Laura Elnitski

Laura Elnitski

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Laura Elnitski

Laura Elnitski

Publications by authors named "Laura Elnitski"

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63Publications

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CAGI experiments: Modeling sequence variant impact on gene splicing using predictions from computational tools.

Hum Mutat 2019 Sep 27;40(9):1252-1260. Epub 2019 Jun 27.

Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.

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http://dx.doi.org/10.1002/humu.23782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744343PMC
September 2019

Aberrant DNA methylation defines isoform usage in cancer, with functional implications.

PLoS Comput Biol 2019 Jul 22;15(7):e1007095. Epub 2019 Jul 22.

Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675117PMC
July 2019

Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.

IEEE/ACM Trans Comput Biol Bioinform 2018 Jul-Aug;15(4):1290-1300. Epub 2015 Oct 30.

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http://dx.doi.org/10.1109/TCBB.2015.2496261DOI Listing
May 2019

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression.

Genome Res 2019 04 18;29(4):657-667. Epub 2019 Mar 18.

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1101/gr.247007.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442386PMC
April 2019

The hypothesis of ultraconserved enhancer dispensability overturned.

Genome Biol 2018 05 8;19(1):57. Epub 2018 May 8.

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1186/s13059-018-1433-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938802PMC
May 2018

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types.

PLoS Comput Biol 2017 Nov 10;13(11):e1005840. Epub 2017 Nov 10.

Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States.

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http://dx.doi.org/10.1371/journal.pcbi.1005840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709060PMC
November 2017

SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures.

Bioinformatics 2017 Sep;33(17):2615-2621

Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860059PMC
September 2017

A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models.

PLoS One 2016 27;11(10):e0163353. Epub 2016 Oct 27.

National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163353PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082879PMC
June 2017

CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies.

World J Gastrointest Oncol 2017 Mar;9(3):105-120

Francisco Sánchez-Vega, Valer Gotea, Yun-Ching Chen, Laura Elnitski, Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852, United States.

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http://dx.doi.org/10.4251/wjgo.v9.i3.105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348626PMC
March 2017

The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation.

Biomolecules 2016 11 22;6(4). Epub 2016 Nov 22.

National Human Genome Research Institute, Rockville, MD 20852, USA.

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http://dx.doi.org/10.3390/biom6040045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5197955PMC
November 2016

Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development.

J Mol Diagn 2016 Mar 5;18(2):283-98. Epub 2016 Feb 5.

Translational and Functional Genomics Branch, National Human Genome Research Institute, Rockville, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2015.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816708PMC
March 2016

The functional relevance of somatic synonymous mutations in melanoma and other cancers.

Pigment Cell Melanoma Res 2015 Nov;28(6):673-84

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1111/pcmr.12413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834044PMC
November 2015

Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype.

Epigenetics Chromatin 2015 17;8:14. Epub 2015 Apr 17.

Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA.

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http://dx.doi.org/10.1186/s13072-015-0007-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424513PMC
May 2015

Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots.

Genomics 2014 May-Jun;103(5-6):349-56. Epub 2014 Apr 13.

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

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http://dx.doi.org/10.1016/j.ygeno.2014.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527313PMC
January 2015

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.

Nucleic Acids Res 2014 Mar 24;42(5):2856-69. Epub 2013 Dec 24.

Departments of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA, Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852, USA and Deparment of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950716PMC
March 2014

Bidirectional promoters as important drivers for the emergence of species-specific transcripts.

PLoS One 2013 27;8(2):e57323. Epub 2013 Feb 27.

DIR/GTB Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057323PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583895PMC
September 2013

Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene.

J Cyst Fibros 2012 Dec 14;11(6):511-7. Epub 2012 May 14.

DIR/GTB Genomic Functional Analysis Section, National Human Genome Research Institute, NIH Rockville, MD 20852, USA.

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http://dx.doi.org/10.1016/j.jcf.2012.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440543PMC
December 2012

Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype.

PLoS One 2012 5;7(3):e32941. Epub 2012 Mar 5.

DIR/GTB Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032941PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293923PMC
July 2012

Genome-wide detection of a TFIID localization element from an initial human disease mutation.

Nucleic Acids Res 2011 Mar 11;39(6):2175-87. Epub 2010 Nov 11.

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852, USA.

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http://dx.doi.org/10.1093/nar/gkq1035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064768PMC
March 2011

Genomic features defining exonic variants that modulate splicing.

Genome Biol 2010 16;11(2):R20. Epub 2010 Feb 16.

Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-2-r20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872880PMC
August 2010

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes.

PLoS One 2010 Aug 18;5(8):e12274. Epub 2010 Aug 18.

National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012274PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923625PMC
August 2010

Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter.

