<h1>Pachter, Lior</h1>
<h2>Article from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2>
<ul>
<li>Sullivan, Delaney K. and Pachter, Lior (2024) <a href="https://authors.library.caltech.edu/records/hfsjy-tmv33">Flexible parsing, interpretation, and editing of technical sequences with splitcode</a>; Bioinformatics; Vol. 40; No. 6; btae331; PMCID PMC11193061; <a href="https://doi.org/10.1093/bioinformatics/btae331">10.1093/bioinformatics/btae331</a></li>
<li>Dorff, Tanya B. and Blanchard, M. Suzette, el al. (2024) <a href="https://authors.library.caltech.edu/records/svck4-6m833">PSCA-CAR T cell therapy in metastatic castration-resistant prostate cancer: a phase 1 trial</a>; Nature Medicine; <a href="https://doi.org/10.1038/s41591-024-02979-8">10.1038/s41591-024-02979-8</a></li>
<li>Sierra, Noemie and Olsman, Noah, el al. (2024) <a href="https://authors.library.caltech.edu/records/gzq6b-6e424">A novel approach to comparative RNA-Seq does not support a conserved set of orthologs underlying animal regeneration</a>; Genome Biology and Evolution; Vol. 16; No. 6; evae120; PMCID PMC11214158; <a href="https://doi.org/10.1093/gbe/evae120">10.1093/gbe/evae120</a></li>
<li>Booeshaghi, Ali Sina and Chen, Xi, el al. (2024) <a href="https://authors.library.caltech.edu/records/q7w89-9xr46">A machine-readable specification for genomics assays</a>; Bioinformatics; Vol. 40; No. 4; btae168; PMCID PMC11009023; <a href="https://doi.org/10.1093/bioinformatics/btae168">10.1093/bioinformatics/btae168</a></li>
<li>Luebbert, Laura and Hoang, Chi, el al. (2024) <a href="https://authors.library.caltech.edu/records/y0p8m-yqm72">Fast and scalable querying of eukaryotic linear motifs with gget elm</a>; Bioinformatics; Vol. 40; No. 3; btae095; PMCID PMC10927331; <a href="https://doi.org/10.1093/bioinformatics/btae095">10.1093/bioinformatics/btae095</a></li>
<li>Gorin, Gennady and Pachter, Lior (2024) <a href="https://authors.library.caltech.edu/records/4bdzc-r3y87">New and notable: Revisiting the &quot;two cultures&quot; through extrinsic noise</a>; Biophysical Journal; Vol. 123; No. 1; 1-3; <a href="https://doi.org/10.1016/j.bpj.2023.11.3400">10.1016/j.bpj.2023.11.3400</a></li>
<li>Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph), el al. (2024) <a href="https://authors.library.caltech.edu/records/axtf4-cb576">Quantifying orthogonal barcodes for sequence census assays</a>; Bioinformatics Advances; Vol. 4; vbad181; PMCID PMC10783946; <a href="https://doi.org/10.1093/bioadv/vbad181">10.1093/bioadv/vbad181</a></li>
<li>Xiong, Lingyun and Liu, Jing, el al. (2023) <a href="https://authors.library.caltech.edu/records/ntw84-7bx60">Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney</a>; Developmental Cell; Vol. 58; No. 21; 2338-2358.e5; PMCID PMC10873092; <a href="https://doi.org/10.1016/j.devcel.2023.08.010">10.1016/j.devcel.2023.08.010</a></li>
<li>Gorin, Gennady and Yoshida, Shawn, el al. (2023) <a href="https://authors.library.caltech.edu/records/5z5v2-jjy66">Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing</a>; Bulletin of Mathematical Biology; Vol. 85; No. 11; 114; <a href="https://doi.org/10.1007/s11538-023-01213-9">10.1007/s11538-023-01213-9</a></li>
<li>Gorin, Gennady and Vastola, John J., el al. (2023) <a href="https://authors.library.caltech.edu/records/x9gbd-0gk44">Studying stochastic systems biology of the cell with single-cell genomics data</a>; Cell Systems; Vol. 14; No. 10; 822-843.e22; PMCID PMC10725240; <a href="https://doi.org/10.1016/j.cels.2023.08.004">10.1016/j.cels.2023.08.004</a></li>
<li>Booeshaghi, A. Sina and Beltrame, Eduardo da Veiga, el al. (2023) <a href="https://authors.library.caltech.edu/records/hs9mc-jb762">Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system</a>; Scientific Reports; Vol. 13; 14834; PMCID PMC10491597; <a href="https://doi.org/10.1038/s41598-023-42035-y">10.1038/s41598-023-42035-y</a></li>
<li>Jackson, Kayla C. and Pachter, Lior (2023) <a href="https://authors.library.caltech.edu/records/ewrjt-pbk58">A standard for sharing spatial transcriptomics data</a>; Cell Genomics; Vol. 3; No. 8; 100374; PMCID PMC10435375; <a href="https://doi.org/10.1016/j.xgen.2023.100374">10.1016/j.xgen.2023.100374</a></li>
<li>Chari, Tara and Pachter, Lior (2023) <a href="https://authors.library.caltech.edu/records/fzh9v-hjh15">The specious art of single-cell genomics</a>; PLOS Computational Biology; Vol. 19; No. 8; e1011288; PMCID PMC10434946; <a href="https://doi.org/10.1371/journal.pcbi.1011288">10.1371/journal.pcbi.1011288</a></li>
<li>Fenelon, Kelli D. and Gao, Fan, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230502-708586900.1">Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos</a>; Frontiers in Cell and Developmental Biology; Vol. 11; Art. No. 1126507; PMCID PMC10083704; <a href="https://doi.org/10.3389/fcell.2023.1126507">10.3389/fcell.2023.1126507</a></li>
<li>Luebbert, Laura and Pachter, Lior (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230725-706344000.34">Efficient querying of genomic reference databases with gget</a>; Bioinformatics; Vol. 39; No. 1; Art. No. btac836; PMCID PMC9835474; <a href="https://doi.org/10.1093/bioinformatics/btac836">10.1093/bioinformatics/btac836</a></li>
<li>Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph), el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230411-694477200.2">Metadata retrieval from sequence databases with ffq</a>; Bioinformatics; Vol. 39; No. 1; Art. No. btac667; PMCID PMC9883619; <a href="https://doi.org/10.1093/bioinformatics/btac667">10.1093/bioinformatics/btac667</a></li>
<li>Gorin, Gennady and Vastola, John J., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230622-883274000.1">Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments</a>; Nature Communications; Vol. 13; Art. No. 7620; PMCID PMC9734650; <a href="https://doi.org/10.1038/s41467-022-34857-7">10.1038/s41467-022-34857-7</a></li>
<li>Gorin, Gennady and Fang, Meichen, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220916-665804000.785">RNA velocity unraveled</a>; PLOS Computational Biology; Vol. 18; No. 9; Art. No. e1010492; PMCID PMC9499228; <a href="https://doi.org/10.1371/journal.pcbi.1010492">10.1371/journal.pcbi.1010492</a></li>
<li>Moses, Lambda and Pachter, Lior (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210513-122736659">Museum of spatial transcriptomics</a>; Nature Methods; Vol. 19; No. 5; 534-546; <a href="https://doi.org/10.1038/s41592-022-01409-2">10.1038/s41592-022-01409-2</a></li>
<li>Gorin, Gennady and Pachter, Lior (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210325-075042340">Modeling bursty transcription and splicing with the chemical master equation</a>; Biophysical Journal; Vol. 121; No. 6; 1056-1069; <a href="https://doi.org/10.1016/j.bpj.2022.02.004">10.1016/j.bpj.2022.02.004</a></li>
<li>Gayoso, Adam and Lopez, Romain, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210503-142332959">A Python library for probabilistic analysis of single-cell omics data</a>; Nature Biotechnology; Vol. 40; No. 2; 163-166; <a href="https://doi.org/10.1038/s41587-021-01206-w">10.1038/s41587-021-01206-w</a></li>
