Robert K Bradley

Robert K Bradley

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Robert K Bradley

Robert K Bradley

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RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing.

Genome Res 2019 10 21;29(10):1591-1604. Epub 2019 Aug 21.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gr.246678.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771400PMC
October 2019

DUX4 Suppresses MHC Class I to Promote Cancer Immune Evasion and Resistance to Checkpoint Blockade.

Dev Cell 2019 Sep 18;50(5):658-671.e7. Epub 2019 Jul 18.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736738PMC
September 2019

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy.

Elife 2019 01 15;8. Epub 2019 Jan 15.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.41740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349399PMC
January 2019

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.

Mol Cell 2018 11;72(3):496-509.e9

Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765183083
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http://dx.doi.org/10.1016/j.molcel.2018.09.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224609PMC
November 2018

Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations.

Cancer Cell 2018 08;34(2):225-241.e8

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373472PMC
August 2018

Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs.

Stem Cell Reports 2018 05 19;10(5):1610-1624. Epub 2018 Apr 19.

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1044A, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22136711183014
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http://dx.doi.org/10.1016/j.stemcr.2018.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995368PMC
May 2018

Most human introns are recognized via multiple and tissue-specific branchpoints.

Genes Dev 2018 04 17;32(7-8):577-591. Epub 2018 Apr 17.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gad.312058.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959240PMC
April 2018

The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity.

Mol Cell 2017 Jul 29;67(2):239-251.e6. Epub 2017 Jun 29.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.05.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536975PMC
July 2017

Congenital myotonic dystrophy-an RNA-mediated disease across a developmental continuum.

Genes Dev 2017 06;31(11):1067-1068

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gad.302893.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538429PMC
June 2017

Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population.

Genome Res 2016 12 19;26(12):1639-1650. Epub 2016 Sep 19.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gr.205070.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131816PMC
December 2016

Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival.

PLoS Genet 2016 Oct 24;12(10):e1006384. Epub 2016 Oct 24.

Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America.

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http://dx.doi.org/10.1371/journal.pgen.1006384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077151PMC
October 2016

RNA splicing factors as oncoproteins and tumour suppressors.

Nat Rev Cancer 2016 07 10;16(7):413-30. Epub 2016 Jun 10.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1038/nrc.2016.51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094465PMC
July 2016

Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis.

Genes Dev 2016 05;30(9):989-1001

Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.

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http://dx.doi.org/10.1101/gad.278424.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863743PMC
May 2016

Widespread intron retention diversifies most cancer transcriptomes.

Genome Med 2015 15;7(1):45. Epub 2015 May 15.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.

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http://dx.doi.org/10.1186/s13073-015-0168-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480902PMC
June 2015

Integrative clinical genomics of advanced prostate cancer.

Cell 2015 May;161(5):1215-1228

Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484602PMC
May 2015

U2AF1 mutations alter splice site recognition in hematological malignancies.

Genome Res 2015 Jan 29;25(1):14-26. Epub 2014 Sep 29.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;

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http://dx.doi.org/10.1101/gr.181016.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317169PMC
January 2015

A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy.

Elife 2015 Jan 7;4. Epub 2015 Jan 7.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.04996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383350PMC
January 2015

Sample processing obscures cancer-specific alterations in leukemic transcriptomes.

Proc Natl Acad Sci U S A 2014 Nov 10;111(47):16802-7. Epub 2014 Nov 10.

Computational Biology Program, Public Health Sciences Division, Basic Sciences Division, and

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http://dx.doi.org/10.1073/pnas.1413374111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250124PMC
November 2014

Massive mitochondrial gene transfer in a parasitic flowering plant clade.

PLoS Genet 2013 14;9(2):e1003265. Epub 2013 Feb 14.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573108PMC
June 2013

Horizontal transfer of expressed genes in a parasitic flowering plant.

BMC Genomics 2012 Jun 8;13:227. Epub 2012 Jun 8.

Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1186/1471-2164-13-227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460754PMC
June 2012

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.

PLoS Biol 2012 Jan 3;10(1):e1001229. Epub 2012 Jan 3.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250501PMC
January 2012

Evolutionary triplet models of structured RNA.

PLoS Comput Biol 2009 Aug 28;5(8):e1000483. Epub 2009 Aug 28.

Biophysics Graduate Group, University of California, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725318PMC
August 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

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.

Genome Biol 2008 Oct 8;9(10):R147. Epub 2008 Oct 8.

Biophysics Graduate Group, University of California-Berkeley, CA 94720-3200, USA.

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http://dx.doi.org/10.1186/gb-2008-9-10-r147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760874PMC
October 2008

Transducers: an emerging probabilistic framework for modeling indels on trees.

Bioinformatics 2007 Dec 5;23(23):3258-62. Epub 2007 Sep 5.

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http://dx.doi.org/10.1093/bioinformatics/btm402DOI 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.

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

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

BMC Bioinformatics 2006 Oct 3;7:428. Epub 2006 Oct 3.

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

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http://dx.doi.org/10.1186/1471-2105-7-428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1622757PMC
October 2006