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Number of items: 178.

2020

Koromila, Theodora and Gao, Fan and Iwasaki, Yasuno et al. (2020) Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. eLife, 9 . Art. No. e59610. ISSN 2050-084X. (In Press) https://resolver.caltech.edu/CaltechAUTHORS:20191125-141648000

Gustafsson, Johan and Robinson, Jonathan and Nielsen, Jens et al. (2020) Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200707-114817234

Mao, Shunfu and Pachter, Lior and Tse, David et al. (2020) RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition. PLoS ONE, 15 (6). Art. No. e0232946. ISSN 1932-6203. PMCID PMC7266320. https://resolver.caltech.edu/CaltechAUTHORS:20200602-124021279

Svensson, Valentine and Gayoso, Adam and Yosef, Nir et al. (2020) Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinformatics, 36 (11). pp. 3418-3421. ISSN 1367-4803. PMCID PMC7267837. https://resolver.caltech.edu/CaltechAUTHORS:20190816-135915873

Booeshaghi, A. Sina and Pachter, Lior (2020) log(x+1)* and log(1+x)*. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200520-084505912

Booeshaghi, A. Sina and Lubock, Nathan B. and Cooper, Aaron R. et al. (2020) Fast and accurate diagnostics from highly multiplexed sequencing assays. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395

Booeshaghi, A. Sina and Pachter, Lior (2020) Decrease in ACE2 mRNA expression in aged mouse lung. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200406-101324270

Yao, Zizhen and Liu, Hanqing and Xie, Fangming et al. (2020) An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200303-153620082

Gorin, Gennady and Svensson, Valentine and Pachter, Lior (2020) RNA velocity and protein acceleration from single-cell multiomics experiments. Genome Biology, 21 . Art. No. 39. ISSN 1465-6906. PMCID PMC7029606. https://resolver.caltech.edu/CaltechAUTHORS:20190607-122759859

Gehring, Jase and Park, Jong Hwee and Chen, Sisi et al. (2020) Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nature Biotechnology, 38 (1). pp. 35-38. ISSN 1087-0156. https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155

2019

Gao, Fan and da Veiga Beltrame, Eduardo and Gehring, Jase A. et al. (2019) The BUS Format for Single-Cell RNA-Seq Processing and Analysis. Journal of Biomolecular Techniques, 30 (S1). S62. ISSN 1524-0215. PMCID PMC6938108. https://resolver.caltech.edu/CaltechAUTHORS:20200106-081503232

Melsted, Páll and Ntranos, Vasilis and Pachter, Lior (2019) Barcode, UMI, Set format and BUStools. Bioinformatics, 35 (21). pp. 4472-4473. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289

Kim, Dong-Wook and Yao, Zizhen and Graybuck, Lucas T. et al. (2019) Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior. Cell, 179 (3). pp. 713-728. ISSN 0092-8674. https://resolver.caltech.edu/CaltechAUTHORS:20191017-094121433

Wright, Matthew and Goin, Dana and Smed, Mette et al. (2019) Investigating the Post-Partum Flare in Rheumatoid Arthritis Using Transcriptome Analysis. Arthritis and Rheumatology, 71 (S10). Art. No. 1940. ISSN 2326-5191. https://resolver.caltech.edu/CaltechAUTHORS:20200206-130336877

Pathi, Amogh and Smed, Mette and Pachter, Lior et al. (2019) The Pre-pregnancy Rheumatoid Arthritis Gene Expression Signature Correlates with Improvement or Worsening of Disease Activity During Pregnancy: A Pilot Study. Arthritis and Rheumatology, 71 (S10). Art. No. 1938. ISSN 2326-5191. https://resolver.caltech.edu/CaltechAUTHORS:20200206-125453251

McCurdy, Shannon and Molinaro, Annette and Pachter, Lior (2019) Factor analysis for survival time prediction with informative censoring and diverse covariates. Statistics in Medicine, 38 (20). pp. 3719-3732. ISSN 0277-6715. https://resolver.caltech.edu/CaltechAUTHORS:20190610-075805993

Svensson, Valentine and da Veiga Beltrame, Eduardo and Pachter, Lior (2019) Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20190910-074005263

Booeshaghi, A. Sina and da Veiga Beltrame, Eduardo and Bannon, Dylan et al. (2019) Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific Reports, 9 . Art. No. 12385. ISSN 2045-2322. PMCID PMC6711986. https://resolver.caltech.edu/CaltechAUTHORS:20190827-103540654

Melsted, Páll and Booeshaghi, A. Sina and Gao, Fan et al. (2019) Modular and efficient pre-processing of single-cell RNA-seq. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20190617-153352518

McGee, Warren A. and Pimentel, Harold and Pachter, Lior et al. (2019) Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20190304-085432513

Ntranos, Vasilis and Yi, Lynn and Melsted, Páll et al. (2019) A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nature Methods, 16 (2). pp. 163-166. ISSN 1548-7091. https://resolver.caltech.edu/CaltechAUTHORS:20190123-095919155

McCurdy, Shannon R. and Ntranos, Vasilis and Pachter, Lior (2019) Deterministic column subset selection for single-cell RNA-Seq. PLoS ONE, 14 (1). Art. No. e0210571. ISSN 1932-6203. PMCID PMC6347249. https://resolver.caltech.edu/CaltechAUTHORS:20181029-133340286

Tambe, Akshay and Pachter, Lior (2019) Barcode identification for single cell genomics. BMC Bioinformatics, 20 . Art. No. 32. ISSN 1471-2105. PMCID PMC6337828. https://resolver.caltech.edu/CaltechAUTHORS:20181029-144423877

2018

Brown, Brielin C. and Bray, Nicolas L. and Pachter, Lior (2018) Expression reflects population structure. PLoS Genetics, 14 (12). Art. No. e1007841. ISSN 1553-7390. PMCID PMC6317812. https://resolver.caltech.edu/CaltechAUTHORS:20181008-162020262

