| 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 |
|
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