Mol Cell Biol 2010 Jul 17;30(14):3493-502. Epub 2010 May 17.

National Institutes of Health, National Human Genome Research Institute, Genetics and Molecular Biology Branch, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1128/MCB.00119-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897556PMC
July 2010

MultiPipMaker: a comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2010 Jun;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471250953.bi1004s30DOI Listing
June 2010

Word-based characterization of promoters involved in human DNA repair pathways.

BMC Genomics 2009 Jul 7;10 Suppl 1:S18. Epub 2009 Jul 7.

Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-S1-S18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709261PMC
July 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Finding Occurrences of Relevant Functional Elements in Genomic Signatures.

Int J Comput Sci 2008 Oct;2(5):599-606

National Human Genome Research Institute, National Institutes of Health, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800375PMC
October 2008

Diversity of core promoter elements comprising human bidirectional promoters.

BMC Genomics 2008 Sep 16;9 Suppl 2:S3. Epub 2008 Sep 16.

National Human Genome Research Institute, National Institutes Health, Rockville, MD 20852, USA.

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http://dx.doi.org/10.1186/1471-2164-9-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559893PMC
September 2008

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus.

Genome Res 2008 Aug 24;18(8):1238-46. Epub 2008 Apr 24.

Genome Technology Branch, National Human Genome Research Institute, NIH, Rockville, MD 20852, USA.

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http://dx.doi.org/10.1101/gr.073817.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493434PMC
August 2008

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

BMC Genomics 2008 ;9 Suppl 1:S2

National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1186/1471-2164-9-S1-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386062PMC
June 2008

Comparative analyses of bidirectional promoters in vertebrates.

BMC Bioinformatics 2008 May 28;9 Suppl 6:S9. Epub 2008 May 28.

Genome Technology Branch, NHGRI, NIH, MD, USA.

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http://dx.doi.org/10.1186/1471-2105-9-S6-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423431PMC
May 2008

The ENCODEdb portal: simplified access to ENCODE Consortium data.

Genome Res 2007 Jun;17(6):954-9

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

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http://dx.doi.org/10.1101/gr.5582207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891354PMC
June 2007

Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

PLoS Comput Biol 2007 Apr 5;3(4):e72. Epub 2007 Mar 5.

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853124PMC
April 2007

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.

Genome Res 2006 Dec 19;16(12):1455-64. Epub 2006 Oct 19.

Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20878, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.4140006
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http://dx.doi.org/10.1101/gr.4140006DOI Listing
December 2006

Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.

Methods Mol Biol 2006 ;338:91-103

Genome Technology Branch, National Institutes of Health, Rockville, MD, USA.

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http://link.springer.com/10.1385/1-59745-097-9:91
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http://dx.doi.org/10.1385/1-59745-097-9:91DOI Listing
September 2006

Galaxy: a platform for interactive large-scale genome analysis.

Genome Res 2005 Oct 16;15(10):1451-5. Epub 2005 Sep 16.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.4086505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089PMC
October 2005

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

Genome Res 2005 Aug 15;15(8):1051-60. Epub 2005 Jul 15.

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.3642605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182217PMC
August 2005

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2005 Apr;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471250953.bi1004s9DOI Listing
April 2005

Molecular determinants of NOTCH4 transcription in vascular endothelium.

Mol Cell Biol 2005 Feb;25(4):1458-74

Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin Medical School, 1300 University Ave., 383 Medical Sciences Center, Madison, WI 53706, USA.

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http://dx.doi.org/10.1128/MCB.25.4.1458-1474.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548019PMC
February 2005

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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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

Genome Res 2004 Apr;14(4):700-7

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1976004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383316PMC
April 2004

Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins.

Genomics 2003 Oct;82(4):417-32

Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/s0888-7543(03)00114-9DOI Listing
October 2003

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

Nucleic Acids Res 2003 Jul;31(13):3518-24

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168985PMC
http://dx.doi.org/10.1093/nar/gkg579DOI Listing
July 2003

GALA, a database for genomic sequence alignments and annotations.

Genome Res 2003 Apr;13(4):732-41

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.603103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430176PMC
April 2003

PipMaker: a World Wide Web server for genomic sequence alignments.

Curr Protoc Bioinformatics 2003 Feb;Chapter 10:Unit 10.2

The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471250953.bi1002s00DOI Listing
February 2003

Distinguishing regulatory DNA from neutral sites.

Genome Res 2003 Jan;13(1):64-72

Departments of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.817703
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http://dx.doi.org/10.1101/gr.817703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430974PMC
January 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002

PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

Genomics 2002 Dec;80(6):681-90

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1006/geno.2002.7018DOI Listing
December 2002