Yi, Lynn and Liu, Lauren and Melsted, Páll et al. (2018) A direct comparison of genome alignment and transcriptome pseudoalignment. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20181029-160959571

Svensson, Valentine and Pachter, Lior (2018) RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq. Molecular Cell, 72 (1). pp. 7-9. ISSN 1097-2765. https://resolver.caltech.edu/CaltechAUTHORS:20181004-091624887

Tunney, Robert and McGlincy, Nicholas J. and Graham, Monica E. et al. (2018) Accurate design of translational output by a neural network model of ribosome distribution. Nature Structural & Molecular Biology, 25 (7). pp. 577-582. ISSN 1545-9985. PMCID PMC6457438. https://resolver.caltech.edu/CaltechAUTHORS:20180423-152534642

Rahman, Atif and Hallgrímsdóttir, Ingileif and Eisen, Michael et al. (2018) Association mapping from sequencing reads using k-mers. eLife, 7 . Art. No. e32920. ISSN 2050-084X. PMCID PMC6044908. https://resolver.caltech.edu/CaltechAUTHORS:20190503-134759852

Yi, Lynn and Pimentel, Harold and Bray, Nicolas L. et al. (2018) Gene-level differential analysis at transcript-level resolution. Genome Biology, 19 . Art. No. 53. ISSN 1474-760X. PMCID PMC5896116. https://resolver.caltech.edu/CaltechAUTHORS:20180416-090553011

Ntranos, Vasilis and Yi, Lynn and Melsted, Páll et al. (2018) Identification of transcriptional signatures for cell types from single-cell RNA-Seq. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20181031-090523070

2017

Goin, Dana E. and Smed, Mette and Jewell, Nicholas et al. (2017) Longitudinal Changes in Gene Expression Associated with Disease Activity during Pregnancy and Post-Partum Among Women with Rheumatoid Arthritis. Arthritis and Rheumatology, 69 (S10). Art. No. 2432. ISSN 2326-5191. https://resolver.caltech.edu/CaltechAUTHORS:20171113-143256428

Goin, Dana E. and Smed, Mette and Pachter, Lior et al. (2017) Transcriptome Analysis in Women with Rheumatoid Arthritis Who Improve or Worsen during Pregnancy. Arthritis and Rheumatology, 69 (S10). Art. No. 2433. ISSN 2326-5191. https://resolver.caltech.edu/CaltechAUTHORS:20171113-145148333

Melsted, Páll and Hateley, Shannon and Joseph, Isaac Charles et al. (2017) Fusion detection and quantification by pseudoalignment. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20181029-134221299

Schaeffer, L. and Pimentel, H. and Bray, N. et al. (2017) Pseudoalignment for metagenomic read assignment. Bioinformatics, 33 (14). pp. 2082-2088. ISSN 1367-4803. PMCID PMC5870846. https://resolver.caltech.edu/CaltechAUTHORS:20170306-131027010

Pimentel, Harold and Bray, Nicolas L. and Puente, Suzette et al. (2017) Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods, 14 (7). pp. 687-690. ISSN 1548-7091. https://resolver.caltech.edu/CaltechAUTHORS:20170612-084553487

Goin, Dana E. and Smed, Mette Kiel and Pachter, Lior et al. (2017) Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study. Arthritis Research and Therapy, 19 (1). Art. No. 104. ISSN 1478-6362. PMCID PMC5445464. https://resolver.caltech.edu/CaltechAUTHORS:20170531-131446160

Li, Bo and Tambe, Akshay and Aviran, Sharon et al. (2017) PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems, 4 (5). pp. 568-574. ISSN 2405-4712. PMCID PMC5758053. https://resolver.caltech.edu/CaltechAUTHORS:20170510-142406445

Yi, Lynn and Pimentel, Harold and Pachter, Lior (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS ONE, 12 (4). Art. No. e0175744. ISSN 1932-6203. PMCID PMC5407828. https://resolver.caltech.edu/CaltechAUTHORS:20170505-103858288

2016

Pimentel, Harold and Sturmfels, Pascal and Bray, Nicolas et al. (2016) The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinformatics, 17 (1). Art. No. 490. ISSN 1471-2105. PMCID PMC5131447. https://resolver.caltech.edu/CaltechAUTHORS:20190506-141348569

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, 15 (6). pp. 447-471. ISSN 2194-6302. PMCID PMC5518956. https://resolver.caltech.edu/CaltechAUTHORS:20170306-150123048

Chen, Xi and Love, J. Christopher and Navin, Nicholas E. et al. (2016) Single-cell analysis at the threshold. Nature Biotechnology, 34 (11). pp. 1111-1118. ISSN 1087-0156. https://resolver.caltech.edu/CaltechAUTHORS:20190503-153138885

Pimentel, Harold and Conboy, John G. and Pachter, Lior (2016) Keep Me Around: Intron Retention Detection and Analysis. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170306-132431515

Hateley, Shannon and Hosamani, Ravikumar and Bhardwaj, Shilpa R. et al. (2016) Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity. Genomics, 108 (3-4). pp. 158-167. ISSN 0888-7543. https://resolver.caltech.edu/CaltechAUTHORS:20170309-154829565

Ntranos, Vasilis and Kamath, Govinda M. and Zhang, Jesse M. et al. (2016) Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biology, 17 (1). Art. No. 112. ISSN 1474-760X. PMCID PMC4881296. https://resolver.caltech.edu/CaltechAUTHORS:20190503-155957743

Bray, Nicolas L. and Pimentel, Harold and Melsted, Páll et al. (2016) Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34 (5). pp. 525-527. ISSN 1087-0156. https://resolver.caltech.edu/CaltechAUTHORS:20190506-110012992

