Lior Pachter - Publications

Electrical Engineering and Computer Science University of California, Berkeley, Berkeley, CA 
Biosystems & Computational Biology (BIO); Artificial Intelligence (AI)

153 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, ... ... Pachter L, et al. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nature Biomedical Engineering. PMID 34211145 DOI: 10.1038/s41551-021-00754-5  0.4
2021 Melsted P, Booeshaghi AS, Liu L, Gao F, Lu L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature Biotechnology. PMID 33795888 DOI: 10.1038/s41587-021-00870-2  0.64
2021 Booeshaghi AS, Pachter L. Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x). Bioinformatics (Oxford, England). PMID 33676365 DOI: 10.1093/bioinformatics/btab085  0.64
2020 Booeshaghi AS, Lubock NB, Cooper AR, Simpkins SW, Bloom JS, Gehring J, Luebbert L, Kosuri S, Pachter L. Reliable and accurate diagnostics from highly multiplexed sequencing assays. Scientific Reports. 10: 21759. PMID 33303831 DOI: 10.1038/s41598-020-78942-7  0.64
2020 Svensson V, da Veiga Beltrame E, Pachter L. A curated database reveals trends in single-cell transcriptomics. Database : the Journal of Biological Databases and Curation. 2020. PMID 33247933 DOI: 10.1093/database/baaa073  0.48
2020 Bloom JS, Jones EM, Gasperini M, Lubock NB, Sathe L, Munugala C, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, ... ... Pachter L, et al. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. Medrxiv : the Preprint Server For Health Sciences. PMID 32909008 DOI: 10.1101/2020.08.04.20167874  0.64
2020 Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. Elife. 9. PMID 32701060 DOI: 10.7554/Elife.59610  0.48
2020 Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Author response: Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos Elife. DOI: 10.7554/Elife.59610.Sa2  0.48
2019 Gao F, da Veiga Beltrame E, Gehring JA, Edljarn Hjoerleifsson KE, Lu L, Melsted P, Ntranos V, Pachter L, Svensson V. The BUS Format for Single-Cell RNA-Seq Processing and Analysis. Journal of Biomolecular Techniques : Jbt. 30: S62. PMID 31897036  0.48
2019 Gehring J, Hwee Park J, Chen S, Thomson M, Pachter L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nature Biotechnology. PMID 31873215 DOI: 10.1038/S41587-019-0372-Z  0.52
2019 Booeshaghi AS, Beltrame EDV, Bannon D, Gehring J, Pachter L. Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific Reports. 9: 12385. PMID 31455877 DOI: 10.1038/S41598-019-48815-9  0.64
2019 Melsted P, Ntranos V, Pachter L. The Barcode, UMI, Set format and BUStools. Bioinformatics (Oxford, England). PMID 31073610 DOI: 10.1093/Bioinformatics/Btz279  0.48
2019 Ntranos V, Yi L, Melsted P, Pachter L. A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nature Methods. PMID 30664774 DOI: 10.1038/S41592-018-0303-9  0.48
2019 Melsted P, Booeshaghi AS, Liu L, Gao F, Min KH, Beltrame E, Lu L, Hjörleifsson KE, Gehring J, Pachter L. Algorithms and infrastructure for accurate pre-processing and analysis of single-cell RNA-seq F1000research. 8. DOI: 10.7490/F1000Research.1117626.1  0.64
2018 Tunney R, McGlincy NJ, Graham ME, Naddaf N, Pachter L, Lareau LF. Accurate design of translational output by a neural network model of ribosome distribution. Nature Structural & Molecular Biology. PMID 29967537 DOI: 10.1038/S41594-018-0080-2  0.44
2017 Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods. PMID 28581496 DOI: 10.1038/Nmeth.4324  0.48
2016 Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. The Lair: a resource for exploratory analysis of published RNA-Seq data. Bmc Bioinformatics. 17: 490. PMID 27905880 DOI: 10.1186/S12859-016-1357-2  0.48
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Erratum: Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34: 888. PMID 27504780 DOI: 10.1038/Nbt0816-888D  0.48
2016 Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biology. 17: 112. PMID 27230763 DOI: 10.1186/S13059-016-0970-8  1
