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Lior Pachter - Publications

Affiliations: 
Electrical Engineering and Computer Science University of California, Berkeley, Berkeley, CA, United States 
Area:
Biosystems & Computational Biology (BIO); Artificial Intelligence (AI)
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Year Citation  Score
2023 Gorin G, Vastola JJ, Pachter L. Studying stochastic systems biology of the cell with single-cell genomics data. Cell Systems. 14: 822-843.e22. PMID 37751736 DOI: 10.1016/j.cels.2023.08.004  0.326
2023 Gorin G, Vastola JJ, Pachter L. Studying stochastic systems biology of the cell with single-cell genomics data. Biorxiv : the Preprint Server For Biology. PMID 37292934 DOI: 10.1101/2023.05.17.541250  0.326
2023 Booeshaghi AS, Chen X, Pachter L. A machine-readable specification for genomics assays. Biorxiv : the Preprint Server For Biology. PMID 36993635 DOI: 10.1101/2023.03.17.533215  0.312
2022 Gorin G, Pachter L. Length biases in single-cell RNA sequencing of pre-mRNA. Biophysical Reports. 3: 100097. PMID 36660179 DOI: 10.1016/j.bpr.2022.100097  0.305
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  0.778
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  0.783
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  0.791
2020 Gorin G, Pachter L. Special function methods for bursty models of transcription. Physical Review. E. 102: 022409. PMID 32942485 DOI: 10.1103/Physreve.102.022409  0.306
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  0.776
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  0.336
2020 Mao S, Pachter L, Tse D, Kannan S. RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition. Plos One. 15: e0232946. PMID 32484809 DOI: 10.1371/Journal.Pone.0232946  0.439
2020 Svensson V, Gayoso A, Yosef N, Pachter L. Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinformatics (Oxford, England). PMID 32176273 DOI: 10.1093/Bioinformatics/Btaa169  0.355
2020 Gorin G, Svensson V, Pachter L. Protein velocity and acceleration from single-cell multiomics experiments. Genome Biology. 21: 39. PMID 32070398 DOI: 10.1186/S13059-020-1945-3  0.337
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  0.369
2019 Kim DW, Yao Z, Graybuck LT, Kim TK, Nguyen TN, Smith KA, Fong O, Yi L, Koulena N, Pierson N, Shah S, Lo L, Pool AH, Oka Y, Pachter L, et al. Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior. Cell. 179: 713-728.e17. PMID 31626771 DOI: 10.1016/J.Cell.2019.09.020  0.755
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  0.745
2019 Melsted P, Ntranos V, Pachter L. The Barcode, UMI, Set format and BUStools. Bioinformatics (Oxford, England). PMID 31073610 DOI: 10.1093/Bioinformatics/Btz279  0.345
2019 McCurdy SR, Ntranos V, Pachter L. Deterministic column subset selection for single-cell RNA-Seq. Plos One. 14: e0210571. PMID 30682053 DOI: 10.1371/Journal.Pone.0210571  0.357
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  0.784
2019 Tambe A, Pachter L. Barcode identification for single cell genomics. Bmc Bioinformatics. 20: 32. PMID 30654736 DOI: 10.1186/S12859-019-2612-0  0.367
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  0.775
2018 Brown BC, Bray NL, Pachter L. Expression reflects population structure. Plos Genetics. 14: e1007841. PMID 30566439 DOI: 10.1371/Journal.Pgen.1007841  0.322
2018 Svensson V, Pachter L. RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq. Molecular Cell. 72: 7-9. PMID 30290149 DOI: 10.1016/J.Molcel.2018.09.026  0.318
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  0.765
2018 Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L. Association mapping from sequencing reads using -mers. Elife. 7. PMID 29897334 DOI: 10.7554/Elife.32920  0.428
2018 Yi L, Pimentel H, Bray NL, Pachter L. Gene-level differential analysis at transcript-level resolution. Genome Biology. 19: 53. PMID 29650040 DOI: 10.1186/S13059-018-1419-Z  0.782
2018 Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment. Bioinformatics (Oxford, England). 33: 2082-2088. PMID 28334086 DOI: 10.1093/Bioinformatics/Btx106  0.367
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  0.358
2017 Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems. PMID 28501650 DOI: 10.1016/J.Cels.2017.04.007  0.509