Pimentel, Harold and Parra, Marilyn and Gee, Sherry L. et al. (2016) A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Research, 44 (2). pp. 838-851. ISSN 0305-1048. PMCID PMC4737145. https://resolver.caltech.edu/CaltechAUTHORS:20170303-131213123

2015

Mittal, Anuradha and Pachter, Lior and Nelson, J. Lee et al. (2015) Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis. PLOS ONE, 10 (12). Art. No. e0145204. ISSN 1932-6203. PMCID PMC4684291. https://resolver.caltech.edu/CaltechAUTHORS:20170303-124807271

Hanchate, Naresh K. and Kondoh, Kunio and Lu, Zhonglua et al. (2015) Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science, 350 (6265). pp. 1251-1255. ISSN 0036-8075. PMCID PMC5642900. https://resolver.caltech.edu/CaltechAUTHORS:20170303-130217211

Paten, Benedict and Diekhans, Mark and Druker, Brian J. et al. (2015) The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association, 22 (6). pp. 1143-1147. ISSN 1067-5027. PMCID PMC5009913. https://resolver.caltech.edu/CaltechAUTHORS:20150721-085701041

Brat, Daniel J. and Pachter, Lior (2015) Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. New England Journal of Medicine, 372 (26). pp. 2481-2498. ISSN 0028-4793. PMCID PMC4530011. https://resolver.caltech.edu/CaltechAUTHORS:20170303-132106100

Singer, Meromit and Pachter, Lior (2015) Controlling for conservation in genome-wide DNA methylation studies. BMC Genomics, 16 . Art. No. 420. ISSN 1471-2164. PMCID PMC4448855. https://resolver.caltech.edu/CaltechAUTHORS:20170303-133219740

Bray, Nicolas L. and Pimentel, Harold and Melsted, Páll et al. (2015) Near-optimal RNA-Seq quantification. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20170303-114628470

Singer, Meromit and Kosti, Idit and Pachter, Lior et al. (2015) A diverse epigenetic landscape at human exons with implication for expression. Nucleic Acids Research, 43 (7). pp. 3498-3508. ISSN 0305-1048. PMCID PMC4402514. https://resolver.caltech.edu/CaltechAUTHORS:20170303-133948010

2014

Tambe, Akshay and Doudna, Jennifer and Pachter, Lior (2014) Identifying RNA contacts from SHAPE-MaP by partial correlation analysis. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-101642083

Singer, Meromit and Pachter, Lior (2014) Bayesian Networks in the Study of Genome-wide DNA Methylation. In: Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics. Oxford University Press , New York, NY, pp. 363-386. ISBN 9780198709022. https://resolver.caltech.edu/CaltechAUTHORS:20170303-140414225

Aviran, Sharon and Pachter, Lior (2014) Rational experiment design for sequencing-based RNA structure mapping. RNA, 20 (12). pp. 1864-1877. ISSN 1355-8382. PMCID PMC4238353. https://resolver.caltech.edu/CaltechAUTHORS:20170303-134607827

Forster, Ryan and Chiba, Kunitoshi and Schaeffer, Lorian et al. (2014) Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells. Stem Cell Reports, 2 (6). pp. 838-852. ISSN 2213-6711. PMCID PMC4050346; PMC4110795. https://resolver.caltech.edu/CaltechAUTHORS:20170303-141031221

Wong, Valerie L. and Ellison, Christopher E. and Eisen, Michael B. et al. (2014) Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum. PLoS ONE, 9 (5). Art. No. e96784. ISSN 1932-6203. PMCID PMC4019546. https://resolver.caltech.edu/CaltechAUTHORS:20190507-112223935

Takayama, Sachiko and Dhahbi, Joseph and Roberts, Adam et al. (2014) Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Research, 24 (5). pp. 821-830. ISSN 1088-9051. PMCID PMC4009611. https://resolver.caltech.edu/CaltechAUTHORS:20170303-142644662

Pimentel, Harold and Parra, Marilynn and Gee, Sherry et al. (2014) A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Research, 42 (6). pp. 4031-4042. ISSN 0305-1048. PMCID PMC3973340. https://resolver.caltech.edu/CaltechAUTHORS:20170303-143819723

2013

Roberts, Adam and Feng, Harvey and Pachter, Lior (2013) Fragment assignment in the cloud with eXpress-D. BMC Bioinformatics, 14 . Art. No. 358. ISSN 1471-2105. PMCID PMC3881492. https://resolver.caltech.edu/CaltechAUTHORS:20170303-144424899

Roberts, Adam and Schaeffer, Lorian and Pachter, Lior (2013) Updating RNA-Seq analyses after re-annotation. Bioinformatics, 29 (13). pp. 1631-1637. ISSN 1367-4803. PMCID PMC3694665. https://resolver.caltech.edu/CaltechAUTHORS:20170303-154642805

Kleinman, Aaron and Harel, Matan and Pachter, Lior (2013) Affine and Projective Tree Metric Theorems. Annals of Combinatorics, 17 (1). pp. 205-228. ISSN 0218-0006. https://resolver.caltech.edu/CaltechAUTHORS:20170303-162557287

Rahman, Atif and Pachter, Lior (2013) CGAL: computing genome assembly likelihoods. Genome Biology, 14 (1). Art. No. R8. ISSN 1465-6906. PMCID PMC3663106. https://resolver.caltech.edu/CaltechAUTHORS:20170303-155431520

Trapnell, Cole and Hendrickson, David G. and Sauvageau, Martin et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology, 31 (1). pp. 46-53. ISSN 1087-0156. PMCID PMC3869392. https://resolver.caltech.edu/CaltechAUTHORS:20170303-161532491

Roberts, Adam and Pachter, Lior (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods, 10 (1). pp. 71-73. ISSN 1548-7091. PMCID PMC3880119. https://resolver.caltech.edu/CaltechAUTHORS:20170303-163300268

2012

Bray, Nicolas and Pachter, Lior (2012) Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions". . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-101423905