<li>Chari, Tara and Weissbourd, Brandon, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210126-133110736">Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types</a>; Science Advances; Vol. 7; No. 48; Art. No. eabh1683; PMCID PMC8626072; <a href="https://doi.org/10.1126/sciadv.abh1683">10.1126/sciadv.abh1683</a></li>
<li>Rahman, Atif and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210930-221100053">SWALO: scaffolding with assembly likelihood optimization</a>; Nucleic Acids Research; Vol. 49; No. 20; Art. No. e117; <a href="https://doi.org/10.1093/nar/gkab717">10.1093/nar/gkab717</a></li>
<li>Adkins, Ricky S. and Aldridge, Andrew I., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201027-075126222">A multimodal cell census and atlas of the mammalian primary motor cortex</a>; Nature; Vol. 598; No. 7879; 86-102; <a href="https://doi.org/10.1038/s41586-021-03950-0">10.1038/s41586-021-03950-0</a></li>
<li>Yao, Zizhen and Liu, Hanqing, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200303-153620082">A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex</a>; Nature; Vol. 598; No. 7879; 103-110; PMCID PMC8494649; <a href="https://doi.org/10.1038/s41586-021-03500-8">10.1038/s41586-021-03500-8</a></li>
<li>Booeshaghi, A. Sina and Yao, Zizhen, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200306-130944112">Isoform cell-type specificity in the mouse primary motor cortex</a>; Nature; Vol. 598; No. 7879; 195-199; PMCID PMC8494650; <a href="https://doi.org/10.1038/s41586-021-03969-3">10.1038/s41586-021-03969-3</a></li>
<li>Booeshaghi, A. Sina and Kil, Yeokyoung, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210129-070700034">Low-cost, scalable, and automated fluid sampling for fluidics applications</a>; HardwareX; Vol. 10; Art. No. e00201; <a href="https://doi.org/10.1016/j.ohx.2021.e00201">10.1016/j.ohx.2021.e00201</a></li>
<li>Booeshaghi, A. Sina and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200520-084505912">Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*</a>; Bioinformatics; Vol. 37; No. 15; 2223-2224; PMCID PMC7989636; <a href="https://doi.org/10.1093/bioinformatics/btab085">10.1093/bioinformatics/btab085</a></li>
<li>Bloom, Joshua S. and Sathe, Laila, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980">Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples</a>; Nature Biomedical Engineering; Vol. 5; No. 7; 657-665; PMCID PMC7480060; <a href="https://doi.org/10.1038/s41551-021-00754-5">10.1038/s41551-021-00754-5</a></li>
<li>Melsted, Páll and Booeshaghi, A. Sina, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210405-142728694">Modular, efficient and constant-memory single-cell RNA-seq preprocessing</a>; Nature Biotechnology; Vol. 39; No. 7; 813-818; <a href="https://doi.org/10.1038/s41587-021-00870-2">10.1038/s41587-021-00870-2</a></li>
<li>Gustafsson, Johan and Robinson, Jonathan, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200707-114817234">BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq</a>; Genome Biology; Vol. 22; Art. No. 174; PMCID PMC8188791; <a href="https://doi.org/10.1186/s13059-021-02386-z">10.1186/s13059-021-02386-z</a></li>
<li>Gorin, Gennady and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210503-100056268">Analysis of Length Biases in Single-Cell RNA Sequencing of Unspliced mRNA by Markov Modeling</a>; Biophysical Journal; Vol. 120; No. 3; 81A; <a href="https://doi.org/10.1016/j.bpj.2020.11.706">10.1016/j.bpj.2020.11.706</a></li>
<li>Vastola, John J. and Gorin, Gennady, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210503-102227319">Learning the Dynamics of Bursty Transcription and Splicing using Ultra-Fast Parameter Inference and New Analytical Solutions of the Chemical Master Equation</a>; Biophysical Journal; Vol. 120; No. 3; 135A; <a href="https://doi.org/10.1016/j.bpj.2020.11.1018">10.1016/j.bpj.2020.11.1018</a></li>
<li>Booeshaghi, A. Sina and Lubock, Nathan B., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395">Reliable and accurate diagnostics from highly multiplexed sequencing assays</a>; Scientific Reports; Vol. 10; Art. No. 21759; PMCID PMC7730459; <a href="https://doi.org/10.1038/s41598-020-78942-7">10.1038/s41598-020-78942-7</a></li>
<li>Svensson, Valentine and da Veiga Beltrame, Eduardo, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190821-092511308">A curated database reveals trends in single cell transcriptomics</a>; Database: The Journal of Biological Databases and Curation; Vol. 2020; Art. No. baaa073; PMCID PMC7698659; <a href="https://doi.org/10.1093/database/baaa073">10.1093/database/baaa073</a></li>
<li>Mehrab, Zakaria and Mobin, Jaiaid, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210309-074448590">A faster implementation of association mapping from k-mers</a>; Bio-protocol; Vol. 10; No. 21; Art. No. e3815; <a href="https://doi.org/10.21769/bioprotoc.3815">10.21769/bioprotoc.3815</a></li>
<li>Gorin, Gennady and Pachter, Lior (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200909-153753998">Special function methods for bursty models of transcription</a>; Physical Review E; Vol. 102; No. 2; Art. No. 022409; <a href="https://doi.org/10.1103/physreve.102.022409">10.1103/physreve.102.022409</a></li>
<li>Koromila, Theodora and Gao, Fan, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191125-141648000">Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos</a>; eLife; Vol. 9; Art. No. e59610; PMCID PMC7417190; <a href="https://doi.org/10.7554/eLife.59610">10.7554/eLife.59610</a></li>
<li>Mao, Shunfu and Pachter, Lior, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200602-124021279">RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition</a>; PLoS ONE; Vol. 15; No. 6; Art. No. e0232946; PMCID PMC7266320; <a href="https://doi.org/10.1371/journal.pone.0232946">10.1371/journal.pone.0232946</a></li>
<li>Svensson, Valentine and Gayoso, Adam, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190816-135915873">Interpretable factor models of single-cell RNA-seq via variational autoencoders</a>; Bioinformatics; Vol. 36; No. 11; 3418-3421; PMCID PMC7267837; <a href="https://doi.org/10.1093/bioinformatics/btaa169">10.1093/bioinformatics/btaa169</a></li>
<li>Gorin, Gennady and Svensson, Valentine, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190607-122759859">RNA velocity and protein acceleration from single-cell multiomics experiments</a>; Genome Biology; Vol. 21; Art. No. 39; PMCID PMC7029606; <a href="https://doi.org/10.1186/s13059-020-1945-3">10.1186/s13059-020-1945-3</a></li>
<li>Gehring, Jase and Park, Jong Hwee, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155">Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins</a>; Nature Biotechnology; Vol. 38; No. 1; 35-38; <a href="https://doi.org/10.1038/s41587-019-0372-z">10.1038/s41587-019-0372-z</a></li>
<li>Gao, Fan and da Veiga Beltrame, Eduardo, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200106-081503232">The BUS Format for Single-Cell RNA-Seq Processing and Analysis</a>; Journal of Biomolecular Techniques; Vol. 30; No. S1; S62; PMCID PMC6938108</li>
