Publications by authors named "Valer Gotea"

23Publications

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics.

Methods Mol Biol 2019 ;1910:177-207

Institute of Anthropology, Adam Mickiewicz University, Poznań, Poland.

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January 2020

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

Hum Mutat 2019 09 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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September 2019

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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November 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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March 2017

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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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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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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January 2015

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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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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December 2012

Transposable elements and their identification.

Methods Mol Biol 2012 ;855:337-59

Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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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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March 2011

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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August 2010

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Genome Res 2010 May 2;20(5):565-77. Epub 2010 Apr 2.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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May 2010

DiRE: identifying distant regulatory elements of co-expressed genes.

Nucleic Acids Res 2008 Jul 17;36(Web Server issue):W133-9. Epub 2008 May 17.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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July 2008

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

Spliceosomal small nuclear RNA genes in 11 insect genomes.

RNA 2007 Jan 9;13(1):5-14. Epub 2006 Nov 9.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815, USA.

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January 2007