2017 Yi L, Pimentel H, Pachter L. Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. Plos One. 12: e0175744. PMID 28448519 DOI: 10.1371/Journal.Pone.0175744  0.764
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  0.369
2016 Fu AQ, Pachter L. Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Statistical Applications in Genetics and Molecular Biology. PMID 27875323 DOI: 10.1515/Sagmb-2016-0002  0.309
2016 Hateley S, Hosamani R, Bhardwaj SR, Pachter L, Bhattacharya S. Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity. Genomics. PMID 27621057 DOI: 10.1016/J.Ygeno.2016.09.002  0.309
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  0.387
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. PMID 27043002 DOI: 10.1038/Nbt.3519  0.355
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  0.347
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  0.36
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  0.541
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  0.548
2015 Joseph I, McCurdy S, Costello JF, Pachter L. Method for combining multiple genomic and clinical datatypes to predict recurrence grade in gliomas F1000research. 6. DOI: 10.7490/F1000Research.1097884.1  0.327
2015 Pimentel H, Parra M, Gee S, Mohandas N, Pachter L, Conboy JG. The Erythroid Intron Retention Program Encompasses Developmentally Stable and Dynamic Networks and Regulates Diverse Gene Classes Blood. 126: 3331-3331. DOI: 10.1182/Blood.V126.23.3331.3331  0.385
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  0.402
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  0.359
2014 Pimentel H, Parra M, Gee S, Mohandas N, Pachter L, Conboy JG. An Erythroid-Specific Intron Retention Program Regulates Expression of Selected Genes during Terminal Erythropoiesis Blood. 124: 449-449. DOI: 10.1182/Blood.V124.21.449.449  0.381
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  0.39
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  0.404
2013 Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biology. 14: R8. PMID 23360652 DOI: 10.1186/Gb-2013-14-1-R8  0.326
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  0.381
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  0.407
2013 Pimentel H, Parra M, Li J, Gee S, Ghanem D, Hu J, An X, Narla M, Pachter L, Conboy JG. A Dynamic Alternative Splicing Program Regulates Gene Expression In A Differentiation Stage-Specific Manner During Terminal Erythropoiesis Blood. 122: 3413-3413. DOI: 10.1182/Blood.V122.21.3413.3413  0.387
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  0.76
2012 Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4: 275-97. PMID 23788555 DOI: 10.1002/9780470559277.Ch120019  0.353
2012 Pachter L. A closer look at RNA editing. Nature Biotechnology. 30: 246-7. PMID 22398619 DOI: 10.1038/Nbt.2156  0.406
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  0.438
2012 Pimentel H, Li J, Parra M, Ghanem D, Gee S, Hu J, An X, Mohandas N, Pachter L, Conboy JG. Abundance of Alternative Splicing Events and Differentiation Stage-Specific Changes in Splicing Suggest A Major Role in Regulation of Gene Expression During Late Erythropoiesis Blood. 120: 978-978. DOI: 10.1182/Blood.V120.21.978.978  0.383
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  0.601
2011 Roberts A, Pachter L. RNA-Seq and find: entering the RNA deep field. Genome Medicine. 3: 74. PMID 22113004 DOI: 10.1186/Gm290  0.37
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  0.526
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  0.543
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  0.41
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  0.414
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  0.426
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  0.392
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  0.351
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  0.34
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  0.624
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  0.392
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  0.456
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  0.315
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  0.777