Mortimer, Stefanie A. and Trapnell, Cole and Aviran, Sharon et al. (2012) SHAPE-Seq: High-Throughput RNA Structure Analysis. In: Current Protocols in Chemical Biology. John Wiley and Sons , New York, NY, pp. 275-297. ISBN 9780470559277. https://resolver.caltech.edu/CaltechAUTHORS:20170303-160835568

Hower, Valerie and Starfield, Richard and Roberts, Adam et al. (2012) Quantifying uniformity of mapped reads. Bioinformatics, 28 (20). pp. 2680-2682. ISSN 1367-4803. PMCID PMC3467739. https://resolver.caltech.edu/CaltechAUTHORS:20170303-164056261

Trapnell, Cole and Roberts, Adam and Goff, Loyal et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7 (3). pp. 562-578. ISSN 1754-2189. PMCID PMC3334321. https://resolver.caltech.edu/CaltechAUTHORS:20170303-165006599

Pachter, Lior (2012) A closer look at RNA editing. Nature Biotechnology, 30 (3). pp. 246-247. ISSN 1087-0156. https://resolver.caltech.edu/CaltechAUTHORS:20170303-164721967

2011

Martin, David I. K. and Singer, Meromit and Dhahbi, Joseph et al. (2011) Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research, 21 (12). pp. 2049-2057. ISSN 1088-9051. PMCID PMC3227095. https://resolver.caltech.edu/CaltechAUTHORS:20170306-101015596

Roberts, Adam and Pachter, Lior (2011) RNA-Seq and find: entering the RNA deep field. Genome Medicine, 3 (11). Art. No. 74. ISSN 1756-994X. PMCID PMC3308029. https://resolver.caltech.edu/CaltechAUTHORS:20170306-093511106

Meacham, Frazer and Boffelli, Dario and Dhahbi, Joseph et al. (2011) Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics, 12 . Art. No. 451. ISSN 1471-2105. PMCID PMC3295828. https://resolver.caltech.edu/CaltechAUTHORS:20170306-095020310

Singer, Meromit and Engström, Alexander and Schönhuth, Alexander et al. (2011) Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains. Statistical Applications in Genetics and Molecular Biology, 10 (1). Art. No. 43. ISSN 2194-6302. https://resolver.caltech.edu/CaltechAUTHORS:20170306-100428893

Roberts, Adam and Pimentel, Harold and Trapnell, Cole et al. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27 (17). pp. 2325-2329. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170306-101954304

Aviran, Sharon and Lucks, Julius B. and Pachter, Lior (2011) RNA structure characterization from chemical mapping experiments. In: 49th Annual Allerton Conference on Communication, Control, and Computing. IEEE , Piscataway, NJ, pp. 1743-1750. ISBN 978-1-4577-1817-5. https://resolver.caltech.edu/CaltechAUTHORS:20170306-092934189

Snir, Sagi and Pachter, Lior (2011) Tracing the Most Parsimonious Indel History. Journal of Computational Biology, 18 (8). pp. 967-986. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170306-102549258

Levy, Dan and Pachter, Lior (2011) The neighbor-net algorithm. Advances in Applied Mathematics, 47 (2). pp. 240-258. ISSN 0196-8858. https://resolver.caltech.edu/CaltechAUTHORS:20170306-113043756

Aviran, Sharon and Trapnell, Cole and Lucks, Julius B. et al. (2011) Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America, 108 (27). pp. 11069-11074. ISSN 0027-8424. PMCID PMC3131376. https://resolver.caltech.edu/CaltechAUTHORS:20170306-103050792

Lucks, Julius B. and Mortimer, Stefanie A. and Trapnell, Cole et al. (2011) Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America, 108 (27). pp. 11063-11068. ISSN 0027-8424. PMCID PMC3131332. https://resolver.caltech.edu/CaltechAUTHORS:20170306-104204159

Pachter, Lior (2011) Models for transcript quantification from RNA-Seq. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-112830219

Roberts, Adam and Trapnell, Cole and Donaghey, Julie et al. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology, 12 (3). Art. No. R22. ISSN 1465-6906. PMCID PMC3129672. https://resolver.caltech.edu/CaltechAUTHORS:20170306-105110860

Hower, Valerie and Evans, Steven N. and Pachter, Lior (2011) Shape-based peak identification for ChIP-Seq. BMC Bioinformatics, 12 . Art. No. 15. ISSN 1471-2105. PMCID PMC3032669. https://resolver.caltech.edu/CaltechAUTHORS:20170306-111327579

2010

Willerth, Stephanie M. and Pedro, Hélder A. M. and Pachter, Lior et al. (2010) Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology. PLOS ONE, 5 (10). Art. No. e13564. ISSN 1932-6203. PMCID PMC2962647. https://resolver.caltech.edu/CaltechAUTHORS:20170306-114844988

Evans, Steven N. and Hower, Valerie and Pachter, Lior (2010) Coverage statistics for sequence census methods. BMC Bioinformatics, 11 . Art. No. 430. ISSN 1471-2105. PMCID PMC2940910. https://resolver.caltech.edu/CaltechAUTHORS:20170306-122114222

Singer, Meromit and Boffelli, Dario and Dhahbi, Joseph et al. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations. PLOS Computational Biology, 6 (8). Art. No. e1000888. ISSN 1553-7358. PMCID PMC2924245. https://resolver.caltech.edu/CaltechAUTHORS:20170306-121310345

Levin, Tera C. and Glazer, Andrew M. and Pachter, Lior et al. (2010) Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study. PLOS ONE, 5 (7). Art. No. e11645. ISSN 1932-6203. PMCID PMC2912228. https://resolver.caltech.edu/CaltechAUTHORS:20170306-123004736

Lapuk, Anna and Marr, Henry and Jakkula, Lakshmi et al. (2010) Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer. Molecular Cancer Research, 8 (7). pp. 961-974. ISSN 1541-7786. PMCID PMC2911965. https://resolver.caltech.edu/CaltechAUTHORS:20170306-123614363

