Michael R Brent

Michael R Brent

UNVERIFIED PROFILE

Are you Michael R Brent?   Register this Author

Register author
Michael R Brent

Michael R Brent

Publications by authors named "Michael R Brent"

Are you Michael R Brent?   Register this Author

51Publications

817Reads

34Profile Views

Seven-Up Is a Novel Regulator of Insulin Signaling.

Genetics 2018 04 27;208(4):1643-1656. Epub 2018 Feb 27.

Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.118.300770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5887154PMC
April 2018

Unintended Side Effects of Transformation Are Very Rare in .

G3 (Bethesda) 2018 03 2;8(3):815-822. Epub 2018 Mar 2.

Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, Missouri 63110

View Article

Download full-text PDF

Source
http://g3journal.org/lookup/doi/10.1534/g3.117.300357
Publisher Site
http://dx.doi.org/10.1534/g3.117.300357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844303PMC
March 2018

NetProphet 2.0: Mapping Transcription Factor Networks by Exploiting Scalable Data Resources.

Bioinformatics 2017 09 12. Epub 2017 Sep 12.

Department of Computer Science and Engineering and Center for Genome Sciences and Systems Biology, Washington University. One Brookings Dr. Saint Louis, MO 63108.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860202PMC
September 2017

Past Roadblocks and New Opportunities in Transcription Factor Network Mapping.

Authors:
Michael R Brent

Trends Genet 2016 11 6;32(11):736-750. Epub 2016 Oct 6.

Departments of Computer Science and Genetics and Center for Genome Sciences and Systems Biology, Washington University, , Saint Louis, MO, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01689525163010
Publisher Site
http://dx.doi.org/10.1016/j.tig.2016.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5117949PMC
November 2016

Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast.

Proc Natl Acad Sci U S A 2016 11 3;113(47):E7428-E7437. Epub 2016 Nov 3.

Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63108;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1603577113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127345PMC
November 2016

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation.

Genome Res 2015 May 2;25(5):690-700. Epub 2015 Feb 2.

Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri 63108, USA; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA; Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.184101.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417117PMC
May 2015

Mapping functional transcription factor networks from gene expression data.

Genome Res 2013 Aug 1;23(8):1319-28. Epub 2013 May 1.

Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, Missouri 63108, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.150904.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730105PMC
August 2013

Role of fat body lipogenesis in protection against the effects of caloric overload in Drosophila.

J Biol Chem 2013 Mar 25;288(12):8028-42. Epub 2013 Jan 25.

Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M112.371047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605622PMC
March 2013

Reduced DICER1 elicits an interferon response in endometrial cancer cells.

Mol Cancer Res 2012 Mar 17;10(3):316-25. Epub 2012 Jan 17.

Department of Surgery, Division of Gynecologic Oncology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1541-7786.MCR-11-0520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307918PMC
March 2012

Toward an integrated model of capsule regulation in Cryptococcus neoformans.

PLoS Pathog 2011 Dec 8;7(12):e1002411. Epub 2011 Dec 8.

Center for Genome Sciences and Systems Biology and Departments of Computer Science and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.ppat.1002411
Publisher Site
http://dx.doi.org/10.1371/journal.ppat.1002411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234223PMC
December 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

View Article

Download full-text PDF

Source
http://compbio.mit.edu/publications/46_modENCODE_Science_10.
Web Search
http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
Publisher Site
http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription.

Proc Natl Acad Sci U S A 2010 Sep 1;107(38):16743-8. Epub 2010 Sep 1.

Center for Genome Sciences and Systems Biology, Washington University, St. Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0912483107
Publisher Site
http://dx.doi.org/10.1073/pnas.0912483107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944743PMC
September 2010

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Bioinformatics 2009 Jul 4;25(13):1587-93. Epub 2009 May 4.

Department of Computer Science and Center for Genome Sciences, Washington University, St. Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732315PMC
July 2009

Benchmarking regulatory network reconstruction with GRENDEL.

Bioinformatics 2009 Mar 2;25(6):801-7. Epub 2009 Feb 2.

Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, MO, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732301PMC
March 2009

Steady progress and recent breakthroughs in the accuracy of automated genome annotation.

Authors:
Michael R Brent

Nat Rev Genet 2008 Jan;9(1):62-73

Center for Genome Sciences, Campus BOX 8510, Washington University, 4444 Forest Park Blvd, Saint Louis, Missouri 63108, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg2220DOI Listing
January 2008

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.

Curr Protoc Bioinformatics 2007 Dec;Chapter 4:Unit 4.8

Washington University, St. Louis, Missouri, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi0408s20DOI Listing
December 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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.

Nat Methods 2007 Aug 24;4(8):659-64. Epub 2007 Jun 24.

Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth1063DOI Listing
August 2007

How does eukaryotic gene prediction work?

Authors:
Michael R Brent

Nat Biotechnol 2007 Aug;25(8):883-5

Center for Genome Sciences, Campus Box 1045, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt0807-883DOI Listing
August 2007

The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.

Bioinformatics 2007 Mar 18;23(5):545-54. Epub 2007 Jan 18.

Laboratory for Computational Genomics, Campus Box 1045, Washington University, St. Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btl659DOI Listing
March 2007

A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.

Genome Res 2007 Feb 8;17(2):212-8. Epub 2007 Jan 8.

Laboratory for Computational Genomics and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.5661407
Publisher Site
http://dx.doi.org/10.1101/gr.5661407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781353PMC
February 2007

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

Genome Biol 2006 7;7 Suppl 1:S3.1-13. Epub 2006 Aug 7.