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  0.412
2009 Mihaescu R, Levy D, Pachter L. Why neighbor-joining works Algorithmica (New York). 54: 1-24. DOI: 10.1007/S00453-007-9116-4  0.76
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  0.468
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  0.766
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  0.364
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  0.713
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  0.418
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  0.811
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  0.772
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  0.79
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  0.707
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Pachter L, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.811
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  0.812
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  0.606
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  0.513
2007 Schwartz AS, Pachter L. Multiple alignment by sequence annealing. Bioinformatics (Oxford, England). 23: e24-9. PMID 17237099 DOI: 10.1093/Bioinformatics/Btl311  0.694
2007 Pachter L, Sturmsfels B. The mathematics of phylogenomics Siam Review. 49: 3-31. DOI: 10.1137/050632634  0.402
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  0.798
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  0.798
2006 Chatterji S, Pachter L. Reference based annotation with GeneMapper. Genome Biology. 7: R29. PMID 16600017 DOI: 10.1186/Gb-2006-7-4-R29  0.647
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  0.757
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  0.427
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  0.314
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  0.355
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  0.668
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  0.378
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  0.446
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  0.329
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  0.787
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  0.441
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  0.373
2004 Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Research. 14: 693-9. PMID 15060012 DOI: 10.1101/Gr.1960404  0.447
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  0.779
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  0.412
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Pachter L, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.806
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  0.425
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.  0.5
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  0.37
2003 Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Research. 31: 3525-6. PMID 12824358 DOI: 10.1093/Nar/Gkg623  0.424
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  0.406
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  0.43
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  0.461
2003 Bray N, Dubchak I, Pachter L. AVID: A global alignment program. Genome Research. 13: 97-102. PMID 12529311 DOI: 10.1101/Gr.789803  0.394
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  0.425
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Pachter L, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.805
2002 Dubchak I, Pachter L. The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics. 3: 18-22. PMID 12002220 DOI: 10.1093/Bib/3.1.18  0.417
2002 Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Research. 12: 832-9. PMID 11997350 DOI: 10.1101/Gr.225502  0.351
2002 Peter A, Schöttler P, Werner M, Beinert N, Dowe G, Burkert P, Mourkioti F, Dentzer L, He Y, Deak P, Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, ... ... Pachter L, et al. Mapping and identification of essential gene functions on the X chromosome of Drosophila. Embo Reports. 3: 34-8. PMID 11751581 DOI: 10.1093/Embo-Reports/Kvf012  0.384
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  0.431
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  0.428
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  0.611