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. PMID 27043002 DOI: 10.1038/Nbt.3519  1
2015 Mittal A, Pachter L, Nelson JL, Kjærgaard H, Smed MK, Gildengorin VL, Zoffmann V, Hetland ML, Jewell NP, Olsen J, Jawaheer D. Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis. Plos One. 10: e0145204. PMID 26683605 DOI: 10.1371/Journal.Pone.0145204  1
2015 Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science (New York, N.Y.). PMID 26541607 DOI: 10.1126/Science.Aad2456  1
2015 Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Research. PMID 26531823 DOI: 10.1093/Nar/Gkv1168  1
2015 Taylor DR, Bernstein BA, Carroll E, Oquendo E, Peyton L, Pachter LM. Keeping the Heat on for Children's Health: A Successful Medical-Legal Partnership Initiative to Prevent Utility Shutoffs in Vulnerable Children. Journal of Health Care For the Poor and Underserved. 26: 676-85. PMID 26320904 DOI: 10.1353/hpu.2015.0074  0.44
2015 Cronholm PF, Forke CM, Wade R, Bair-Merritt MH, Davis M, Harkins-Schwarz M, Pachter LM, Fein JA. Adverse Childhood Experiences: Expanding the Concept of Adversity. American Journal of Preventive Medicine. 49: 354-61. PMID 26296440 DOI: 10.1016/j.amepre.2015.02.001  0.4
2015 Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047  1
2015 Singer M, Pachter L. Controlling for conservation in genome-wide DNA methylation studies. Bmc Genomics. 16: 420. PMID 26024968 DOI: 10.1186/S12864-015-1604-3  1
2015 Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y. A diverse epigenetic landscape at human exons with implication for expression. Nucleic Acids Research. 43: 3498-508. PMID 25765649 DOI: 10.1093/Nar/Gkv153  1
2015 Pachter LM, Kodjo C. New Century Scholars: A Mentorship Program to Increase Workforce Diversity in Academic Pediatrics. Academic Medicine : Journal of the Association of American Medical Colleges. PMID 25692562 DOI: 10.1097/ACM.0000000000000669  0.4
2015 Weller SC, Baer RD, de Alba Garcia JG, Glazer M, Trotter R, Salcedo Rocha AL, Klein RE, Pachter LM. Variation and Persistence in Latin American Beliefs About Evil Eye Cross-Cultural Research. 49: 174-203. DOI: 10.1177/1069397114539268  0.4
2015 Pachter LM, Weller SC, Baer RD, de Alba Garcia JEG, Glazer M, Trotter R, Klein RE, Gonzalez E. Culture and Dehydration: A Comparative Study of Caída de la Mollera (Fallen Fontanel) in Three Latino Populations Journal of Immigrant and Minority Health. DOI: 10.1007/s10903-015-0259-0  0.4
2015 Taylor DR, Bernstein BA, Carroll E, Oquendo E, Peyton L, Pachter LM. Keeping the heat on for children’s health: A successful medical– legal partnership initiative to prevent utility shutoffs in vulnerable children Journal of Health Care For the Poor and Underserved. 26: 676-685.  0.4
2014 Pachter LM, Cheng TL. Prevention of noncommunicable diseases. Jama. 312: 2572-3. PMID 25514311 DOI: 10.1001/jama.2014.15140  0.4
2014 Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. Rna (New York, N.Y.). 20: 1864-77. PMID 25332375 DOI: 10.1261/Rna.043844.113  1
2014 Forster R, Chiba K, Schaeffer L, Regalado SG, Lai CS, Gao Q, Kiani S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, et al. Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Stem Cell Reports. 2: 838-52. PMID 24936470 DOI: 10.1016/J.Stemcr.2014.05.001  1
2014 Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB. Structural variation among wild and industrial strains of Penicillium chrysogenum. Plos One. 9: e96784. PMID 24824901 DOI: 10.1371/Journal.Pone.0096784  1
2014 Thompson DA, Pachter LM, Keller D. Efforts to diversify the academic pediatric workforce. Jama Pediatrics. 168: 390-1. PMID 24710589 DOI: 10.1001/jamapediatrics.2013.4867  0.4
2014 Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D. Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Research. 24: 821-30. PMID 24558263 DOI: 10.1101/Gr.162412.113  1