<li>Melsted, Páll and Ntranos, Vasilis, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289">Barcode, UMI, Set format and BUStools</a>; Bioinformatics; Vol. 35; No. 21; 4472-4473; <a href="https://doi.org/10.1093/bioinformatics/btz279">10.1093/bioinformatics/btz279</a></li>
<li>Kim, Dong-Wook and Yao, Zizhen, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191017-094121433">Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior</a>; Cell; Vol. 179; No. 3; 713-728; PMCID PMC7534821; <a href="https://doi.org/10.1016/j.cell.2019.09.020">10.1016/j.cell.2019.09.020</a></li>
<li>Wright, Matthew and Goin, Dana, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200206-130336877">Investigating the Post-Partum Flare in Rheumatoid Arthritis Using Transcriptome Analysis</a>; Arthritis and Rheumatology; Vol. 71; No. S10; Art. No. 1940; <a href="https://doi.org/10.1002/art.41108">10.1002/art.41108</a></li>
<li>Pathi, Amogh and Smed, Mette, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200206-125453251">The Pre-pregnancy Rheumatoid Arthritis Gene Expression Signature Correlates with Improvement or Worsening of Disease Activity During Pregnancy: A Pilot Study</a>; Arthritis and Rheumatology; Vol. 71; No. S10; Art. No. 1938; <a href="https://doi.org/10.1002/art.41108">10.1002/art.41108</a></li>
<li>McCurdy, Shannon and Molinaro, Annette, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190610-075805993">Factor analysis for survival time prediction with informative censoring and diverse covariates</a>; Statistics in Medicine; Vol. 38; No. 20; 3719-3732; <a href="https://doi.org/10.1002/sim.8151">10.1002/sim.8151</a></li>
<li>Booeshaghi, A. Sina and da Veiga Beltrame, Eduardo, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190827-103540654">Principles of open source bioinstrumentation applied to the poseidon syringe pump system</a>; Scientific Reports; Vol. 9; 12385; PMCID PMC6711986; <a href="https://doi.org/10.1038/s41598-019-48815-9">10.1038/s41598-019-48815-9</a></li>
<li>Ntranos, Vasilis and Yi, Lynn, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190123-095919155">A discriminative learning approach to differential expression analysis for single-cell RNA-seq</a>; Nature Methods; Vol. 16; No. 2; 163-166; <a href="https://doi.org/10.1038/s41592-018-0303-9">10.1038/s41592-018-0303-9</a></li>
<li>McCurdy, Shannon R. and Ntranos, Vasilis, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181029-133340286">Deterministic column subset selection for single-cell RNA-Seq</a>; PLoS ONE; Vol. 14; No. 1; Art. No. e0210571; PMCID PMC6347249; <a href="https://doi.org/10.1371/journal.pone.0210571">10.1371/journal.pone.0210571</a></li>
<li>Tambe, Akshay and Pachter, Lior (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181029-144423877">Barcode identification for single cell genomics</a>; BMC Bioinformatics; Vol. 20; Art. No. 32; PMCID PMC6337828; <a href="https://doi.org/10.1186/s12859-019-2612-0">10.1186/s12859-019-2612-0</a></li>
<li>Brown, Brielin C. and Bray, Nicolas L., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181008-162020262">Expression reflects population structure</a>; PLoS Genetics; Vol. 14; No. 12; Art. No. e1007841; PMCID PMC6317812; <a href="https://doi.org/10.1371/journal.pgen.1007841">10.1371/journal.pgen.1007841</a></li>
<li>Svensson, Valentine and Pachter, Lior (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181004-091624887">RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq</a>; Molecular Cell; Vol. 72; No. 1; 7-9; <a href="https://doi.org/10.1016/j.molcel.2018.09.026">10.1016/j.molcel.2018.09.026</a></li>
<li>Tunney, Robert and McGlincy, Nicholas J., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20180423-152534642">Accurate design of translational output by a neural network model of ribosome distribution</a>; Nature Structural &amp; Molecular Biology; Vol. 25; No. 7; 577-582; PMCID PMC6457438; <a href="https://doi.org/10.1038/s41594-018-0080-2">10.1038/s41594-018-0080-2</a></li>
<li>Rahman, Atif and Hallgrímsdóttir, Ingileif, el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190503-134759852">Association mapping from sequencing reads using k-mers</a>; eLife; Vol. 7; Art. No. e32920; PMCID PMC6044908; <a href="https://doi.org/10.7554/elife.32920">10.7554/elife.32920</a></li>
<li>Yi, Lynn and Pimentel, Harold, el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20180416-090553011">Gene-level differential analysis at transcript-level resolution</a>; Genome Biology; Vol. 19; Art. No. 53; PMCID PMC5896116; <a href="https://doi.org/10.1186/s13059-018-1419-z">10.1186/s13059-018-1419-z</a></li>
<li>Goin, Dana E. and Smed, Mette, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20171113-143256428">Longitudinal Changes in Gene Expression Associated with Disease Activity during Pregnancy and Post-Partum Among Women with Rheumatoid Arthritis</a>; Arthritis and Rheumatology; Vol. 69; No. S10; Art. No. 2432; <a href="https://doi.org/10.1002/art.40321">10.1002/art.40321</a></li>
<li>Goin, Dana E. and Smed, Mette, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20171113-145148333">Transcriptome Analysis in Women with Rheumatoid Arthritis Who Improve or Worsen during Pregnancy</a>; Arthritis and Rheumatology; Vol. 69; No. S10; Art. No. 2433; <a href="https://doi.org/10.1002/art.40321">10.1002/art.40321</a></li>
<li>Schaeffer, L. and Pimentel, H., el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-131027010">Pseudoalignment for metagenomic read assignment</a>; Bioinformatics; Vol. 33; No. 14; 2082-2088; PMCID PMC5870846; <a href="https://doi.org/10.1093/bioinformatics/btx106">10.1093/bioinformatics/btx106</a></li>
<li>Pimentel, Harold and Bray, Nicolas L., el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170612-084553487">Differential analysis of RNA-seq incorporating quantification uncertainty</a>; Nature Methods; Vol. 14; No. 7; 687-690; <a href="https://doi.org/10.1038/nmeth.4324">10.1038/nmeth.4324</a></li>
<li>Goin, Dana E. and Smed, Mette Kiel, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170531-131446160">Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study</a>; Arthritis Research and Therapy; Vol. 19; No. 1; Art. No. 104; PMCID PMC5445464; <a href="https://doi.org/10.1186/s13075-017-1312-2">10.1186/s13075-017-1312-2</a></li>
<li>Li, Bo and Tambe, Akshay, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170510-142406445">PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays</a>; Cell Systems; Vol. 4; No. 5; 568-574; PMCID PMC5758053; <a href="https://doi.org/10.1016/j.cels.2017.04.007">10.1016/j.cels.2017.04.007</a></li>
<li>Yi, Lynn and Pimentel, Harold, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170505-103858288">Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways</a>; PLoS ONE; Vol. 12; No. 4; Art. No. e0175744; PMCID PMC5407828; <a href="https://doi.org/10.1371/journal.pone.0175744">10.1371/journal.pone.0175744</a></li>
