Lior Pachter

Lior Pachter

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Lior Pachter

Publications by authors named "Lior Pachter"

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Factor analysis for survival time prediction with informative censoring and diverse covariates.

Stat Med 2019 Sep 4;38(20):3719-3732. Epub 2019 Jun 4.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.

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http://dx.doi.org/10.1002/sim.8151DOI Listing
September 2019

Principles of open source bioinstrumentation applied to the poseidon syringe pump system.

Sci Rep 2019 Aug 27;9(1):12385. Epub 2019 Aug 27.

Department of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.

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http://dx.doi.org/10.1038/s41598-019-48815-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711986PMC
August 2019

The Barcode, UMI, Set format and BUStools.

Bioinformatics 2019 May 9. Epub 2019 May 9.

Department of Computing & Mathematical Sciences. California Institute of Technology, Pasadena, CA, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz279DOI Listing
May 2019

A discriminative learning approach to differential expression analysis for single-cell RNA-seq.

Nat Methods 2019 02 21;16(2):163-166. Epub 2019 Jan 21.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

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http://dx.doi.org/10.1038/s41592-018-0303-9DOI Listing
February 2019

Barcode identification for single cell genomics.

BMC Bioinformatics 2019 Jan 17;20(1):32. Epub 2019 Jan 17.

Departments of Biology and Computing & Mathematical Sciences, California Institute of Technology, 116 Kerckhoff Laboratory, Pasadena, CA, 91125, USA.

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http://dx.doi.org/10.1186/s12859-019-2612-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337828PMC
January 2019

Deterministic column subset selection for single-cell RNA-Seq.

PLoS One 2019 25;14(1):e0210571. Epub 2019 Jan 25.

Division of Biology and Biological Engineering, Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210571PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347249PMC
January 2019

Expression reflects population structure.

PLoS Genet 2018 12 19;14(12):e1007841. Epub 2018 Dec 19.

Division of Biology and Biological Engineering, California Institute of Technology, Padadena, California, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1007841
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http://dx.doi.org/10.1371/journal.pgen.1007841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317812PMC
December 2018

RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.

Mol Cell 2018 10;72(1):7-9

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765183079
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http://dx.doi.org/10.1016/j.molcel.2018.09.026DOI Listing
October 2018

Accurate design of translational output by a neural network model of ribosome distribution.

Nat Struct Mol Biol 2018 07 2;25(7):577-582. Epub 2018 Jul 2.

California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41594-018-0080-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457438PMC
July 2018

Association mapping from sequencing reads using -mers.

Elife 2018 06 13;7. Epub 2018 Jun 13.

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, United States.

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http://dx.doi.org/10.7554/eLife.32920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044908PMC
June 2018

Gene-level differential analysis at transcript-level resolution.

Genome Biol 2018 04 12;19(1):53. Epub 2018 Apr 12.

Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA.

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http://dx.doi.org/10.1186/s13059-018-1419-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896116PMC
April 2018

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

PLoS One 2017 27;12(4):e0175744. Epub 2017 Apr 27.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175744PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407828PMC
September 2017

Differential analysis of RNA-seq incorporating quantification uncertainty.

Nat Methods 2017 Jul 5;14(7):687-690. Epub 2017 Jun 5.

Division of Biology and Biological Engineering, Caltech, Pasadena, California, USA.

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http://dx.doi.org/10.1038/nmeth.4324DOI Listing
July 2017

PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.

Cell Syst 2017 05 10;4(5):568-574.e7. Epub 2017 May 10.

Departments of Biology and Computing & Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758053PMC
May 2017

Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study.

Arthritis Res Ther 2017 05 25;19(1):104. Epub 2017 May 25.

UCSF Benioff Children's Hospital Oakland, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, USA.

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http://dx.doi.org/10.1186/s13075-017-1312-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445464PMC
May 2017

The Lair: a resource for exploratory analysis of published RNA-Seq data.

BMC Bioinformatics 2016 Dec 1;17(1):490. Epub 2016 Dec 1.

Department of Computer Science, University of California, Berkeley, 387 Soda Hall, Berkeley, 94720, USA.

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http://dx.doi.org/10.1186/s12859-016-1357-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131447PMC
December 2016

Single-cell analysis at the threshold.

Nat Biotechnol 2016 11;34(11):1111-1118

Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/nbt.3721DOI Listing
November 2016

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

Genomics 2016 10 10;108(3-4):158-167. Epub 2016 Sep 10.

Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2016.09.002DOI Listing
October 2016

Near-optimal probabilistic RNA-seq quantification.