2014 Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG. A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Research. 42: 4031-42. PMID 24442673 DOI: 10.1093/nar/gkt1388  1
2014 Di Rocco S, Sturmfels B. Preface Lecture Notes in Mathematics. 2108: v-vi. DOI: 10.1007/978-3-319-04870-3  1
2013 Roberts A, Feng H, Pachter L. Fragment assignment in the cloud with eXpress-D. Bmc Bioinformatics. 14: 358. PMID 24314033 DOI: 10.1186/1471-2105-14-358  1
2013 Roberts A, Schaeffer L, Pachter L. Updating RNA-Seq analyses after re-annotation. Bioinformatics (Oxford, England). 29: 1631-7. PMID 23677943 DOI: 10.1093/Bioinformatics/Btt197  1
2013 Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biology. 14: R8. PMID 23360652 DOI: 10.1186/Gb-2013-14-1-R8  1
2013 Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 31: 46-53. PMID 23222703 DOI: 10.1038/Nbt.2450  1
2013 Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods. 10: 71-3. PMID 23160280 DOI: 10.1038/Nmeth.2251  1
2013 Kleinman A, Harel M, Pachter L. Affine and Projective Tree Metric Theorems Annals of Combinatorics. 17: 205-228. DOI: 10.1007/S00026-012-0173-2  1
2012 Hower V, Starfield R, Roberts A, Pachter L. Quantifying uniformity of mapped reads. Bioinformatics (Oxford, England). 28: 2680-2. PMID 22815359 DOI: 10.1093/bioinformatics/bts451  1
2012 Philp JC, Maselli J, Pachter LM, Cabana MD. Complementary and alternative medicine use and adherence with pediatric asthma treatment. Pediatrics. 129: e1148-54. PMID 22492763 DOI: 10.1542/peds.2011-2467  0.4
2012 Pachter L. A closer look at RNA editing. Nature Biotechnology. 30: 246-7. PMID 22398619 DOI: 10.1038/Nbt.2156  1
2012 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/Nprot.2012.016  1
2012 Blekherman G, Hauenstein J, Ottem JC, Ranestad K, Sturmfels B. Algebraic boundaries of Hilbert™s SOS cones Compositio Mathematica. 148: 1717-1735. DOI: 10.1112/S0010437X12000437  0.56
2011 Singer M, Engström A, Schönhuth A, Pachter L. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains. Statistical Applications in Genetics and Molecular Biology. 10. PMID 23089814 DOI: 10.2202/1544-6115.1677  1
2011 Roberts A, Pachter L. RNA-Seq and find: entering the RNA deep field. Genome Medicine. 3: 74. PMID 22113004 DOI: 10.1186/Gm290  1
2011 Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. Bmc Bioinformatics. 12: 451. PMID 22099972 DOI: 10.1186/1471-2105-12-451  1
2011 Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research. 21: 2049-57. PMID 21908772 DOI: 10.1101/Gr.122721.111  1
2011 Snir S, Pachter L. Tracing the most parsimonious indel history. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 967-86. PMID 21728862 DOI: 10.1089/Cmb.2010.0325  1
2011 Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (Oxford, England). 27: 2325-9. PMID 21697122 DOI: 10.1093/Bioinformatics/Btr355  1
2011 Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108  0.4
2011 Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. 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: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108  0.4
2011 Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 12: R22. PMID 21410973 DOI: 10.1186/Gb-2011-12-3-R22  1
2011 Hower V, Evans SN, Pachter L. Shape-based peak identification for ChIP-Seq. Bmc Bioinformatics. 12: 15. PMID 21226895 DOI: 10.1186/1471-2105-12-15  1
2011 Taylor T, Pachter LM, Bastian JF, Stein MT. Gerardo: asthma and cultural beliefs in a Latino family. Journal of Developmental and Behavioral Pediatrics : Jdbp. 32: 75-7. PMID 21206360 DOI: 10.1097/DBP.0b013e318203e087  0.4
2011 Aviran S, Lucks JB, Pachter L. RNA structure characterization from chemical mapping experiments 2011 49th Annual Allerton Conference On Communication, Control, and Computing, Allerton 2011. 1743-1750. DOI: 10.1109/Allerton.2011.6120379  1
2011 Levy D, Pachter L. The neighbor-net algorithm Advances in Applied Mathematics. 47: 240-258. DOI: 10.1016/J.Aam.2010.09.002  1
2010 Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. Plos One. 5: e13564. PMID 21042592 DOI: 10.1371/Journal.Pone.0013564  1