<li>Pimentel, Harold and Sturmfels, Pascal, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190506-141348569">The Lair: a resource for exploratory analysis of published RNA-Seq data</a>; BMC Bioinformatics; Vol. 17; No. 1; Art. No. 490; PMCID PMC5131447; <a href="https://doi.org/10.1186/s12859-016-1357-2">10.1186/s12859-016-1357-2</a></li>
<li>Fu, Audrey Qiuyan and Pachter, Lior (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-150123048">Estimating intrinsic and extrinsic noise from single-cell gene expression measurements</a>; Statistical Applications in Genetics and Molecular Biology; Vol. 15; No. 6; 447-471; PMCID PMC5518956; <a href="https://doi.org/10.1515/sagmb-2016-0002">10.1515/sagmb-2016-0002</a></li>
<li>Chen, Xi and Love, J. Christopher, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190503-153138885">Single-cell analysis at the threshold</a>; Nature Biotechnology; Vol. 34; No. 11; 1111-1118; <a href="https://doi.org/10.1038/nbt.3721">10.1038/nbt.3721</a></li>
<li>Hateley, Shannon and Hosamani, Ravikumar, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-154829565">Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity</a>; Genomics; Vol. 108; No. 3-4; 158-167; <a href="https://doi.org/10.1016/j.ygeno.2016.09.002">10.1016/j.ygeno.2016.09.002</a></li>
<li>Ntranos, Vasilis and Kamath, Govinda M., el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190503-155957743">Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts</a>; Genome Biology; Vol. 17; No. 1; Art. No. 112; PMCID PMC4881296; <a href="https://doi.org/10.1186/s13059-016-0970-8">10.1186/s13059-016-0970-8</a></li>
<li>Bray, Nicolas L. and Pimentel, Harold, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190506-110012992">Near-optimal probabilistic RNA-seq quantification</a>; Nature Biotechnology; Vol. 34; No. 5; 525-527; <a href="https://doi.org/10.1038/nbt.3519">10.1038/nbt.3519</a></li>
<li>Pimentel, Harold and Parra, Marilyn, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-131213123">A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis</a>; Nucleic Acids Research; Vol. 44; No. 2; 838-851; PMCID PMC4737145; <a href="https://doi.org/10.1093/nar/gkv1168">10.1093/nar/gkv1168</a></li>
<li>Mittal, Anuradha and Pachter, Lior, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-124807271">Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis</a>; PLOS ONE; Vol. 10; No. 12; Art. No. e0145204; PMCID PMC4684291; <a href="https://doi.org/10.1371/journal.pone.0145204">10.1371/journal.pone.0145204</a></li>
<li>Hanchate, Naresh K. and Kondoh, Kunio, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-130217211">Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis</a>; Science; Vol. 350; No. 6265; 1251-1255; PMCID PMC5642900; <a href="https://doi.org/10.1126/science.aad2456">10.1126/science.aad2456</a></li>
<li>Paten, Benedict and Diekhans, Mark, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150721-085701041">The NIH BD2K center for big data in translational genomics</a>; Journal of the American Medical Informatics Association; Vol. 22; No. 6; 1143-1147; PMCID PMC5009913; <a href="https://doi.org/10.1093/jamia/ocv047">10.1093/jamia/ocv047</a></li>
<li>Brat, Daniel J. and Pachter, Lior, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-132106100">Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas</a>; New England Journal of Medicine; Vol. 372; No. 26; 2481-2498; PMCID PMC4530011; <a href="https://doi.org/10.1056/NEJMoa1402121">10.1056/NEJMoa1402121</a></li>
<li>Singer, Meromit and Pachter, Lior (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-133219740">Controlling for conservation in genome-wide DNA methylation studies</a>; BMC Genomics; Vol. 16; Art. No. 420; PMCID PMC4448855; <a href="https://doi.org/10.1186/s12864-015-1604-3">10.1186/s12864-015-1604-3</a></li>
<li>Singer, Meromit and Kosti, Idit, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-133948010">A diverse epigenetic landscape at human exons with implication for expression</a>; Nucleic Acids Research; Vol. 43; No. 7; 3498-3508; PMCID PMC4402514; <a href="https://doi.org/10.1093/nar/gkv153">10.1093/nar/gkv153</a></li>
<li>Aviran, Sharon and Pachter, Lior (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-134607827">Rational experiment design for sequencing-based RNA structure mapping</a>; RNA; Vol. 20; No. 12; 1864-1877; PMCID PMC4238353; <a href="https://doi.org/10.1261/rna.043844.113">10.1261/rna.043844.113</a></li>
<li>Forster, Ryan and Chiba, Kunitoshi, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-141031221">Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells</a>; Stem Cell Reports; Vol. 2; No. 6; 838-852; PMCID PMC4050346; <a href="https://doi.org/10.1016/j.stemcr.2014.05.001">10.1016/j.stemcr.2014.05.001</a></li>
<li>Wong, Valerie L. and Ellison, Christopher E., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190507-112223935">Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum</a>; PLoS ONE; Vol. 9; No. 5; Art. No. e96784; PMCID PMC4019546; <a href="https://doi.org/10.1371/journal.pone.0096784">10.1371/journal.pone.0096784</a></li>
<li>Takayama, Sachiko and Dhahbi, Joseph, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-142644662">Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity</a>; Genome Research; Vol. 24; No. 5; 821-830; PMCID PMC4009611; <a href="https://doi.org/10.1101/gr.162412.113">10.1101/gr.162412.113</a></li>
<li>Pimentel, Harold and Parra, Marilynn, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-143819723">A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis</a>; Nucleic Acids Research; Vol. 42; No. 6; 4031-4042; PMCID PMC3973340; <a href="https://doi.org/10.1093/nar/gkt1388">10.1093/nar/gkt1388</a></li>
<li>Roberts, Adam and Feng, Harvey, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-144424899">Fragment assignment in the cloud with eXpress-D</a>; BMC Bioinformatics; Vol. 14; Art. No. 358; PMCID PMC3881492; <a href="https://doi.org/10.1186/1471-2105-14-358">10.1186/1471-2105-14-358</a></li>
<li>Roberts, Adam and Schaeffer, Lorian, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-154642805">Updating RNA-Seq analyses after re-annotation</a>; Bioinformatics; Vol. 29; No. 13; 1631-1637; PMCID PMC3694665; <a href="https://doi.org/10.1093/bioinformatics/btt197">10.1093/bioinformatics/btt197</a></li>
<li>Kleinman, Aaron and Harel, Matan, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-162557287">Affine and Projective Tree Metric Theorems</a>; Annals of Combinatorics; Vol. 17; No. 1; 205-228; <a href="https://doi.org/10.1007/s00026-012-0173-2">10.1007/s00026-012-0173-2</a></li>
<li>Rahman, Atif and Pachter, Lior (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-155431520">CGAL: computing genome assembly likelihoods</a>; Genome Biology; Vol. 14; No. 1; Art. No. R8; PMCID PMC3663106; <a href="https://doi.org/10.1186/gb-2013-14-1-r8">10.1186/gb-2013-14-1-r8</a></li>
<li>Trapnell, Cole and Hendrickson, David G., el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-161532491">Differential analysis of gene regulation at transcript resolution with RNA-seq</a>; Nature Biotechnology; Vol. 31; No. 1; 46-53; PMCID PMC3869392; <a href="https://doi.org/10.1038/nbt.2450">10.1038/nbt.2450</a></li>
