Publications by authors named "Roger A Hoskins"

37Publications

Reports from CAGI: The Critical Assessment of Genome Interpretation.

Hum Mutat 2017 09;38(9):1039-1041

Department of Plant and Microbial Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/humu.23290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606199PMC
September 2017

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Nat Biotechnol 2014 Apr 16;32(4):341-6. Epub 2014 Mar 16.

1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [3].

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http://search.proquest.com/openview/5a27f43084800d7458173e64
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http://www.nature.com/doifinder/10.1038/nbt.2850
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http://dx.doi.org/10.1038/nbt.2850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4037530PMC
April 2014

Drosophila P elements preferentially transpose to replication origins.

Proc Natl Acad Sci U S A 2011 Sep 6;108(38):15948-53. Epub 2011 Sep 6.

Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1073/pnas.1112960108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179094PMC
September 2011

The Drosophila gene disruption project: progress using transposons with distinctive site specificities.

Genetics 2011 Jul 21;188(3):731-43. Epub 2011 Apr 21.

Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1534/genetics.111.126995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176542PMC
July 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.

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

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

PLoS Genet 2010 Dec 2;6(12):e1001228. Epub 2010 Dec 2.

Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996329PMC
December 2010

A molecularly defined duplication set for the X chromosome of Drosophila melanogaster.

Genetics 2010 Dec 27;186(4):1111-25. Epub 2010 Sep 27.

Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1534/genetics.110.121285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998297PMC
December 2010

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

Drosophila by the dozen.

Genome Biol 2007 ;8(7):309

Berkeley Drosophila Genome Project, Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2007-8-7-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323228PMC
February 2008

Thirty-one flavors of Drosophila rab proteins.

Genetics 2007 Jun 3;176(2):1307-22. Epub 2007 Apr 3.

Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.106.066761
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http://dx.doi.org/10.1534/genetics.106.066761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894592PMC
June 2007

High-throughput plasmid cDNA library screening.

Nat Protoc 2006 ;1(2):624-32

Department of Genome Sciences, Earnest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nprot.2006.90DOI Listing
September 2007

Exploring strategies for protein trapping in Drosophila.

Genetics 2007 Mar 18;175(3):1089-104. Epub 2006 Dec 18.

Department of Genetics, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1534/genetics.106.065995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1840052PMC
March 2007

P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster.

Science 2006 Dec 30;314(5806):1747-51. Epub 2006 Nov 30.

Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1134426DOI Listing
December 2006

BAC clones generated from sheared DNA.

Genomics 2007 Feb 13;89(2):291-9. Epub 2006 Nov 13.

Children's Hospital and Research Center at Oakland, 747 52nd Street, Oakland, CA 94609, USA.

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http://dx.doi.org/10.1016/j.ygeno.2006.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1909752PMC
February 2007

Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

Nucleic Acids Res 2005 Dec 2;33(21):e185. Epub 2005 Dec 2.

Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gni184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1301602PMC
December 2005

The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.

Genetics 2004 Jun;167(2):761-81

Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1534/genetics.104.026427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470905PMC
June 2004

Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development.

Curr Biol 2003 Aug;13(16):1388-96

Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T630, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/s0960-9822(03)00546-3DOI Listing
August 2003

Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?

Genetica 2003 Mar;117(2-3):227-37

Departamento de Genética, Universidade Federal do Rio de Janeiro, Caixa Postal 68011 CEP 21944-970, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1023/a:1022900313650DOI Listing
March 2003