2010 Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L. MetMap enables genome-scale Methyltyping for determining methylation states in populations. Plos Computational Biology. 6: e1000888. PMID 20856582 DOI: 10.1371/Journal.Pcbi.1000888  1
2010 Evans SN, Hower V, Pachter L. Coverage statistics for sequence census methods. Bmc Bioinformatics. 11: 430. PMID 20718980 DOI: 10.1186/1471-2105-11-430  1
2010 Levin TC, Glazer AM, Pachter L, Brem RB, Eisen MB. Exploring the genetic basis of variation in gene predictions with a synthetic association study. Plos One. 5: e11645. PMID 20686598 DOI: 10.1371/Journal.Pone.0011645  1
2010 Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Molecular Cancer Research : McR. 8: 961-74. PMID 20605923 DOI: 10.1158/1541-7786.Mcr-09-0528  1
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/Nbt.1621  1
2010 Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biology. 8: e1000343. PMID 20351773 DOI: 10.1371/Journal.Pbio.1000343  1
2010 Pachter LM, Bernstein BA, Szalacha LA, García Coll C. Perceived racism and discrimination in children and youths: an exploratory study. Health & Social Work. 35: 61-9. PMID 20218454  0.4
2010 Pachter LM. Child health care disparities: findings from the annual report on children's health care. Academic Pediatrics. 10: 87-8. PMID 20206905 DOI: 10.1016/j.acap.2010.01.009  0.4
2010 Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WO. Disordered microbial communities in asthmatic airways. Plos One. 5: e8578. PMID 20052417 DOI: 10.1371/Journal.Pone.0008578  1
2010 Pachter LM, Szalacha LA, Bernstein BA, Coll CG. Perceptions of Racism in Children and Youth (PRaCY): properties of a self-report instrument for research on children's health and development. Ethnicity & Health. 15: 33-46. PMID 20013438 DOI: 10.1080/13557850903383196  0.4
2009 Horn IB, Cora-Bramble D, Cheng TL, Jenkins R, Pachter L, Joseph J. Starting early: a life-course perspective on child health disparities--research recommendations. Pediatrics. 124: S257-61. PMID 19861478 DOI: 10.1542/Peds.2009-1100O  0.4
2009 Pachter LM, Coll CG. Racism and child health: a review of the literature and future directions. Journal of Developmental and Behavioral Pediatrics : Jdbp. 30: 255-63. PMID 19525720 DOI: 10.1097/DBP.0b013e3181a7ed5a  0.4
2009 Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. Plos Computational Biology. 5: e1000392. PMID 19478997 DOI: 10.1371/Journal.Pcbi.1000392  1
2009 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England). 25: 1105-11. PMID 19289445 DOI: 10.1093/Bioinformatics/Btp120  1
2009 Mihaescu R, Levy D, Pachter L. Why neighbor-joining works Algorithmica (New York). 54: 1-24. DOI: 10.1007/S00453-007-9116-4  1
2008 Bradley RK, Pachter L, Holmes I. Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (Oxford, England). 24: 2677-83. PMID 18796475 DOI: 10.1093/Bioinformatics/Btn495  1
2008 Mihaescu R, Pachter L. Combinatorics of least-squares trees. Proceedings of the National Academy of Sciences of the United States of America. 105: 13206-11. PMID 18779558 DOI: 10.1073/Pnas.0802089105  1
2008 Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O. Comparison of pattern detection methods in microarray time series of the segmentation clock. Plos One. 3: e2856. PMID 18682743 DOI: 10.1371/Journal.Pone.0002856  1
2008 Eickmeyer K, Huggins P, Pachter L, Yoshida R. On the optimality of the neighbor-joining algorithm. Algorithms For Molecular Biology : Amb. 3: 5. PMID 18447942 DOI: 10.1186/1748-7188-3-5  1
2008 Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. Viral population estimation using pyrosequencing. Plos Computational Biology. 4: e1000074. PMID 18437230 DOI: 10.1371/Journal.Pcbi.1000074  1
2008 Kostanecka A, Power T, Clarke A, Watkins M, Hausman CL, Blum NJ. Behavioral health screening in urban primary care settings: construct validity of the PSC-17. Journal of Developmental and Behavioral Pediatrics : Jdbp. 29: 124-8. PMID 18408533 DOI: 10.1097/Dbp.0B013E31816A0D9E  0.4