<li>Roberts, Adam and Pachter, Lior (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-163300268">Streaming fragment assignment for real-time analysis of sequencing experiments</a>; Nature Methods; Vol. 10; No. 1; 71-73; PMCID PMC3880119; <a href="https://doi.org/10.1038/nmeth.2251">10.1038/nmeth.2251</a></li>
<li>Hower, Valerie and Starfield, Richard, el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-164056261">Quantifying uniformity of mapped reads</a>; Bioinformatics; Vol. 28; No. 20; 2680-2682; PMCID PMC3467739; <a href="https://doi.org/10.1093/bioinformatics/bts451">10.1093/bioinformatics/bts451</a></li>
<li>Trapnell, Cole and Roberts, Adam, el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-165006599">Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks</a>; Nature Protocols; Vol. 7; No. 3; 562-578; PMCID PMC3334321; <a href="https://doi.org/10.1038/nprot.2012.016">10.1038/nprot.2012.016</a></li>
<li>Pachter, Lior (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-164721967">A closer look at RNA editing</a>; Nature Biotechnology; Vol. 30; No. 3; 246-247; <a href="https://doi.org/10.1038/nbt.2156">10.1038/nbt.2156</a></li>
<li>Martin, David I. K. and Singer, Meromit, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-101015596">Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states</a>; Genome Research; Vol. 21; No. 12; 2049-2057; PMCID PMC3227095; <a href="https://doi.org/10.1101/gr.122721.111">10.1101/gr.122721.111</a></li>
<li>Roberts, Adam and Pachter, Lior (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-093511106">RNA-Seq and find: entering the RNA deep field</a>; Genome Medicine; Vol. 3; No. 11; Art. No. 74; PMCID PMC3308029; <a href="https://doi.org/10.1186/gm290">10.1186/gm290</a></li>
<li>Meacham, Frazer and Boffelli, Dario, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-095020310">Identification and correction of systematic error in high-throughput sequence data</a>; BMC Bioinformatics; Vol. 12; Art. No. 451; PMCID PMC3295828; <a href="https://doi.org/10.1186/1471-2105-12-451">10.1186/1471-2105-12-451</a></li>
<li>Singer, Meromit and Engström, Alexander, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-100428893">Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains</a>; Statistical Applications in Genetics and Molecular Biology; Vol. 10; No. 1; Art. No. 43; <a href="https://doi.org/10.2202/1544-6115.1677">10.2202/1544-6115.1677</a></li>
<li>Roberts, Adam and Pimentel, Harold, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-101954304">Identification of novel transcripts in annotated genomes using RNA-Seq</a>; Bioinformatics; Vol. 27; No. 17; 2325-2329; <a href="https://doi.org/10.1093/bioinformatics/btr355">10.1093/bioinformatics/btr355</a></li>
<li>Snir, Sagi and Pachter, Lior (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-102549258">Tracing the Most Parsimonious Indel History</a>; Journal of Computational Biology; Vol. 18; No. 8; 967-986; <a href="https://doi.org/10.1089/cmb.2010.0325">10.1089/cmb.2010.0325</a></li>
<li>Levy, Dan and Pachter, Lior (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-113043756">The neighbor-net algorithm</a>; Advances in Applied Mathematics; Vol. 47; No. 2; 240-258; <a href="https://doi.org/10.1016/j.aam.2010.09.002">10.1016/j.aam.2010.09.002</a></li>
<li>Lucks, Julius B. and Mortimer, Stefanie A., el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-104204159">Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 27; 11063-11068; PMCID PMC3131332; <a href="https://doi.org/10.1073/pnas.1106501108">10.1073/pnas.1106501108</a></li>
<li>Aviran, Sharon and Trapnell, Cole, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-103050792">Modeling and automation of sequencing-based characterization of RNA structure</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 27; 11069-11074; PMCID PMC3131376; <a href="https://doi.org/10.1073/pnas.1106541108">10.1073/pnas.1106541108</a></li>
<li>Roberts, Adam and Trapnell, Cole, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-105110860">Improving RNA-Seq expression estimates by correcting for fragment bias</a>; Genome Biology; Vol. 12; No. 3; Art. No. R22; PMCID PMC3129672; <a href="https://doi.org/10.1186/gb-2011-12-3-r22">10.1186/gb-2011-12-3-r22</a></li>
<li>Hower, Valerie and Evans, Steven N., el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-111327579">Shape-based peak identification for ChIP-Seq</a>; BMC Bioinformatics; Vol. 12; Art. No. 15; PMCID PMC3032669; <a href="https://doi.org/10.1186/1471-2105-12-15">10.1186/1471-2105-12-15</a></li>
<li>Willerth, Stephanie M. and Pedro, Hélder A. M., el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-114844988">Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology</a>; PLOS ONE; Vol. 5; No. 10; Art. No. e13564; PMCID PMC2962647; <a href="https://doi.org/10.1371/journal.pone.0013564">10.1371/journal.pone.0013564</a></li>
<li>Evans, Steven N. and Hower, Valerie, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-122114222">Coverage statistics for sequence census methods</a>; BMC Bioinformatics; Vol. 11; Art. No. 430; PMCID PMC2940910; <a href="https://doi.org/10.1186/1471-2105-11-430">10.1186/1471-2105-11-430</a></li>
<li>Singer, Meromit and Boffelli, Dario, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-121310345">MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations</a>; PLOS Computational Biology; Vol. 6; No. 8; Art. No. e1000888; PMCID PMC2924245; <a href="https://doi.org/10.1371/journal.pcbi.1000888">10.1371/journal.pcbi.1000888</a></li>
<li>Levin, Tera C. and Glazer, Andrew M., el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-123004736">Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study</a>; PLOS ONE; Vol. 5; No. 7; Art. No. e11645; PMCID PMC2912228; <a href="https://doi.org/10.1371/journal.pone.0011645">10.1371/journal.pone.0011645</a></li>
<li>Lapuk, Anna and Marr, Henry, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-123614363">Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer</a>; Molecular Cancer Research; Vol. 8; No. 7; 961-974; PMCID PMC2911965; <a href="https://doi.org/10.1158/1541-7786.MCR-09-0528">10.1158/1541-7786.MCR-09-0528</a></li>
<li>Trapnell, Cole and Williams, Brian A., el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20100601-111602154">Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation</a>; Nature Biotechnology; Vol. 28; No. 5; 511-515; PMCID PMC3146043; <a href="https://doi.org/10.1038/nbt.1621">10.1038/nbt.1621</a></li>
<li>Bradley, Robert K. and Li, Xiao-Yong, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-125457377">Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species</a>; PLoS Biology; Vol. 8; No. 3; Art. No. e1000343; PMCID PMC2843597; <a href="https://doi.org/10.1371/journal.pbio.1000343">10.1371/journal.pbio.1000343</a></li>
<li>Hilty, Markus and Burke, Conor, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-131319458">Disordered Microbial Communities in Asthmatic Airways</a>; PLOS ONE; Vol. 5; No. 1; Art. No. e8578; PMCID PMC2798952; <a href="https://doi.org/10.1371/journal.pone.0008578">10.1371/journal.pone.0008578</a></li>