Trapnell, Cole and Williams, Brian A. and Pertea, Geo et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28 (5). pp. 511-515. ISSN 1087-0156. PMCID PMC3146043. https://resolver.caltech.edu/CaltechAUTHORS:20100601-111602154

Bradley, Robert K. and Li, Xiao-Yong and Trapnell, Cole et al. (2010) Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species. PLoS Biology, 8 (3). Art. No. e1000343. ISSN 1545-7885. PMCID PMC2843597. https://resolver.caltech.edu/CaltechAUTHORS:20170306-125457377

Hilty, Markus and Burke, Conor and Pedro, Helder et al. (2010) Disordered Microbial Communities in Asthmatic Airways. PLOS ONE, 5 (1). Art. No. e8578. ISSN 1932-6203. PMCID PMC2798952. https://resolver.caltech.edu/CaltechAUTHORS:20170306-131319458

2009

Morton, Jason and Pachter, Lior and Shiu, Anne et al. (2009) Convex Rank Tests and Semigraphoids. SIAM Journal on Discrete Mathematics, 23 (3). pp. 1117-1134. ISSN 0895-4801. https://resolver.caltech.edu/CaltechAUTHORS:20170306-133921221

Trapnell, Cole and Pachter, Lior and Salzberg, Steven L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25 (9). pp. 1105-1111. ISSN 1367-4803. PMCID PMC2672628. https://resolver.caltech.edu/CaltechAUTHORS:20170306-141357019

Bradley, Robert K. and Roberts, Adam and Smoot, Michael et al. (2009) Fast Statistical Alignment. PLOS Computational Biology, 5 (5). Art. No. e1000392. ISSN 1553-7358. PMCID PMC2684580. https://resolver.caltech.edu/CaltechAUTHORS:20170306-135830452

Mihaescu, Radu and Levy, Dan and Pachter, Lior (2009) Why neighbor-joining works. Algorithmica, 54 (1). pp. 1-24. ISSN 0178-4617. https://resolver.caltech.edu/CaltechAUTHORS:20170307-094400293

2008

Bradley, Robert K. and Pachter, Lior and Holmes, Ian (2008) Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics, 24 (23). pp. 2677-2683. ISSN 1367-4803. PMCID PMC2732270. https://resolver.caltech.edu/CaltechAUTHORS:20170307-103825678

Mihaescu, Radu and Pachter, Lior (2008) Combinatorics of least squares trees. Proceedings of the National Academy of Sciences of the United States of America, 105 (36). pp. 13206-13211. ISSN 0027-8424. PMCID PMC2533170. https://resolver.caltech.edu/CaltechAUTHORS:20170306-144249240

Dequéant, Mary-Lee and Ahnert, Sebastian and Edelsbrunner, Herbert et al. (2008) Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock. PLOS ONE, 3 (8). Art. No. e2856. ISSN 1932-6203. PMCID PMC2481401. https://resolver.caltech.edu/CaltechAUTHORS:20170307-104539290

Satija, Rahul and Pachter, Lior and Hein, Jotun (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics, 24 (10). pp. 1236-1242. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170307-111036850

Huggins, Peter and Pachter, Lior (2008) Selecting universities: personal preference and rankings. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170306-145946949

Tesler, Glenn and Eriksson, Nicholas and Pachter, Lior et al. (2008) Viral Population Estimation Using Pyrosequencing. PLoS Computational Biology, 4 (5). Art. No. e1000074. ISSN 1553-7358. PMCID PMC2323617. https://resolver.caltech.edu/CaltechAUTHORS:20170306-133352205

Eickmeyer, Kord and Huggins, Peter and Pachter, Lior et al. (2008) On the optimality of the neighbor-joining algorithm. Algorithms for Molecular Biology, 3 . Art. No. 5. ISSN 1748-7188. PMCID PMC2430562. https://resolver.caltech.edu/CaltechAUTHORS:20170306-143033087

2007

Stark, Alexander and Pachter, Lior (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450 (7167). pp. 219-232. ISSN 0028-0836. PMCID PMC2474711. https://resolver.caltech.edu/CaltechAUTHORS:20170307-112926954

Clark, Andrew G. and Pachter, Lior (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167). pp. 203-218. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20170307-113900780

Begun, David J. and Holloway, Alisha K. and Stevens, Kristian et al. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biology, 5 (11). Art. No. e310. ISSN 1545-7885. PMCID PMC2062478. https://resolver.caltech.edu/CaltechAUTHORS:20170307-114846354

Huggins, Peter and Pachter, Lior and Sturmfels, Bernd (2007) Towards the Human Genotope. Bulletin of Mathematical Biology, 69 (8). pp. 2723-2735. ISSN 0092-8240. https://resolver.caltech.edu/CaltechAUTHORS:20170307-095818473

Beerenwinkel, Niko and Pachter, Lior and Sturmfels, Bernd (2007) Epistasis and Shapes of Fitness Landscapes. Statistica Sinica, 17 (4). pp. 1317-1342. ISSN 1017-0405. https://resolver.caltech.edu/CaltechAUTHORS:20170307-094958898

Morton, Jason and Pachter, Lior and Shiu, Anne et al. (2007) The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies. Statistical Applications in Genetics and Molecular Biology, 6 . Art. No. 21. ISSN 2194-6302. (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170306-154012533

Chatterji, Sourav and Pachter, Lior (2007) Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics, 90 (1). pp. 44-48. ISSN 0888-7543. PMCID PMC2034525. https://resolver.caltech.edu/CaltechAUTHORS:20170307-130932831

Birney, Ewan and Pachter, Lior (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 0028-0836. PMCID PMC2212820. https://resolver.caltech.edu/CaltechAUTHORS:20170307-121815071