2008 Satija R, Pachter L, Hein J. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics (Oxford, England). 24: 1236-42. PMID 18353788 DOI: 10.1093/Bioinformatics/Btn104  1
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Pachter L, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  1
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Pachter L, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.68
2007 Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Plos Biology. 5: e310. PMID 17988176 DOI: 10.1371/Journal.Pbio.0050310  1
2007 Huggins P, Pachter L, Sturmfels B. Toward the human genotope. Bulletin of Mathematical Biology. 69: 2723-35. PMID 17874271 DOI: 10.1007/S11538-007-9244-7  1
2007 Morton J, Pachter L, Shiu A, Sturmfels B. The cyclohedron test for finding periodic genes in time course expression studies. Statistical Applications in Genetics and Molecular Biology. 6: Article 21. PMID 17764440 DOI: 10.2202/1544-6115.1286  1
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Pachter L, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  1
2007 Pachter L. Interpreting the unculturable majority. Nature Methods. 4: 479-80. PMID 17538628 DOI: 10.1038/Nmeth0607-479  1
2007 Chatterji S, Pachter L. Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics. 90: 44-8. PMID 17499477 DOI: 10.1016/J.Ygeno.2007.03.008  1
2007 Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, Lenski RE. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. Bmc Evolutionary Biology. 7: 60. PMID 17433106 DOI: 10.1186/1471-2148-7-60  1
2007 Schwartz AS, Pachter L. Multiple alignment by sequence annealing. Bioinformatics (Oxford, England). 23: e24-9. PMID 17237099 DOI: 10.1093/Bioinformatics/Btl311  1
2007 Pachter L, Sturmsfels B. The mathematics of phylogenomics Siam Review. 49: 3-31. DOI: 10.1137/050632634  1
2007 Schumacher C, Chandler PR, Pachter M, Pachter LS. Optimization of air vehicles operations using mixed-integer linear programming Journal of the Operational Research Society. 58: 516-527. DOI: 10.1057/Palgrave.Jors.2602176  1
2007 Beerenwinkel N, Pachter L, Sturmfels B. Epistasis and shapes of fitness landscapes Statistica Sinica. 17: 1317-1342.  1
2006 Dumont-Mathieu TM, Bernstein BA, Dworkin PH, Pachter LM. Role of pediatric health care professionals in the provision of parenting advice: a qualitative study with mothers from 4 minority ethnocultural groups. Pediatrics. 118: e839-48. PMID 16950970 DOI: 10.1542/peds.2005-2604  0.4
2006 Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. Plos Computational Biology. 2: e73. PMID 16789815 DOI: 10.1371/Journal.Pcbi.0020073  1
2006 Dewey CN, Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics. 15: R51-6. PMID 16651369 DOI: 10.1093/Hmg/Ddl056  1
2006 Chatterji S, Pachter L. Reference based annotation with GeneMapper. Genome Biology. 7: R29. PMID 16600017 DOI: 10.1186/Gb-2006-7-4-R29  1
2006 Pachter LM, Auinger P, Palmer R, Weitzman M. Do parenting and the home environment, maternal depression, neighborhood, and chronic poverty affect child behavioral problems differently in different racial-ethnic groups? Pediatrics. 117: 1329-38. PMID 16585331 DOI: 10.1542/peds.2005-1784  0.4
2006 Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Current Biology : Cb. 16: 460-71. PMID 16458514 DOI: 10.1016/J.Cub.2006.01.050  1
2006 Caspi A, Pachter L. Identification of transposable elements using multiple alignments of related genomes. Genome Research. 16: 260-70. PMID 16354754 DOI: 10.1101/Gr.4361206  1
2006 Levy D, Yoshida R, Pachter L. Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Molecular Biology and Evolution. 23: 491-8. PMID 16280538 DOI: 10.1093/Molbev/Msj059  1
2006 Snir S, Pachter L. Phylogenetic profiling of insertions and deletions in vertebrate genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 265-280. DOI: 10.1007/11732990_23  1