Nat Biotechnol 2016 05 4;34(5):525-7. Epub 2016 Apr 4.

Department of Computer Science, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nbt.3519DOI Listing
May 2016

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts.

Genome Biol 2016 05 26;17(1):112. Epub 2016 May 26.

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1186/s13059-016-0970-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881296PMC
May 2016

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

Nucleic Acids Res 2016 Jan 3;44(2):838-51. Epub 2015 Nov 3.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

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http://dx.doi.org/10.1093/nar/gkv1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737145PMC
January 2016

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.

Science 2015 Dec 5;350(6265):1251-5. Epub 2015 Nov 5.

Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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https://cole-trapnell-lab.github.io/pdfs/papers/hanchate-olf
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http://www.sciencemag.org/cgi/doi/10.1126/science.aad2456
Publisher Site
http://dx.doi.org/10.1126/science.aad2456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642900PMC
December 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Controlling for conservation in genome-wide DNA methylation studies.

BMC Genomics 2015 May 30;16:420. Epub 2015 May 30.

Division of Computer Science, University of California at Berkeley, 94720, Berkeley, CA, USA.

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http://dx.doi.org/10.1186/s12864-015-1604-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448855PMC
May 2015

A diverse epigenetic landscape at human exons with implication for expression.

Nucleic Acids Res 2015 Apr 12;43(7):3498-508. Epub 2015 Mar 12.

Department of Molecular & Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA

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http://dx.doi.org/10.1093/nar/gkv153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402514PMC
April 2015

Structural variation among wild and industrial strains of Penicillium chrysogenum.

PLoS One 2014 13;9(5):e96784. Epub 2014 May 13.

Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096784PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019546PMC
January 2015

Rational experiment design for sequencing-based RNA structure mapping.

RNA 2014 Dec 20;20(12):1864-77. Epub 2014 Oct 20.

Center for Computational Biology and Departments of Molecular and Cell Biology and Mathematics, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1261/rna.043844.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238353PMC
December 2014

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Nucleic Acids Res 2014 Apr 17;42(6):4031-42. Epub 2014 Jan 17.

Department of Computer Science, University of California, Berkeley, CA 94720, USA, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065, USA, Department of Mathematics, University of California, Berkeley, CA 94720, USA and Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkt1388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973340PMC
April 2014

Fragment assignment in the cloud with eXpress-D.

BMC Bioinformatics 2013 Dec 7;14:358. Epub 2013 Dec 7.

Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/1471-2105-14-358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3881492PMC
December 2013

Updating RNA-Seq analyses after re-annotation.

Bioinformatics 2013 Jul 14;29(13):1631-7. Epub 2013 May 14.

Department of Computer Science, University of Calofornia Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694665PMC
July 2013

Streaming fragment assignment for real-time analysis of sequencing experiments.

Nat Methods 2013 Jan 18;10(1):71-3. Epub 2012 Nov 18.

Department of Computer Science, University of California, Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nmeth.2251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880119PMC
January 2013

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Nat Biotechnol 2013 Jan 9;31(1):46-53. Epub 2012 Dec 9.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869392PMC
January 2013

CGAL: computing genome assembly likelihoods.

Genome Biol 2013 Jan 29;14(1):R8. Epub 2013 Jan 29.

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http://dx.doi.org/10.1186/gb-2013-14-1-r8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663106PMC
January 2013

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Curr Protoc Chem Biol 2012 Dec;4(4):275-97

Department of Molecular and Cell Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/9780470559277.ch120019DOI Listing
December 2012

Quantifying uniformity of mapped reads.

Bioinformatics 2012 Oct 18;28(20):2680-2. Epub 2012 Jul 18.

Department of Mathematics, University of Miami, Coral Gables, FL 33146, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467739PMC
October 2012

A closer look at RNA editing.

Authors:
Lior Pachter

Nat Biotechnol 2012 Mar 7;30(3):246-7. Epub 2012 Mar 7.

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http://dx.doi.org/10.1038/nbt.2156DOI Listing
March 2012

Improving RNA-Seq expression estimates by correcting for fragment bias.

Genome Biol 2011 16;12(3):R22. Epub 2011 Mar 16.

Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-r22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672PMC
January 2012

Identification and correction of systematic error in high-throughput sequence data.

BMC Bioinformatics 2011 Nov 21;12:451. Epub 2011 Nov 21.

Department of Mathematics, University of California, Berkeley, 970 Evans Hall #3840, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/1471-2105-12-451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295828PMC
November 2011

RNA-Seq and find: entering the RNA deep field.