<li>Morton, Jason and Pachter, Lior, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-133921221">Convex Rank Tests and Semigraphoids</a>; SIAM Journal on Discrete Mathematics; Vol. 23; No. 3; 1117-1134; <a href="https://doi.org/10.1137/080715822">10.1137/080715822</a></li>
<li>Trapnell, Cole and Pachter, Lior, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-141357019">TopHat: discovering splice junctions with RNA-Seq</a>; Bioinformatics; Vol. 25; No. 9; 1105-1111; PMCID PMC2672628; <a href="https://doi.org/10.1093/bioinformatics/btp120">10.1093/bioinformatics/btp120</a></li>
<li>Mihaescu, Radu and Levy, Dan, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-094400293">Why neighbor-joining works</a>; Algorithmica; Vol. 54; No. 1; 1-24; <a href="https://doi.org/10.1007/s00453-007-9116-4">10.1007/s00453-007-9116-4</a></li>
<li>Bradley, Robert K. and Roberts, Adam, el al. (2009) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-135830452">Fast Statistical Alignment</a>; PLOS Computational Biology; Vol. 5; No. 5; Art. No. e1000392; PMCID PMC2684580; <a href="https://doi.org/10.1371/journal.pcbi.1000392">10.1371/journal.pcbi.1000392</a></li>
<li>Bradley, Robert K. and Pachter, Lior, el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-103825678">Specific alignment of structured RNA: stochastic grammars and sequence annealing</a>; Bioinformatics; Vol. 24; No. 23; 2677-2683; PMCID PMC2732270; <a href="https://doi.org/10.1093/bioinformatics/btn495">10.1093/bioinformatics/btn495</a></li>
<li>Mihaescu, Radu and Pachter, Lior (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-144249240">Combinatorics of least squares trees</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 36; 13206-13211; PMCID PMC2533170; <a href="https://doi.org/10.1073/pnas.0802089105">10.1073/pnas.0802089105</a></li>
<li>Dequéant, Mary-Lee and Ahnert, Sebastian, el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-104539290">Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock</a>; PLOS ONE; Vol. 3; No. 8; Art. No. e2856; PMCID PMC2481401; <a href="https://doi.org/10.1371/journal.pone.0002856">10.1371/journal.pone.0002856</a></li>
<li>Satija, Rahul and Pachter, Lior, el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-111036850">Combining statistical alignment and phylogenetic footprinting to detect regulatory elements</a>; Bioinformatics; Vol. 24; No. 10; 1236-1242; <a href="https://doi.org/10.1093/bioinformatics/btn104">10.1093/bioinformatics/btn104</a></li>
<li>Tesler, Glenn and Eriksson, Nicholas, el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-133352205">Viral Population Estimation Using Pyrosequencing</a>; PLoS Computational Biology; Vol. 4; No. 5; Art. No. e1000074; PMCID PMC2323617; <a href="https://doi.org/10.1371/journal.pcbi.1000074">10.1371/journal.pcbi.1000074</a></li>
<li>Eickmeyer, Kord and Huggins, Peter, el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-143033087">On the optimality of the neighbor-joining algorithm</a>; Algorithms for Molecular Biology; Vol. 3; Art. No. 5; PMCID PMC2430562; <a href="https://doi.org/10.1186/1748-7188-3-5">10.1186/1748-7188-3-5</a></li>
<li>Stark, Alexander and Pachter, Lior (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-112926954">Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures</a>; Nature; Vol. 450; No. 7167; 219-232; PMCID PMC2474711; <a href="https://doi.org/10.1038/nature06340">10.1038/nature06340</a></li>
<li>Clark, Andrew G. and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-113900780">Evolution of genes and genomes on the Drosophila phylogeny</a>; Nature; Vol. 450; No. 7167; 203-218; <a href="https://doi.org/10.1038/nature06341">10.1038/nature06341</a></li>
<li>Huggins, Peter and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-095818473">Towards the Human Genotope</a>; Bulletin of Mathematical Biology; Vol. 69; No. 8; 2723-2735; <a href="https://doi.org/10.1007/s11538-007-9244-7">10.1007/s11538-007-9244-7</a></li>
<li>Begun, David J. and Holloway, Alisha K., el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-114846354">Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans</a>; PLoS Biology; Vol. 5; No. 11; Art. No. e310; PMCID PMC2062478; <a href="https://doi.org/10.1371/journal.pbio.0050310">10.1371/journal.pbio.0050310</a></li>
<li>Beerenwinkel, Niko and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-094958898">Epistasis and Shapes of Fitness Landscapes</a>; Statistica Sinica; Vol. 17; No. 4; 1317-1342; <a href="https://doi.org/10.48550/arXiv.0603034">10.48550/arXiv.0603034</a></li>
<li>Morton, Jason and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-154012533">The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies</a>; Statistical Applications in Genetics and Molecular Biology; Vol. 6; Art. No. 21; <a href="https://doi.org/10.2202/1544-6115.1286">10.2202/1544-6115.1286</a></li>
<li>Chatterji, Sourav and Pachter, Lior (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-130932831">Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor</a>; Genomics; Vol. 90; No. 1; 44-48; PMCID PMC2034525; <a href="https://doi.org/10.1016/j.ygeno.2007.03.008">10.1016/j.ygeno.2007.03.008</a></li>
<li>Birney, Ewan and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-121815071">Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project</a>; Nature; Vol. 447; No. 7146; 799-816; PMCID PMC2212820; <a href="https://doi.org/10.1038/nature05874">10.1038/nature05874</a></li>
<li>Margulies, Elliott H. and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-125526948">Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome</a>; Genome Research; Vol. 17; No. 6; 760-774; PMCID PMC1891336; <a href="https://doi.org/10.1101/gr.6034307">10.1101/gr.6034307</a></li>
<li>Pachter, Lior (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-131612759">Interpreting the unculturable majority</a>; Nature Methods; Vol. 4; No. 6; 479-480; <a href="https://doi.org/10.1038/nmeth0607-479">10.1038/nmeth0607-479</a></li>
<li>Beerenwinkel, Niko and Pachter, Lior, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-131928305">Analysis of epistatic interactions and fitness landscapes using a new geometric approach</a>; BMC Evolutionary Biology; Vol. 7; Art. No. 60; PMCID PMC1865543; <a href="https://doi.org/10.1186/1471-2148-7-60">10.1186/1471-2148-7-60</a></li>
<li>Pachter, Lior and Sturmfels, Bernd (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-085456375">The Mathematics of Phylogenomics</a>; SIAM Review; Vol. 49; No. 1; 3-31; <a href="https://doi.org/10.1137/050632634">10.1137/050632634</a></li>
<li>Schwartz, Ariel S. and Pachter, Lior (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-134453947">Multiple alignment by sequence annealing</a>; Bioinformatics; Vol. 23; No. 2; e24-e29; <a href="https://doi.org/10.1093/bioinformatics/btl311">10.1093/bioinformatics/btl311</a></li>