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  0.686
1998 Kleitman D, Pachter L. Finding Convex Sets Among Points in the Plane Discrete & Computational Geometry. 19: 405-410. DOI: 10.1007/Pl00009358  0.445
Low-probability matches (unlikely to be authored by this person)
2021 Gustafsson J, Robinson J, Nielsen J, Pachter L. BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. Genome Biology. 22: 174. PMID 34103073 DOI: 10.1186/s13059-021-02386-z  0.292
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  0.292
2023 Sullivan DK, Pachter L. Flexible parsing and preprocessing of technical sequences with splitcode. Biorxiv : the Preprint Server For Biology. PMID 36993532 DOI: 10.1101/2023.03.20.533521  0.289
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  0.289
2023 Carilli M, Gorin G, Choi Y, Chari T, Pachter L. Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data. Biorxiv : the Preprint Server For Biology. PMID 36712140 DOI: 10.1101/2023.01.13.523995  0.288
2023 Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, ... ... Pachter L, et al. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. Biorxiv : the Preprint Server For Biology. PMID 37292896 DOI: 10.1101/2023.05.15.540865  0.287
2019 McCurdy S, Molinaro A, Pachter L. Factor analysis for survival time prediction with informative censoring and diverse covariates. Statistics in Medicine. PMID 31162708 DOI: 10.1002/Sim.8151  0.286
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  0.285
2014 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Erratum: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature Protocols. 9: 2513-2513. DOI: 10.1038/Nprot1014-2513A  0.283
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  0.282
2023 Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq. Biorxiv : the Preprint Server For Biology. PMID 38045414 DOI: 10.1101/2023.11.21.568164  0.28
2018 Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L. Author response: Association mapping from sequencing reads using k-mers Elife. DOI: 10.7554/Elife.32920.033  0.276
2007 Pachter L. Interpreting the unculturable majority. Nature Methods. 4: 479-80. PMID 17538628 DOI: 10.1038/Nmeth0607-479  0.273
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  0.271
2023 Booeshaghi AS, Sullivan DK, Pachter L. Universal preprocessing of single-cell genomics data. Biorxiv : the Preprint Server For Biology. PMID 37745572 DOI: 10.1101/2023.09.14.543267  0.271
2023 Gálvez-Merchán Á, Min KHJ, Pachter L, Booeshaghi AS. Metadata retrieval from sequence databases with ffq. Bioinformatics (Oxford, England). PMID 36610997 DOI: 10.1093/bioinformatics/btac667  0.27
2021 Rahman A, Pachter L. SWALO: scaffolding with assembly likelihood optimization. Nucleic Acids Research. PMID 34417615 DOI: 10.1093/nar/gkab717  0.27
2020 Mehrab Z, Mobin J, Tahmid IA, Pachter L, Rahman A. Reference-free Association Mapping from Sequencing Reads Using k-mers. Bio-Protocol. 10: e3815. PMID 33659468 DOI: 10.21769/BioProtoc.3815  0.269
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  0.269
2023 Luebbert L, Sullivan DK, Carilli M, Hjörleifsson KE, Winnett AV, Chari T, Pachter L. Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. Biorxiv : the Preprint Server For Biology. PMID 38168363 DOI: 10.1101/2023.12.11.571168  0.267
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  0.267
2016 Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA. Single-cell analysis at the threshold. Nature Biotechnology. 34: 1111-1118. PMID 27824834 DOI: 10.1038/Nbt.3721  0.265
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  0.264
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  0.263
2021 Booeshaghi AS, Yao Z, van Velthoven C, Smith K, Tasic B, Zeng H, Pachter L. Isoform cell-type specificity in the mouse primary motor cortex. Nature. 598: 195-199. PMID 34616073 DOI: 10.1038/s41586-021-03969-3  0.261
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  0.259
2004 Pachter L, Speyer D. Reconstructing trees from subtree weights Applied Mathematics Letters. 17: 615-621. DOI: 10.1016/S0893-9659(04)90095-X  0.253
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  0.251