Margulies, Elliott H. and Pachter, Lior (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17 (6). pp. 760-774. ISSN 1088-9051. PMCID PMC1891336. https://resolver.caltech.edu/CaltechAUTHORS:20170307-125526948

Pachter, Lior (2007) Interpreting the unculturable majority. Nature Methods, 4 (6). pp. 479-480. ISSN 1548-7091. https://resolver.caltech.edu/CaltechAUTHORS:20170307-131612759

Beerenwinkel, Niko and Pachter, Lior and Sturmfels, Bernd et al. (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evolutionary Biology, 7 . Art. No. 60. ISSN 1471-2148. PMCID PMC1865543. https://resolver.caltech.edu/CaltechAUTHORS:20170307-131928305

Pachter, Lior and Sturmfels, Bernd (2007) The Mathematics of Phylogenomics. SIAM Review, 49 (1). pp. 3-31. ISSN 0036-1445. https://resolver.caltech.edu/CaltechAUTHORS:20170307-085456375

Schwartz, Ariel S. and Pachter, Lior (2007) Multiple alignment by sequence annealing. Bioinformatics, 23 (2). e24-e29. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170307-134453947

Pachter, Lior (2007) An introduction to reconstructing ancestral genomes. In: Modeling and Simulation of Biological Networks. Proceedings of Symposia in Applied Mathematics. No.64. American Mathematical Society , Providence, RI, pp. 10-29. ISBN 978-0-8218-3964-5. https://resolver.caltech.edu/CaltechAUTHORS:20170307-135106127

2006

Morton, Jason and Pachter, Lior and Shiu, Anne et al. (2006) Geometry of rank tests. In: Proceedings of the 3rd European Workshop on Probabilistic Graphical Models. Action M Agency , Prague, Czech Republic, Art. No.7. ISBN 9788086742144. https://resolver.caltech.edu/CaltechAUTHORS:20170307-095347077

Dewey, Colin N. and Huggins, Peter M. and Woods, Kevin et al. (2006) Parametric Alignment of Drosophila Genomes. PLoS Computational Biology, 2 (6). Art. No. e73. ISSN 1553-734X. PMCID PMC1480539. https://resolver.caltech.edu/CaltechAUTHORS:20170307-090954418

Dewey, Colin N. and Pachter, Lior (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics, 15 (Suppl. 1). R51-R56. ISSN 0964-6906. https://resolver.caltech.edu/CaltechAUTHORS:20170307-162320251

Chatterji, Sourav and Pachter, Lior (2006) Reference based annotation with GeneMapper. Genome Biology, 7 (4). Art. No. R29. ISSN 1465-6906. PMCID PMC1557983. https://resolver.caltech.edu/CaltechAUTHORS:20170307-162728814

Snir, Sagi and Pachter, Lior (2006) Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science. No.3909. Springer , Berlin, pp. 265-280. ISBN 978-3-540-33295-4. https://resolver.caltech.edu/CaltechAUTHORS:20170307-163715632

Lall, Sabbi and Grün, Dominic and Krek, Azra et al. (2006) A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans. Current Biology, 16 (5). pp. 460-471. ISSN 0960-9822. https://resolver.caltech.edu/CaltechAUTHORS:20170307-164849681

Levy, Dan and Yoshida, Ruriko and Pachter, Lior (2006) Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates. Molecular Biology and Evolution, 23 (3). pp. 491-498. ISSN 0737-4038. https://resolver.caltech.edu/CaltechAUTHORS:20170307-164418033

Caspi, Anat and Pachter, Lior (2006) Identification of transposable elements using multiple alignments of related genomes. Genome Research, 16 (2). pp. 260-270. ISSN 1088-9051. PMCID PMC1361722. https://resolver.caltech.edu/CaltechAUTHORS:20170308-111109017

2005

Schwartz, Ariel S. and Myers, Eugene W. and Pachter, Lior (2005) Alignment Metric Accuracy. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-100435592

Pachter, Lior and Sturmfels, Bernd, eds. (2005) Algebraic Statistics for Computational Biology. Cambridge University Press , New York, NY. ISBN 9780521857000. https://resolver.caltech.edu/CaltechAUTHORS:20170308-112102236

Levy, Dan and Yoshida, Ruriko and Pachter, Lior (2005) Neighbor joining with phylogenetic diversity estimates. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-090555699

Chen, Kevin and Pachter, Lior (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Computational Biology, 1 (2). Art. No. e24. ISSN 1553-734X. PMCID PMC1185649. https://resolver.caltech.edu/CaltechAUTHORS:20170308-124940796

Chatterji, Sourav and Pachter, Lior (2005) Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. Journal of Computational Biology, 12 (6). pp. 599-608. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170308-125857130

McAuliffe, Jon D. and Jordan, Michael I. and Pachter, Lior (2005) Subtree power analysis and species selection for comparative genomics. Proceedings of the National Academy of Sciences of the United States of America, 102 (22). pp. 7900-7905. ISSN 0027-8424. PMCID PMC1142384. https://resolver.caltech.edu/CaltechAUTHORS:20190503-150942109

McAuliffe, Jon D. and Jordan, Michael I. and Pachter, Lior (2005) Subtree power analysis finds optimal species for comparative genomics. Proceedings of the National Academy of Sciences of the United States of America, 102 (22). pp. 7900-7905. ISSN 0027-8424. PMCID PMC1142384. https://resolver.caltech.edu/CaltechAUTHORS:20170307-090057219

Alexandersson, Marina and Bray, Nicolas and Pachter, Lior (2005) Pair hidden Markov models. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley , New York, NY, Art. No. 4:4.2:17. ISBN 9780470011539. https://resolver.caltech.edu/CaltechAUTHORS:20170308-113640795

2004

Hillier, LaDeana W. and Pachter, Lior (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018). pp. 695-716. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20170308-130340353