<li>Dewey, Colin N. and Huggins, Peter M., el al. (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-090954418">Parametric Alignment of Drosophila Genomes</a>; PLoS Computational Biology; Vol. 2; No. 6; Art. No. e73; PMCID PMC1480539; <a href="https://doi.org/10.1371/journal.pcbi.0020073">10.1371/journal.pcbi.0020073</a></li>
<li>Dewey, Colin N. and Pachter, Lior (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-162320251">Evolution at the nucleotide level: the problem of multiple whole-genome alignment</a>; Human Molecular Genetics; Vol. 15; No. Suppl. 1; R51-R56; <a href="https://doi.org/10.1093/hmg/ddl056">10.1093/hmg/ddl056</a></li>
<li>Chatterji, Sourav and Pachter, Lior (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-162728814">Reference based annotation with GeneMapper</a>; Genome Biology; Vol. 7; No. 4; Art. No. R29; PMCID PMC1557983; <a href="https://doi.org/10.1186/gb-2006-7-4-r29">10.1186/gb-2006-7-4-r29</a></li>
<li>Lall, Sabbi and Grün, Dominic, el al. (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-164849681">A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans</a>; Current Biology; Vol. 16; No. 5; 460-471; <a href="https://doi.org/10.1016/j.cub.2006.01.050">10.1016/j.cub.2006.01.050</a></li>
<li>Levy, Dan and Yoshida, Ruriko, el al. (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-164418033">Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates</a>; Molecular Biology and Evolution; Vol. 23; No. 3; 491-498; <a href="https://doi.org/10.1093/molbev/msj059">10.1093/molbev/msj059</a></li>
<li>Caspi, Anat and Pachter, Lior (2006) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-111109017">Identification of transposable elements using multiple alignments of related genomes</a>; Genome Research; Vol. 16; No. 2; 260-270; PMCID PMC1361722; <a href="https://doi.org/10.1101/gr.4361206">10.1101/gr.4361206</a></li>
<li>Chatterji, Sourav and Pachter, Lior (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-125857130">Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling</a>; Journal of Computational Biology; Vol. 12; No. 6; 599-608; <a href="https://doi.org/10.1089/cmb.2005.12.599">10.1089/cmb.2005.12.599</a></li>
<li>Chen, Kevin and Pachter, Lior (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-124940796">Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities</a>; PLoS Computational Biology; Vol. 1; No. 2; Art. No. e24; PMCID PMC1185649; <a href="https://doi.org/10.1371/journal.pcbi.0010024">10.1371/journal.pcbi.0010024</a></li>
<li>McAuliffe, Jon D. and Jordan, Michael I., el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190503-150942109">Subtree power analysis and species selection for comparative genomics</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 22; 7900-7905; PMCID PMC1142384; <a href="https://doi.org/10.1073/pnas.0502790102">10.1073/pnas.0502790102</a></li>
<li>McAuliffe, Jon D. and Jordan, Michael I., el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-090057219">Subtree power analysis finds optimal species for comparative genomics</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 22; 7900-7905; PMCID PMC1142384; <a href="https://doi.org/10.1073/pnas.0502790102">10.1073/pnas.0502790102</a></li>
<li>Hillier, LaDeana W. and Pachter, Lior, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-130340353">Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution</a>; Nature; Vol. 432; No. 7018; 695-716; <a href="https://doi.org/10.1038/nature03154">10.1038/nature03154</a></li>
<li>Boffelli, Dario and Weer, Claire V., el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-131651119">Intraspecies sequence comparisons for annotating genomes</a>; Genome Research; Vol. 14; No. 12; 2406-2411; PMCID PMC534664; <a href="https://doi.org/10.1101/gr.3199704">10.1101/gr.3199704</a></li>
<li>Pachter, Lior and Sturmfels, Bernd (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-081738298">Parametric Inference for Biological Sequence Analysis</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16138-16143; PMCID PMC528961; <a href="https://doi.org/10.1073/pnas.0406011101">10.1073/pnas.0406011101</a></li>
<li>Pachter, Lior and Sturmfels, Bernd (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-073504137">Tropical Geometry of Statistical Models</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16132-16137; PMCID PMC528960; <a href="https://doi.org/10.1073/pnas.0406010101">10.1073/pnas.0406010101</a></li>
<li>Feingold, E. A. and Pachter, L., el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-133717579">The ENCODE (ENCyclopedia Of DNA Elements) Project</a>; Science; Vol. 306; No. 5696; 636-640; <a href="https://doi.org/10.1126/science.1105136">10.1126/science.1105136</a></li>
<li>McAuliffe, Jon D. and Pachter, Lior, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-135943475">Multiple-sequence functional annotation and the generalized hidden Markov phylogeny</a>; Bioinformatics; Vol. 20; No. 12; 1850-1860; <a href="https://doi.org/10.1093/bioinformatics/bth153">10.1093/bioinformatics/bth153</a></li>
<li>Frazer, Kelly A. and Pachter, Lior, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-140652072">VISTA: computational tools for comparative genomics</a>; Nucleic Acids Research; Vol. 32; No. Suppl. 2; W273-W279; PMCID PMC441596; <a href="https://doi.org/10.1093/nar/gkh458">10.1093/nar/gkh458</a></li>
<li>Pachter, L. and Speyer, D. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-080948323">Reconstructing Trees from Subtree Weights</a>; Applied Mathematics Letters; Vol. 17; No. 6; 615-621; <a href="https://doi.org/10.1016/S0893-9659(04)90095-X">10.1016/S0893-9659(04)90095-X</a></li>
<li>Gibbs, Richard A. and Pachter, Lior, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-145138306">Genome sequence of the Brown Norway rat yields insights into mammalian evolution</a>; Nature; Vol. 428; No. 6982; 493-521; <a href="https://doi.org/10.1038/nature02426">10.1038/nature02426</a></li>
<li>Yap, Von Bing and Pachter, Lior (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-144803591">Identification of Evolutionary Hotspots in the Rodent Genomes</a>; Genome Research; Vol. 14; No. 4; 574-579; PMCID PMC383301; <a href="https://doi.org/10.1101/gr.1967904">10.1101/gr.1967904</a></li>
<li>Chakrabarti, Kushal and Pachter, Lior (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-142044905">Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER</a>; Genome Research; Vol. 14; No. 4; 716-720; PMCID PMC383318; <a href="https://doi.org/10.1101/gr.1957004">10.1101/gr.1957004</a></li>
<li>Bray, Nicolas and Pachter, Lior (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-074220313">MAVID: Constrained ancestral alignment of multiple sequences</a>; Genome Research; Vol. 14; No. 4; 693-699; PMCID PMC383315; <a href="https://doi.org/10.1101/gr.1960404">10.1101/gr.1960404</a></li>
<li>Dewey, Colin and Wu, Jia Qian, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-144150791">Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat</a>; Genome Research; Vol. 14; No. 4; 661-664; PMCID PMC383310; <a href="https://doi.org/10.1101/gr.1939804">10.1101/gr.1939804</a></li>