2006 Morton J, Pachter L, Shiu A, Sturmfels B, Wienand O. Geometry of rank tests Proceedings of the 3rd European Workshop On Probabilistic Graphical Models, Pgm 2006. 207-214.  1
2005 Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. Plos Computational Biology. 1: 106-12. PMID 16110337 DOI: 10.1371/Journal.Pcbi.0010024  1
2005 Chatterji S, Pachter L. Large multiple organism gene finding by collapsed Gibbs sampling. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 599-608. PMID 16108706 DOI: 10.1089/Cmb.2005.12.599  1
2005 McAuliffe JD, Jordan MI, Pachter L. Subtree power analysis and species selection for comparative genomics. Proceedings of the National Academy of Sciences of the United States of America. 102: 7900-5. PMID 15911755 DOI: 10.1073/Pnas.0502790102  1
2005 Pachter L, Sturmfels B. Biology Algebraic Statistics For Computational Biology. 125-160. DOI: 10.1017/CBO9780511610684.007  1
2005 Pachter L, Sturmfels B. Computation Algebraic Statistics For Computational Biology. 43-84. DOI: 10.1017/CBO9780511610684.005  1
2005 Pachter L, Sturmfels B. Statistics Algebraic Statistics For Computational Biology. 3-42. DOI: 10.1017/CBO9780511610684.004  1
2005 Pachter L, Sturmfels B. Algebraic statistics for computational biology Algebraic Statistics For Computational Biology. 1-420. DOI: 10.1017/CBO9780511610684  1
2005 Pachter LM. The Effects of Culture on Child Health Pediatrics. 1646-1651. DOI: 10.1016/B978-0-323-01199-0.50262-0  0.4
2005 Agarwal PK, Akutsu T, Amihood A, Apostolico A, Benham C, Benson G, Blanchette M, El-Mabrouk N, Gascuel O, Giancarlo R, Guigo R, Hallet M, Huson D, Kucherov G, Lacey M, ... ... Pachter L, et al. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692: V-VI.  1
2004 Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, Rubin EM. Intraspecies sequence comparisons for annotating genomes. Genome Research. 14: 2406-11. PMID 15545499 DOI: 10.1101/Gr.3199704  1
2004 Pachter L, Sturmfels B. Tropical geometry of statistical models. Proceedings of the National Academy of Sciences of the United States of America. 101: 16132-7. PMID 15534224 DOI: 10.1073/Pnas.0406010101  1
2004 Pachter L, Sturmfels B. Parametric inference for biological sequence analysis. Proceedings of the National Academy of Sciences of the United States of America. 101: 16138-43. PMID 15534223 DOI: 10.1073/Pnas.0406011101  1
2004 Stein MT, Pachter LM, Schwartz L, Taras H. Disruptive classroom behavior in an amish school-age child with muscular dystrophy. Journal of Developmental and Behavioral Pediatrics : Jdbp. 25: S102-6. PMID 15502525  0.4
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Pachter L, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  1
2004 Stein MT, Pachter LM, Schwartz L, Taras H. Disruptive classroom behavior in an Amish school-age child with muscular dystrophy. Journal of Developmental and Behavioral Pediatrics : Jdbp. 25: 280-4. PMID 15308929 DOI: 10.1097/00004703-200408000-00008  0.4
2004 Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Research. 32: W273-9. PMID 15215394 DOI: 10.1093/Nar/Gkh458  1
2004 Chakrabarti K, Pachter L. Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Research. 14: 716-20. PMID 15060015 DOI: 10.1101/Gr.1957004  1
2004 Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Research. 14: 693-9. PMID 15060012 DOI: 10.1101/Gr.1960404  1
2004 Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research. 14: 661-4. PMID 15060007 DOI: 10.1101/Gr.1939804  1
2004 Yap VB, Pachter L. Identification of evolutionary hotspots in the rodent genomes. Genome Research. 14: 574-9. PMID 15059998 DOI: 10.1101/Gr.1967904  1
2004 McAuliffe JD, Pachter L, Jordan MI. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics (Oxford, England). 20: 1850-60. PMID 14988105 DOI: 10.1093/Bioinformatics/Bth153  1
2004 Pachter LM, Dumont-Mathieu T. Parenting in culturally divergent settings Handbook of Parenting: Theory and Research For Practice. 88-97. DOI: 10.4135/9781848608160.n6  0.4