Boffelli, Dario and Weer, Claire V. and Weng, Li et al. (2004) Intraspecies sequence comparisons for annotating genomes. Genome Research, 14 (12). pp. 2406-2411. ISSN 1088-9051. PMCID PMC534664. https://resolver.caltech.edu/CaltechAUTHORS:20170308-131651119

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, 101 (46). pp. 16138-16143. ISSN 0027-8424. PMCID PMC528961. https://resolver.caltech.edu/CaltechAUTHORS:20170307-081738298

Pachter, Lior and Sturmfels, Bernd (2004) Tropical Geometry of Statistical Models. Proceedings of the National Academy of Sciences of the United States of America, 101 (46). pp. 16132-16137. ISSN 0027-8424. PMCID PMC528960. https://resolver.caltech.edu/CaltechAUTHORS:20170307-073504137

Feingold, E. A. and Pachter, L. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-640. ISSN 0036-8075. https://resolver.caltech.edu/CaltechAUTHORS:20170308-133717579

Guigó, Roderic and Birney, Ewan and Brent, Michael et al. (2004) Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170307-100841641

McAuliffe, Jon D. and Pachter, Lior and Jordan, Michael I. (2004) Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics, 20 (12). pp. 1850-1860. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170308-135943475

Frazer, Kelly A. and Pachter, Lior and Poliakov, Alexander et al. (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research, 32 (Suppl. 2). W273-W279. ISSN 0305-1048. PMCID PMC441596. https://resolver.caltech.edu/CaltechAUTHORS:20170308-140652072

Pachter, L. and Speyer, D. (2004) Reconstructing Trees from Subtree Weights. Applied Mathematics Letters, 17 (6). pp. 615-621. ISSN 0893-9659. https://resolver.caltech.edu/CaltechAUTHORS:20170307-080948323

Gibbs, Richard A. and Pachter, Lior (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428 (6982). pp. 493-521. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20170308-145138306

Dewey, Colin and Wu, Jia Qian and Cawley, Simon et al. (2004) Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat. Genome Research, 14 (4). pp. 661-664. ISSN 1088-9051. PMCID PMC383310. https://resolver.caltech.edu/CaltechAUTHORS:20170308-144150791

Yap, Von Bing and Pachter, Lior (2004) Identification of Evolutionary Hotspots in the Rodent Genomes. Genome Research, 14 (4). pp. 574-579. ISSN 1088-9051. PMCID PMC383301. https://resolver.caltech.edu/CaltechAUTHORS:20170308-144803591

Bray, Nicolas and Pachter, Lior (2004) MAVID: Constrained ancestral alignment of multiple sequences. Genome Research, 14 (4). pp. 693-699. ISSN 1088-9051. PMCID PMC383315. https://resolver.caltech.edu/CaltechAUTHORS:20170307-074220313

Chakrabarti, Kushal and Pachter, Lior (2004) Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER. Genome Research, 14 (4). pp. 716-720. ISSN 1088-9051. PMCID PMC383318. https://resolver.caltech.edu/CaltechAUTHORS:20170308-142044905

Chatterji, Sourav and Pachter, Lior (2004) Multiple organism gene finding by collapsed Gibbs sampling. In: Proceedings of the eighth annual international conference on Computational molecular biology (RECOMB '04). ACM , New York, NY, pp. 187-193. ISBN 1-58113-755-9. https://resolver.caltech.edu/CaltechAUTHORS:20170308-141248581

2003

Cawley, Simon L. and Pachter, Lior (2003) HMM sampling and applications to gene finding and alternative splicing. Bioinformatics, 19 (Suppl 2). ii36-ii41. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170308-151105303

Lam, Fumei and Pachter, Lior (2003) Forcing numbers of stop signs. Theoretical Computer Science, 303 (2-3). pp. 409-416. ISSN 0304-3975. https://resolver.caltech.edu/CaltechAUTHORS:20170308-151538288

Bray, Nicolas and Pachter, Lior (2003) MAVID multiple alignment server. Nucleic Acids Research, 31 (13). pp. 3525-3526. ISSN 1362-4962. PMCID PMC169029. https://resolver.caltech.edu/CaltechAUTHORS:20170308-152103068

Cawley, Simon and Pachter, Lior and Alexandersson, Marina (2003) SLAM web server for comparative gene finding and alignment. Nucleic Acids Research, 31 (13). pp. 3507-3509. ISSN 1362-4962. PMCID PMC168989. https://resolver.caltech.edu/CaltechAUTHORS:20170308-152527629

Lam, Fumei and Alexandersson, Marina and Pachter, Lior (2003) Picking Alignments from (Steiner) Trees. Journal of Computational Biology, 10 (3-4). pp. 509-520. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170308-153301235

Alexandersson, Marina and Cawley, Simon and Pachter, Lior (2003) SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research, 13 (3). pp. 496-502. ISSN 1088-9051. PMCID PMC430255. https://resolver.caltech.edu/CaltechAUTHORS:20170308-154151410

Boffelli, Dario and McAuliffe, Jon and Ovcharenko, Dmitriy et al. (2003) Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome. Science, 299 (5611). pp. 1391-1394. ISSN 0036-8075. https://resolver.caltech.edu/CaltechAUTHORS:20170308-154624549

Bray, Nick and Dubchak, Inna and Pachter, Lior (2003) AVID: A Global Alignment Program. Genome Research, 13 (1). pp. 97-102. ISSN 1088-9051. PMCID PMC430967. https://resolver.caltech.edu/CaltechAUTHORS:20170308-155631683

Couronne, Olivier and Poliakov, Alexander and Bray, Nicolas et al. (2003) Strategies and Tools for Whole-Genome Alignments. Genome Research, 13 (1). pp. 73-80. ISSN 1088-9051. PMCID PMC430965. https://resolver.caltech.edu/CaltechAUTHORS:20170308-160145750