2023 Luebbert L, Pachter L. Efficient querying of genomic reference databases with gget. Bioinformatics (Oxford, England). 39. PMID 36610989 DOI: 10.1093/bioinformatics/btac836  0.251
2018 Svensson V, Pachter L. Mapping scRNA-seq data onto cell type taxonomies F1000research. 7. DOI: 10.7490/F1000Research.1116276.1  0.248
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  0.245
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  0.245
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  0.244
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  0.243
2023 Gorin G, Yoshida S, Pachter L. Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing. Bulletin of Mathematical Biology. 85: 114. PMID 37828255 DOI: 10.1007/s11538-023-01213-9  0.233
2022 Gorin G, Vastola JJ, Fang M, Pachter L. Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nature Communications. 13: 7620. PMID 36494337 DOI: 10.1038/s41467-022-34857-7  0.23
2015 Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, ... ... Pachter L, et al. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. The New England Journal of Medicine. 372: 2481-98. PMID 26061751 DOI: 10.1056/Nejmoa1402121  0.229
2023 Chari T, Gorin G, Pachter L. Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data. Biorxiv : the Preprint Server For Biology. PMID 37745403 DOI: 10.1101/2023.09.17.558131  0.228
2023 Booeshaghi AS, Min KHJ, Gehring J, Pachter L. Quantifying orthogonal barcodes for sequence census assays. Bioinformatics Advances. 4: vbad181. PMID 38213823 DOI: 10.1093/bioadv/vbad181  0.224
2014 Forster R, Chiba K, Schaeffer L, Regalado S, Lai C, Gao Q, Kiani S, Farin H, Clevers H, Cost G, Chan A, Rebar E, Urnov F, Gregory P, Pachter L, et al. Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells Stem Cell Reports. 3: 215. DOI: 10.1016/J.Stemcr.2014.06.014  0.222
2003 Lam F, Pachter L. Forcing numbers of stop signs Theoretical Computer Science. 303: 409-416. DOI: 10.1016/S0304-3975(02)00499-1  0.22
2022 Gorin G, Pachter L. Modeling bursty transcription and splicing with the chemical master equation. Biophysical Journal. PMID 35143775 DOI: 10.1016/j.bpj.2022.02.004  0.218
2023 Moses L, Einarsson PH, Jackson K, Luebbert L, Booeshaghi AS, Antonsson S, Bray N, Melsted P, Pachter L. Voyager: exploratory single-cell genomics data analysis with geospatial statistics. Biorxiv : the Preprint Server For Biology. PMID 37645732 DOI: 10.1101/2023.07.20.549945  0.213
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  0.21
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  0.209
2023 Chari T, Pachter L. The specious art of single-cell genomics. Plos Computational Biology. 19: e1011288. PMID 37590228 DOI: 10.1371/journal.pcbi.1011288  0.207
2020 Moses L, Pachter L. Museum of Spatial Transcriptomics F1000research. 9. DOI: 10.7490/F1000Research.1118091.1  0.203
2017 Goin DE, Smed MK, Pachter L, Purdom E, Nelson JL, Kjærgaard H, Olsen J, Hetland ML, Zoffmann V, Ottesen B, Jawaheer D. Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study. Arthritis Research & Therapy. 19: 104. PMID 28545501 DOI: 10.1186/S13075-017-1312-2  0.202
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  0.198
2021 Chari T, Weissbourd B, Gehring J, Ferraioli A, Leclère L, Herl M, Gao F, Chevalier S, Copley RR, Houliston E, Anderson DJ, Pachter L. Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across medusa cell types. Science Advances. 7: eabh1683. PMID 34826233 DOI: 10.1126/sciadv.abh1683  0.194
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  0.191
2022 Gorin G, Fang M, Chari T, Pachter L. RNA velocity unraveled. Plos Computational Biology. 18: e1010492. PMID 36094956 DOI: 10.1371/journal.pcbi.1010492  0.189
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Pachter L, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8  0.187
2002 Pachter L, Alexandersson M, Cawley S. Applications of generalized pair hidden Markov models to alignment and gene finding problems. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 389-99. PMID 12015888 DOI: 10.1089/10665270252935520  0.18
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  0.177
2023 Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Miao Z, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. Developmental Cell. PMID 37673062 DOI: 10.1016/j.devcel.2023.08.010  0.175