2004 Pachter L, Speyer D. Reconstructing trees from subtree weights Applied Mathematics Letters. 17: 615-621. DOI: 10.1016/S0893-9659(04)90095-X  1
2004 Schumacher C, Chandler P, Pachter M, Pachter L. UAV task assignment with timing constraints via mixed-integer linear programming Collection of Technical Papers - Aiaa 3rd "Unmanned-Unlimited" Technical Conference, Workshop, and Exhibit. 1: 238-252.  1
2004 Schumacher C, Chandler P, Pachter M, Pachter L. Constrained optimization for UAV task assignment Collection of Technical Papers - Aiaa Guidance, Navigation, and Control Conference. 5: 3152-3165.  1
2004 Chatterji S, Pachter L. Multiple organism gene finding by collapsed Gibbs sampling Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 187-193.  1
2003 Cawley SL, Pachter L. HMM sampling and applications to gene finding and alternative splicing. Bioinformatics (Oxford, England). 19: ii36-41. PMID 14534169 DOI: 10.1093/bioinformatics/btg1057  1
2003 Baer RD, Weller SC, de Alba Garcia JG, Glazer M, Trotter R, Pachter L, Klein RE. A cross-cultural approach to the study of the folk illness nervios. Culture, Medicine and Psychiatry. 27: 315-37. PMID 14510097 DOI: 10.1023/A:1025351231862  0.4
2003 Lam F, Alexandersson M, Pachter L. Picking alignments from (Steiner) trees. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 509-20. PMID 12935341 DOI: 10.1089/10665270360688156  1
2003 Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Research. 31: 3525-6. PMID 12824358 DOI: 10.1093/Nar/Gkg623  1
2003 Cawley S, Pachter L, Alexandersson M. SLAM web server for comparative gene finding and alignment. Nucleic Acids Research. 31: 3507-9. PMID 12824355 DOI: 10.1093/Nar/Gkg583  1
2003 Alexandersson M, Cawley S, Pachter L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Research. 13: 496-502. PMID 12618381 DOI: 10.1101/Gr.424203  1
2003 Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (New York, N.Y.). 299: 1391-4. PMID 12610304 DOI: 10.1126/Science.1081331  1
2003 Bray N, Dubchak I, Pachter L. AVID: A global alignment program. Genome Research. 13: 97-102. PMID 12529311 DOI: 10.1101/Gr.789803  1
2003 Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Strategies and tools for whole-genome alignments. Genome Research. 13: 73-80. PMID 12529308 DOI: 10.1101/Gr.762503  1
2003 Lam F, Pachter L. Forcing numbers of stop signs Theoretical Computer Science. 303: 409-416. DOI: 10.1016/S0304-3975(02)00499-1  1
2002 Weller SC, Baer RD, de Alba Garcia JG, Glazer M, Trotter R, Pachter L, Klein RE. Regional variation in Latino descriptions of susto. Culture, Medicine and Psychiatry. 26: 449-72. PMID 12572769 DOI: 10.1023/A:1021743405946  0.4
2002 Flores G, Fuentes-Afflick E, Barbot O, Carter-Pokras O, Claudio L, Lara M, McLaurin JA, Pachter L, Ramos-Gomez FJ, Mendoza F, Valdez RB, Villarruel AM, Zambrana RE, Greenberg R, Weitzman M, et al. The health of Latino children: urgent priorities, unanswered questions, and a research agenda. Jama. 288: 82-90. PMID 12090866 DOI: 10.1001/Jama.288.1.82  0.4
2001 Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, ... ... Pachter L, et al. From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies. Genome Research. 11: 710-30. PMID 11337470 DOI: 10.1101/Gr.173801  1
2000 Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics (Oxford, England). 16: 1046-7. PMID 11159318 DOI: 10.1093/Bioinformatics/16.11.1046  1
2000 Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Research. 10: 1304-6. PMID 10984448 DOI: 10.1101/Gr.142200  1
2000 Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research. 10: 950-8. PMID 10899144 DOI: 10.1101/Gr.10.7.950  1
1999 Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary-based approach for gene annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 419-30. PMID 10582576 DOI: 10.1089/106652799318364  1
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