2002

Waterston, Robert H. and Pachter, Lior (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420 (6915). pp. 520-562. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20170309-090859678

Pachter, Lior and Alexandersson, Marina and Cawley, Simon (2002) Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. Journal of Computational Biology, 9 (2). pp. 389-399. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635

Benos, Panayiotis and Pachter, Lior (2002) From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies. Genome Research, 11 (5). pp. 710-730. ISSN 1088-9051. PMCID PMC311117. https://resolver.caltech.edu/CaltechAUTHORS:20170309-100309238

Loots, Gabriela G. and Ovcharenko, Ivan and Pachter, Lior et al. (2002) rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites. Genome Research, 12 (5). pp. 832-839. ISSN 1088-9051. PMCID PMC186580. https://resolver.caltech.edu/CaltechAUTHORS:20170309-093325277

Pachter, Lior and Lam, Fumei and Alexandersson, Marina (2002) Picking alignments from (Steiner) trees. In: Proceedings of the sixth annual international conference on Computational biology (RECOMB '02). ACM , New York, NY, pp. 246-253. ISBN 1-58113-498-3. https://resolver.caltech.edu/CaltechAUTHORS:20170309-094423019

Dubchak, Inna and Pachter, Lior (2002) The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics, 3 (1). pp. 18-22. ISSN 1467-5463. https://resolver.caltech.edu/CaltechAUTHORS:20170309-093904962

Peter, Annette and Pachter, Lior (2002) Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Reports, 3 (1). pp. 34-38. ISSN 1469-221X. PMCID PMC1083931. https://resolver.caltech.edu/CaltechAUTHORS:20170309-095230836

2001

Pachter, L. S. and Pachter, M. (2001) Optimal paths for avoiding a radiating source. In: Proceedings of the 40th IEEE Conference on Decision and Control. Vol.4. IEEE , Piscataway, NJ, pp. 3581-3586. ISBN 0-78057061-9. https://resolver.caltech.edu/CaltechAUTHORS:20170309-101645949

Pachter, Lior and Alexandersson, Marina and Cawley, Simon (2001) Applications of generalized pair hidden Markov models to alignment and gene finding problems. In: Proceedings of the fifth annual international conference on Computational biology (RECOMB '01). ACM , New York, NY, pp. 241-248. ISBN 1-58113-353-7. https://resolver.caltech.edu/CaltechAUTHORS:20170309-084730577

2000

Mayor, Chris and Brudno, Michael and Schwartz, Jody R. et al. (2000) VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16 (11). pp. 1046-1047. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170309-104254761

Dubchak, Inna and Brudno, Michael and Loots, Gabriela G. et al. (2000) Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons. Genome Research, 10 (9). pp. 1304-1306. ISSN 1088-9051. PMCID PMC310906. https://resolver.caltech.edu/CaltechAUTHORS:20170309-111029375

Batzoglou, Serafim and Pachter, Lior and Mesirov, Jill P. et al. (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. Genome Research, 10 (7). pp. 950-958. ISSN 1088-9051. PMCID PMC310911. https://resolver.caltech.edu/CaltechAUTHORS:20170309-110441139

Batzoglou, Serafim and Pachter, Lior and Mesirov, Jill et al. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. In: Proceedings of the fourth annual international conference on Computational molecular biology (RECOMB '00). ACM , New York, NY, pp. 46-53. ISBN 1-58113-186-0. https://resolver.caltech.edu/CaltechAUTHORS:20170309-111631818

1999

Pachter, Lior and Batzoglou, Serafim and Spitkovsky, Valentin I. et al. (1999) A Dictionary-Based Approach for Gene Annotation. Journal of Computational Biology, 6 (3-4). pp. 419-430. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170309-113000311

Pachter, Lior and Batzoglou, Serafim and Spitkovsky, Valentin I. et al. (1999) A dictionary based approach for gene annotation. In: Proceedings of the third annual international conference on Computational molecular biology (RECOMB '99). ACM , New York, NY, pp. 285-294. ISBN 1-58113-069-4. https://resolver.caltech.edu/CaltechAUTHORS:20170309-113403506

1998

Pachter, Lior and Kim, Peter (1998) Forcing matchings on square grids. Discrete Mathematics, 190 (1-3). pp. 287-294. ISSN 0012-365X. https://resolver.caltech.edu/CaltechAUTHORS:20170309-141622723

Kleitman, D. and Pachter, L. (1998) Finding Convex Sets Among Points in the Plane. Discrete and Computational Geometry, 19 (3). pp. 405-410. ISSN 0179-5376. https://resolver.caltech.edu/CaltechAUTHORS:20170309-114305555

Batzoglou, Serafim and Berger, Bonnie and Kleitman, Daniel J. et al. (1998) Recent Developments in Computational Gene Recognition. Documenta Mathematica, ICM I . pp. 649-658. ISSN 1431-0635. https://resolver.caltech.edu/CaltechAUTHORS:20170309-142440565

1997

Pachter, Lior (1997) Constructing status injective graphs. Discrete Applied Mathematics, 80 (1). pp. 107-113. ISSN 0166-218X. https://resolver.caltech.edu/CaltechAUTHORS:20170309-143338663

Pachter, Lior (1997) Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes. Electronic Journal of Combinatorics, 4 (1). Art. No. R29. ISSN 1077-8926. https://resolver.caltech.edu/CaltechAUTHORS:20170309-144854496

1995

Pachter, Lior and Snevily, Hunter S. and Voxman, Bill (1995) On pebbling graphs. In: Proceedings of the Twenty-sixth Southeastern International Conference on Combinatorics, Graph Theory and Computing. Congressus Numerantium. No.107. Utilitas Mathematica Publishing , Winnipeg, MB, pp. 65-80. https://resolver.caltech.edu/CaltechAUTHORS:20170309-150137723

This list was generated on Sat Aug 8 03:57:11 2020 PDT.