Genome Med 2011 Nov 22;3(11):74. Epub 2011 Nov 22.

Department of Computer Science, UC Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gm290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308029PMC
November 2011

Identification of novel transcripts in annotated genomes using RNA-Seq.

Bioinformatics 2011 Sep 21;27(17):2325-9. Epub 2011 Jun 21.

Department of Computer Science, UC Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr355DOI Listing
September 2011

Tracing the most parsimonious indel history.

J Comput Biol 2011 Aug 5;18(8):967-86. Epub 2011 Jul 5.

Department of Evolutionary Biology and the Institute of Evolution, Haifa University, Haifa, Israel.

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http://dx.doi.org/10.1089/cmb.2010.0325DOI Listing
August 2011

Modeling and automation of sequencing-based characterization of RNA structure.

Proc Natl Acad Sci U S A 2011 Jul 3;108(27):11069-74. Epub 2011 Jun 3.

Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1106541108
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http://dx.doi.org/10.1073/pnas.1106541108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131376PMC
July 2011

Shape-based peak identification for ChIP-Seq.

BMC Bioinformatics 2011 Jan 12;12:15. Epub 2011 Jan 12.

Department of Mathematics, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1186/1471-2105-12-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032669PMC
January 2011

Development of a low bias method for characterizing viral populations using next generation sequencing technology.

PLoS One 2010 Oct 22;5(10):e13564. Epub 2010 Oct 22.

Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013564PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2962647PMC
October 2010

Coverage statistics for sequence census methods.

BMC Bioinformatics 2010 Aug 18;11:430. Epub 2010 Aug 18.

Department of Mathematics, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1186/1471-2105-11-430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940910PMC
August 2010

MetMap enables genome-scale Methyltyping for determining methylation states in populations.

PLoS Comput Biol 2010 Aug 19;6(8):e1000888. Epub 2010 Aug 19.

Computer Science Division, University of California at Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924245PMC
August 2010

Exploring the genetic basis of variation in gene predictions with a synthetic association study.

PLoS One 2010 Jul 29;5(7):e11645. Epub 2010 Jul 29.

Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011645PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912228PMC
July 2010

TopHat: discovering splice junctions with RNA-Seq.

Bioinformatics 2009 May 16;25(9):1105-11. Epub 2009 Mar 16.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672628PMC
May 2009

Fast statistical alignment.

PLoS Comput Biol 2009 May 29;5(5):e1000392. Epub 2009 May 29.

Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684580PMC
May 2009

Specific alignment of structured RNA: stochastic grammars and sequence annealing.

Bioinformatics 2008 Dec 16;24(23):2677-83. Epub 2008 Sep 16.

Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732270PMC
December 2008

Combinatorics of least-squares trees.

Proc Natl Acad Sci U S A 2008 Sep 8;105(36):13206-11. Epub 2008 Sep 8.

Departments of Mathematics and Computer Science, University of California, Berkeley, CA 94704, USA.

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http://dx.doi.org/10.1073/pnas.0802089105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533170PMC
September 2008

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Bioinformatics 2008 May 18;24(10):1236-42. Epub 2008 Mar 18.

Department of Statistics, Oxford University, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn104DOI Listing
May 2008

Viral population estimation using pyrosequencing.

PLoS Comput Biol 2008 May 9;4(4):e1000074. Epub 2008 May 9.

Department of Statistics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1000074
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http://dx.doi.org/10.1371/journal.pcbi.1000074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323617PMC
May 2008

On the optimality of the neighbor-joining algorithm.

Algorithms Mol Biol 2008 Apr 30;3. Epub 2008 Apr 30.

Department of Mathematics, University of California at Berkeley Berkeley, CA 94720-3840, USA.

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April 2008

Toward the human genotope.

Bull Math Biol 2007 Nov 15;69(8):2723-35. Epub 2007 Sep 15.

Department of Mathematics, University of California at Berkeley, Berkeley, USA.

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November 2007

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

The cyclohedron test for finding periodic genes in time course expression studies.

Stat Appl Genet Mol Biol 2007 15;6:Article 21. Epub 2007 Aug 15.

University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.2202/1544-6115.1286DOI Listing
September 2007

Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor.

Genomics 2007 Jul 11;90(1):44-8. Epub 2007 May 11.

Genome Center, University of California at Davis, Davis, CA 95616, USA.

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http://dx.doi.org/10.1016/j.ygeno.2007.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034525PMC
July 2007

Interpreting the unculturable majority.