2023 Fenelon KD, Gao F, Borad P, Abbasi S, Pachter L, Koromila T. Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos. Frontiers in Cell and Developmental Biology. 11: 1126507. PMID 37051467 DOI: 10.3389/fcell.2023.1126507  0.172
2011 Levy D, Pachter L. The neighbor-net algorithm Advances in Applied Mathematics. 47: 240-258. DOI: 10.1016/J.Aam.2010.09.002  0.162
2022 Moses L, Pachter L. Museum of spatial transcriptomics. Nature Methods. PMID 35273392 DOI: 10.1038/s41592-022-01409-2  0.161
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  0.158
2022 Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y, Samaran J, Misrachi G, Nazaret A, Clivio O, ... ... Pachter L, et al. A Python library for probabilistic analysis of single-cell omics data. Nature Biotechnology. PMID 35132262 DOI: 10.1038/s41587-021-01206-w  0.157
2023 Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. Biorxiv : the Preprint Server For Biology. PMID 37205355 DOI: 10.1101/2023.05.06.539585  0.148
2023 Jackson KC, Pachter L. A standard for sharing spatial transcriptomics data. Cell Genomics. 3: 100374. PMID 37601972 DOI: 10.1016/j.xgen.2023.100374  0.145
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  0.122
2024 Luebbert L, Hoang C, Kumar M, Pachter L. Fast and scalable querying of eukaryotic linear motifs with gget elm. Bioinformatics (Oxford, England). PMID 38377393 DOI: 10.1093/bioinformatics/btae095  0.12
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  0.108
2005 Pachter L, Sturmfels B. Biology Algebraic Statistics For Computational Biology. 125-160. DOI: 10.1017/CBO9780511610684.007  0.105
2009 Morton J, Pachter L, Shiu A, Sturmfels B, Wienand O. Convex Rank Tests and Semigraphoids Siam Journal On Discrete Mathematics. 23: 1117-1134. DOI: 10.1137/080715822  0.093
2023 Torok Z, Luebbert L, Feldman J, Duffy A, Nevue AA, Wongso S, Mello CV, Fairhall A, Pachter L, Gonzalez WG, Lois C. Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons. Biorxiv : the Preprint Server For Biology. PMID 37292888 DOI: 10.1101/2023.05.17.541057  0.082
2005 Pachter L, Sturmfels B. Algebraic statistics for computational biology Algebraic Statistics For Computational Biology. 1-420. DOI: 10.1017/CBO9780511610684  0.08
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  0.08
2023 Gorin G, Pachter L. The telegraph process is not a subordinator. Biorxiv : the Preprint Server For Biology. PMID 36711462 DOI: 10.1101/2023.01.17.524309  0.074
1997 Pachter L. Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes The Electronic Journal of Combinatorics. 4. DOI: 10.37236/1314  0.073
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  0.073
2021 Booeshaghi AS, Kil YA, Min KHJ, Gehring J, Pachter L. Low-cost, scalable, and automated fluid sampling for fluidics applications. Hardwarex. 10: e00201. PMID 35607693 DOI: 10.1016/j.ohx.2021.e00201  0.07
2005 Pachter L, Sturmfels B. Statistics Algebraic Statistics For Computational Biology. 3-42. DOI: 10.1017/CBO9780511610684.004  0.063
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  0.058
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  0.057
2022 Moses L, Pachter L. Publisher Correction: Museum of spatial transcriptomics. Nature Methods. PMID 35440782 DOI: 10.1038/s41592-022-01494-3  0.055
2023 Booeshaghi AS, Beltrame EDV, Bannon D, Gehring J, Pachter L. Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific Reports. 13: 14834. PMID 37684312 DOI: 10.1038/s41598-023-42035-y  0.054
2002 Pachter LM, Weller SC, Baer RD, de Alba Garcia JE, Trotter RT, Glazer M, Klein R. Variation in asthma beliefs and practices among mainland Puerto Ricans, Mexican-Americans, Mexicans, and Guatemalans. The Journal of Asthma : Official Journal of the Association For the Care of Asthma. 39: 119-34. PMID 11995676 DOI: 10.1081/Jas-120002193  0.054
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  0.053
2015 Pachter LM, Weller SC, Baer RD, de Alba Garcia JE, 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 / Center For Minority Public Health. PMID 26239172 DOI: 10.1007/S10903-015-0259-0  0.05
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.  0.049
2005 Pachter L, Sturmfels B. Computation Algebraic Statistics For Computational Biology. 43-84. DOI: 10.1017/CBO9780511610684.005  0.047