South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2006-7-s1-s3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810552PMC
September 2006

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Genome Biol 2006 7;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

Laboratory for Computational Genomics and Department of Computer Science, Washington University, One Brookings Drive, St, Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2006-7-s1-s5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810554PMC
September 2006

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Genome Biol 2006 7;7 Suppl 1:S8.1-9. Epub 2006 Aug 7.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
Publisher Site
http://dx.doi.org/10.1186/gb-2006-7-s1-s8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810557PMC
September 2006

Using ESTs to improve the accuracy of de novo gene prediction.

BMC Bioinformatics 2006 Jul 3;7:327. Epub 2006 Jul 3.

Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, One Brookings Drive, St, Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-7-327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534067PMC
July 2006

Iterative gene prediction and pseudogene removal improves genome annotation.

Genome Res 2006 May;16(5):678-85

Laboratory for Computational Genomics, Department of Computer Science Washington University, Saint Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.4766206
Publisher Site
http://dx.doi.org/10.1101/gr.4766206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457044PMC
May 2006

Using multiple alignments to improve gene prediction.

J Comput Biol 2006 Mar;13(2):379-93

Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://www.liebertpub.com/doi/10.1089/cmb.2006.13.379
Publisher Site
http://dx.doi.org/10.1089/cmb.2006.13.379DOI Listing
March 2006

Genome annotation past, present, and future: how to define an ORF at each locus.

Authors:
Michael R Brent

Genome Res 2005 Dec;15(12):1777-86

Laboratory for Computational Genomics and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3866105DOI Listing
December 2005

Begin at the beginning: predicting genes with 5' UTRs.

Genome Res 2005 May;15(5):742-7

Laboratory for Computational Genomics, Washington University, St. Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3696205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088303PMC
May 2005

Gene finding in the chicken genome.

BMC Bioinformatics 2005 May 30;6:131. Epub 2005 May 30.

Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-6-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174864PMC
May 2005

Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions.

Genome Res 2005 Apr;15(4):577-82

Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3329005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074372PMC
April 2005

Gene prediction and verification in a compact genome with numerous small introns.

Genome Res 2004 Nov 12;14(11):2330-5. Epub 2004 Oct 12.

Laboratory for Computational Genomics and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.2816704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC525692PMC
November 2004

Reexamining the vocabulary spurt.

Dev Psychol 2004 Jul;40(4):621-32

Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1037/0012-1649.40.4.621DOI Listing
July 2004

Recent advances in gene structure prediction.

Curr Opin Struct Biol 2004 Jun;14(3):264-72

Laboratory for Computational Genomics, Campus Box 1045, Washington University, One Brookings Drive, St Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sbi.2004.05.007DOI Listing
June 2004

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

Genome Res 2004 Apr;14(4):665-71

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.1959604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383311PMC
April 2004

Eval: a software package for analysis of genome annotations.

BMC Bioinformatics 2003 Oct 17;4:50. Epub 2003 Oct 17.

Department of Computer Science and Engineering, Washington University, St, Louis, MO 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-4-50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC270064PMC
October 2003

The DNA sequence of human chromosome 7.

Authors:
Ladeana W Hillier Robert S Fulton Lucinda A Fulton Tina A Graves Kymberlie H Pepin Caryn Wagner-McPherson Dan Layman Jason Maas Sara Jaeger Rebecca Walker Kristine Wylie Mandeep Sekhon Michael C Becker Michelle D O'Laughlin Mark E Schaller Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Matt Cordes Hui Du Hui Sun Jennifer Edwards Holland Bradshaw-Cordum Johar Ali Stephanie Andrews Amber Isak Andrew Vanbrunt Christine Nguyen Feiyu Du Betty Lamar Laura Courtney Joelle Kalicki Philip Ozersky Lauren Bielicki Kelsi Scott Andrea Holmes Richard Harkins Anthony Harris Cynthia Madsen Strong Shunfang Hou Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Shawn Leonard Theresa Rohlfing Susan M Rock Aye-Mon Tin-Wollam Amanda Abbott Patrick Minx Rachel Maupin Catrina Strowmatt Phil Latreille Nancy Miller Doug Johnson Jennifer Murray Jeffrey P Woessner Michael C Wendl Shiaw-Pyng Yang Brian R Schultz John W Wallis John Spieth Tamberlyn A Bieri Joanne O Nelson Nicolas Berkowicz Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Joseph A Bedell Elaine R Mardis Sandra W Clifton Stephanie L Chissoe Marco A Marra Christopher Raymond Eric Haugen Will Gillett Yang Zhou Rose James Karen Phelps Shawn Iadanoto Kerry Bubb Elizabeth Simms Ruth Levy James Clendenning Rajinder Kaul W James Kent Terrence S Furey Robert A Baertsch Michael R Brent Evan Keibler Paul Flicek Peer Bork Mikita Suyama Jeffrey A Bailey Matthew E Portnoy David Torrents Asif T Chinwalla Warren R Gish Sean R Eddy John D McPherson Maynard V Olson Evan E Eichler Eric D Green Robert H Waterston Richard K Wilson

Nature 2003 Jul;424(6945):157-64

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature01782DOI Listing
July 2003

Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.

Proc Natl Acad Sci U S A 2003 Feb 27;100(3):1140-5. Epub 2003 Jan 27.

Research Group in Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra/Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0337561100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298740PMC
February 2003

Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

Genome Res 2003 Jan;13(1):46-54

Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.830003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430948PMC
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.

View Article

Download full-text PDF

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

Predicting full-length transcripts.

Authors:
Michael R Brent

Trends Biotechnol 2002 Jul;20(7):273-5; discussion 275

View Article

Download full-text PDF

Source
July 2002