Authors:
Lior Pachter

Nat Methods 2007 Jun;4(6):479-80

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http://dx.doi.org/10.1038/nmeth0607-479DOI Listing
June 2007

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
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June 2007

Analysis of epistatic interactions and fitness landscapes using a new geometric approach.

BMC Evol Biol 2007 Apr 13;7:60. Epub 2007 Apr 13.

Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1186/1471-2148-7-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865543PMC
April 2007

Multiple alignment by sequence annealing.

Bioinformatics 2007 Jan;23(2):e24-9

EECS, Computer Science Division, University of California Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl311DOI Listing
January 2007

Reference based annotation with GeneMapper.

Genome Biol 2006 5;7(4):R29. Epub 2006 Apr 5.

Department of Computer Science, University of California at Berkeley, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557983PMC
September 2006

Parametric alignment of Drosophila genomes.

PLoS Comput Biol 2006 Jun 23;2(6):e73. Epub 2006 Jun 23.

Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0020073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480539PMC
June 2006

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Hum Mol Genet 2006 Apr;15 Spec No 1:R51-6

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.

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http://www.hmg.oxfordjournals.org/cgi/doi/10.1093/hmg/ddl056
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April 2006

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.

Mol Biol Evol 2006 Mar 9;23(3):491-8. Epub 2005 Nov 9.

Department of Mathematics, University of California, Berkeley, USA.

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March 2006

A genome-wide map of conserved microRNA targets in C. elegans.

Curr Biol 2006 Mar 2;16(5):460-71. Epub 2006 Feb 2.

Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA.

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March 2006

Identification of transposable elements using multiple alignments of related genomes.

Genome Res 2006 Feb 14;16(2):260-70. Epub 2005 Dec 14.

University of California, San Francisco/University of California, Berkeley Joint Graduate Group in Bioengineering, Berkeley, CA 97210, USA.

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http://dx.doi.org/10.1101/gr.4361206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361722PMC
February 2006

Large multiple organism gene finding by collapsed Gibbs sampling.

J Comput Biol 2005 Jul-Aug;12(6):599-608

Department of Computer Science, University of California at Berkeley, Berkeley, CA 94720.

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October 2005

Bioinformatics for whole-genome shotgun sequencing of microbial communities.

PLoS Comput Biol 2005 Jul;1(2):106-12

Department of Electrical Engineering and Computer Science, University of California, Berkeley, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185649PMC
July 2005

Subtree power analysis and species selection for comparative genomics.

Proc Natl Acad Sci U S A 2005 May 23;102(22):7900-5. Epub 2005 May 23.

Department of Statistics and Mathematics, University of California, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142384PMC
May 2005

Intraspecies sequence comparisons for annotating genomes.

Genome Res 2004 Dec 15;14(12):2406-11. Epub 2004 Nov 15.

US Dept. of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534664PMC
December 2004

Parametric inference for biological sequence analysis.

Proc Natl Acad Sci U S A 2004 Nov 8;101(46):16138-43. Epub 2004 Nov 8.

Department of Mathematics, University of California, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528961PMC
November 2004

Tropical geometry of statistical models.

Proc Natl Acad Sci U S A 2004 Nov 8;101(46):16132-7. Epub 2004 Nov 8.

Department of Mathematics, University of California, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528960PMC
November 2004

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.

Bioinformatics 2004 Aug 26;20(12):1850-60. Epub 2004 Feb 26.

Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth153DOI Listing
August 2004

VISTA: computational tools for comparative genomics.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W273-9

Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/nar/gkh458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441596PMC
July 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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April 2004

Identification of evolutionary hotspots in the rodent genomes.

Genome Res 2004 Apr;14(4):574-9

Department of Mathematics, University of California, Berkeley, California 94720-3840, USA.

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http://dx.doi.org/10.1101/gr.1967904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383301PMC
April 2004

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

Genome Res 2004 Apr;14(4):661-4

Department of Electrical Engineering, University of California-Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.1939804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383310PMC
April 2004

MAVID: constrained ancestral alignment of multiple sequences.

Genome Res 2004 Apr;14(4):693-9

Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.1960404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383315PMC
April 2004

Visualization of multiple genome annotations and alignments with the K-BROWSER.

Genome Res 2004 Apr;14(4):716-20

Department of Computer Science, University of California, Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.1957004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383318PMC
April 2004

HMM sampling and applications to gene finding and alternative splicing.

Bioinformatics 2003 Oct;19 Suppl 2:ii36-41

Affymetrix, Emeryville, CA 94608, USA.

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October 2003