<li>Cawley, Simon L. and Pachter, Lior (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-151105303">HMM sampling and applications to gene finding and alternative splicing</a>; Bioinformatics; Vol. 19; No. Suppl 2; ii36-ii41; <a href="https://doi.org/10.1093/bioinformatics/btg1057">10.1093/bioinformatics/btg1057</a></li>
<li>Lam, Fumei and Pachter, Lior (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-151538288">Forcing numbers of stop signs</a>; Theoretical Computer Science; Vol. 303; No. 2-3; 409-416; <a href="https://doi.org/10.1016/S0304-3975(02)00499-1">10.1016/S0304-3975(02)00499-1</a></li>
<li>Bray, Nicolas and Pachter, Lior (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-152103068">MAVID multiple alignment server</a>; Nucleic Acids Research; Vol. 31; No. 13; 3525-3526; PMCID PMC169029; <a href="https://doi.org/10.1093/nar/gkg623">10.1093/nar/gkg623</a></li>
<li>Cawley, Simon and Pachter, Lior, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-152527629">SLAM web server for comparative gene finding and alignment</a>; Nucleic Acids Research; Vol. 31; No. 13; 3507-3509; PMCID PMC168989; <a href="https://doi.org/10.1093/nar/gkg583">10.1093/nar/gkg583</a></li>
<li>Lam, Fumei and Alexandersson, Marina, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-153301235">Picking Alignments from (Steiner) Trees</a>; Journal of Computational Biology; Vol. 10; No. 3-4; 509-520; <a href="https://doi.org/10.1089/10665270360688156">10.1089/10665270360688156</a></li>
<li>Alexandersson, Marina and Cawley, Simon, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-154151410">SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model</a>; Genome Research; Vol. 13; No. 3; 496-502; PMCID PMC430255; <a href="https://doi.org/10.1101/gr.424203">10.1101/gr.424203</a></li>
<li>Boffelli, Dario and McAuliffe, Jon, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-154624549">Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome</a>; Science; Vol. 299; No. 5611; 1391-1394; <a href="https://doi.org/10.1126/science.1081331">10.1126/science.1081331</a></li>
<li>Bray, Nick and Dubchak, Inna, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-155631683">AVID: A Global Alignment Program</a>; Genome Research; Vol. 13; No. 1; 97-102; PMCID PMC430967; <a href="https://doi.org/10.1101/gr.789803">10.1101/gr.789803</a></li>
<li>Couronne, Olivier and Poliakov, Alexander, el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170308-160145750">Strategies and Tools for Whole-Genome Alignments</a>; Genome Research; Vol. 13; No. 1; 73-80; PMCID PMC430965; <a href="https://doi.org/10.1101/gr.762503">10.1101/gr.762503</a></li>
<li>Waterston, Robert H. and Pachter, Lior, el al. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-090859678">Initial sequencing and comparative analysis of the mouse genome</a>; Nature; Vol. 420; No. 6915; 520-562; <a href="https://doi.org/10.1038/nature01262">10.1038/nature01262</a></li>
<li>Pachter, Lior and Alexandersson, Marina, el al. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635">Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems</a>; Journal of Computational Biology; Vol. 9; No. 2; 389-399; <a href="https://doi.org/10.1089/10665270252935520">10.1089/10665270252935520</a></li>
<li>Loots, Gabriela G. and Ovcharenko, Ivan, el al. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-093325277">rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites</a>; Genome Research; Vol. 12; No. 5; 832-839; PMCID PMC186580; <a href="https://doi.org/10.1101/gr.225502">10.1101/gr.225502</a></li>
<li>Benos, Panayiotis and Pachter, Lior (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-100309238">From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies</a>; Genome Research; Vol. 11; No. 5; 710-730; PMCID PMC311117; <a href="https://doi.org/10.1101/gr.173801">10.1101/gr.173801</a></li>
<li>Dubchak, Inna and Pachter, Lior (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-093904962">The computational challenges of applying comparative-based computational methods to whole genomes</a>; Briefings in Bioinformatics; Vol. 3; No. 1; 18-22; <a href="https://doi.org/10.1093/bib/3.1.18">10.1093/bib/3.1.18</a></li>
<li>Peter, Annette and Pachter, Lior (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-095230836">Mapping and identification of essential gene functions on the X chromosome of Drosophila</a>; EMBO Reports; Vol. 3; No. 1; 34-38; PMCID PMC1083931; <a href="https://doi.org/10.1093/embo-reports/kvf012">10.1093/embo-reports/kvf012</a></li>
<li>Mayor, Chris and Brudno, Michael, el al. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-104254761">VISTA : visualizing global DNA sequence alignments of arbitrary length</a>; Bioinformatics; Vol. 16; No. 11; 1046-1047; <a href="https://doi.org/10.1093/bioinformatics/16.11.1046">10.1093/bioinformatics/16.11.1046</a></li>
<li>Dubchak, Inna and Brudno, Michael, el al. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-111029375">Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons</a>; Genome Research; Vol. 10; No. 9; 1304-1306; PMCID PMC310906; <a href="https://doi.org/10.1101/gr.142200">10.1101/gr.142200</a></li>
<li>Batzoglou, Serafim and Pachter, Lior, el al. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-110441139">Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction</a>; Genome Research; Vol. 10; No. 7; 950-958; PMCID PMC310911; <a href="https://doi.org/10.1101/gr.10.7.950">10.1101/gr.10.7.950</a></li>
<li>Pachter, Lior and Batzoglou, Serafim, el al. (1999) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-113000311">A Dictionary-Based Approach for Gene Annotation</a>; Journal of Computational Biology; Vol. 6; No. 3-4; 419-430; <a href="https://doi.org/10.1089/106652799318364">10.1089/106652799318364</a></li>
<li>Pachter, Lior and Kim, Peter (1998) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-141622723">Forcing matchings on square grids</a>; Discrete Mathematics; Vol. 190; No. 1-3; 287-294; <a href="https://doi.org/10.1016/S0012-365X(97)00266-5">10.1016/S0012-365X(97)00266-5</a></li>
<li>Kleitman, D. and Pachter, L. (1998) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-114305555">Finding Convex Sets Among Points in the Plane</a>; Discrete and Computational Geometry; Vol. 19; No. 3; 405-410; <a href="https://doi.org/10.1007/PL00009358">10.1007/PL00009358</a></li>
<li>Batzoglou, Serafim and Berger, Bonnie, el al. (1998) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-142440565">Recent Developments in Computational Gene Recognition</a>; Documenta Mathematica; Vol. ICM I; 649-658</li>
<li>Pachter, Lior (1997) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-143338663">Constructing status injective graphs</a>; Discrete Applied Mathematics; Vol. 80; No. 1; 107-113; <a href="https://doi.org/10.1016/S0166-218X(97)00073-5">10.1016/S0166-218X(97)00073-5</a></li>
<li>Pachter, Lior (1997) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170309-144854496">Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes</a>; Electronic Journal of Combinatorics; Vol. 4; No. 1; Art. No. R29</li>
</ul>