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  0.046
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.  0.044
2014 Van Niel C, Pachter LM, Wade R, Felitti VJ, Stein MT. Adverse events in children: predictors of adult physical and mental conditions. Journal of Developmental and Behavioral Pediatrics : Jdbp. 35: 549-51. PMID 25225793 DOI: 10.1097/DBP.0000000000000102  0.043
2007 Beerenwinkel N, Pachter L, Sturmfels B. Epistasis and shapes of fitness landscapes Statistica Sinica. 17: 1317-1342.  0.04
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.  0.036
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  0.035
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  0.035
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  0.031
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  0.031
2015 Pachter LM. Transition and continuity: Message from the new editor Journal of Developmental and Behavioral Pediatrics. 36: 59-60. DOI: 10.1097/DBP.0000000000000141  0.03
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  0.03
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.  0.029
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  0.029
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  0.027
1997 Pachter L. Constructing status injective graphs Discrete Applied Mathematics. 80: 107-113. DOI: 10.1016/S0166-218X(97)00073-5  0.027
2009 Mitchell A, Connolly M, Bedrosian A, Pachter L, Miller G. QS475. In States of Hepatic Cirrhosis, Liver Dendritic Cells Control the Hepatic Cytokine Milieu and Gain Enhanced Capacity to Stimulate Innate and Adaptive Immunity Journal of Surgical Research. 151: 304. DOI: 10.1016/j.jss.2008.11.790  0.026
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  0.025
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  0.024
1998 Pachter L, Kim P. Forcing matchings on square grids Discrete Mathematics. 190: 287-294. DOI: 10.1016/S0012-365X(97)00266-5  0.024
2023 Gorin G, Pachter L. New and notable: Revisiting the "two cultures" through extrinsic noise. Biophysical Journal. 123: 1-3. PMID 38041403 DOI: 10.1016/j.bpj.2023.11.3400  0.023
2012 Cohen DJ, Newman E, Iqbal S, Chang RY, Potmesil M, Ryan T, Donahue B, Chandra A, Liu M, Utate M, Hiotis S, Pachter LH, Hochster H, Muggia F. Postoperative intraperitoneal 5-fluoro-2'-deoxyuridine added to chemoradiation in patients curatively resected (R0) for locally advanced gastric and gastroesophageal junction adenocarcinoma. Annals of Surgical Oncology. 19: 478-85. PMID 21769462 DOI: 10.1245/s10434-011-1940-8  0.021
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  0.018
2015 Melis M, Masi A, Pinna A, Cohen S, Hatzaras I, Berman R, Pachter LH, Newman E. Does lymph node ratio affect prognosis in gastroesophageal cancer? American Journal of Surgery. PMID 26003203 DOI: 10.1016/j.amjsurg.2014.12.042  0.015
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.  0.013
2000 Guth AA, Pachter L. Domestic violence and the trauma surgeon. American Journal of Surgery. 179: 134-40. PMID 10970242  0.01
2014 Pachter LM, Cheng TL. Prevention of noncommunicable diseases. Jama. 312: 2572-3. PMID 25514311 DOI: 10.1001/jama.2014.15140  0.01
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  0.01
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  0.01
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  0.01
2005 Pachter LM. The Effects of Culture on Child Health Pediatrics. 1646-1651. DOI: 10.1016/B978-0-323-01199-0.50262-0  0.01
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 DOI: 10.1097/00004703-200410001-00021  0.01
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  0.01
2001 Flores G, Fuentes-Afflick E, Carter-Pokras O, Claudio L, Lamberty G, Lara M, Pachter L, Ramos Gomez F, Mendoza F, Valdez RB, Zambrana RE, Greenberg R, Weitzman M. Why ethnicity and race are so important in child health services research today. Archives of Pediatrics & Adolescent Medicine. 155: 1178-9. PMID 11576022  0.01
1973 Pachter L. Management of bleeding diverticulums. The New England Journal of Medicine. 289: 753. PMID 4542246 DOI: 10.1056/NEJM197310042891423  0.01
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