arXiv.1212.3076
• Levy, Dan and Yoshida, Ruriko, et el. (2017) Neighbor joining with phylogenetic diversity estimates; 10.48550/arXiv.0508001
• Pachter, Lior (2017) Models for transcript quantification from RNA-Seq; 10.48550/arXiv.1104.3889
• Pimentel, Harold and Conboy, John G., et el. (2017) Keep Me Around: Intron Retention Detection and Analysis; 10.48550/arXiv.1510.00696
• Bray, Nicolas L. and Pimentel, Harold, et el. (2017) Near-optimal RNA-Seq quantification; 10.48550/arXiv.1505.02710v2
• Pimentel, Harold and Sturmfels, Pascal, et el. (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, et el. (2016) Single-cell analysis at the threshold; Nature Biotechnology; Vol. 34; No. 11; 1111-1118; 10.1038/nbt.3721
• Hateley, Shannon and Hosamani, Ravikumar, et el. (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., et el. (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, et el. (2016) Near-optimal probabilistic RNA-seq quantification; Nature Biotechnology; Vol. 34; No. 5; 525-527; 10.1038/nbt.3519
• Pimentel, Harold and Parra, Marilyn, et el. (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, et el. (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, et el. (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, et el. (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, et el. (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, et el. (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
• Singer, Meromit and Pachter, Lior (2014) Bayesian Networks in the Study of Genome-wide DNA Methylation; ISBN 9780198709022; Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics; 363-386; 10.1093/acprof:oso/9780198709022.003.0014
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• 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., et el. (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
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• 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
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• Singer, Meromit and Boffelli, Dario, et el. (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
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• Morton, Jason and Pachter, Lior, et el. (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, et el. (2009) TopHat: discovering splice junctions with RNA-Seq; Bioinformatics; Vol. 25; No. 9; 1105-1111; PMCID PMC2672628; 10.1093/bioinformatics/btp120
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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
• 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
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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
• 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
• 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
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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
• Pachter, Lior (2007) An introduction to reconstructing ancestral genomes; ISBN 978-0-8218-3964-5; Modeling and Simulation of Biological Networks; 10-29; 10.48550/arXiv.0612046
• Morton, Jason and Pachter, Lior, et el. (2006) Geometry of rank tests; ISBN 9788086742144; Proceedings of the 3rd European Workshop on Probabilistic Graphical Models; Art. No.7; 10.48550/arXiv.0605173
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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
• Snir, Sagi and Pachter, Lior (2006) Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes; ISBN 978-3-540-33295-4; Research in Computational Molecular Biology; 265-280; 10.1007/11732990_23
• 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
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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, 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
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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
• 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., 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
• 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
• 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
• 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
• Chatterji, Sourav and Pachter, Lior (2004) Multiple organism gene finding by collapsed Gibbs sampling; ISBN 1-58113-755-9; Proceedings of the eighth annual international conference on Computational molecular biology (RECOMB '04); 187-193; 10.1145/974614.974639
• 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
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• 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
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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
• Pachter, L. S. and Pachter, M. (2001) Optimal paths for avoiding a radiating source; ISBN 9780780370616; Proceedings of the 40th IEEE Conference on Decision and Control : December 4-7, 2001 : Hyatt Regency Grand Cypress, Orlando, Florida, USA; 3581-3586; 10.1109/CDC.2001.980415
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• 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
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