Publications by authors named "Filipe G Vieira"

27Publications

ngsLD: evaluating linkage disequilibrium using genotype likelihoods.

Bioinformatics 2019 10;35(19):3855-3856

Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btz200DOI Listing
October 2019

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice.

Genome Res 2017 06 6;27(6):1029-1038. Epub 2017 Apr 6.

Department of Integrative Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.204800.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453317PMC
June 2017

Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes.

Mol Ecol Resour 2017 Mar 7;17(2):209-220. Epub 2016 Nov 7.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.

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http://dx.doi.org/10.1111/1755-0998.12610DOI Listing
March 2017

Estimating IBD tracts from low coverage NGS data.

Bioinformatics 2016 07 22;32(14):2096-102. Epub 2016 Apr 22.

Department of Biology, University of Copenhagen, Copenhagen, Denmark and Department of Integrative Biology, University of California, Berkeley, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw212DOI Listing
July 2016

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Authors:
Monika Gulia-Nuss Andrew B Nuss Jason M Meyer Daniel E Sonenshine R Michael Roe Robert M Waterhouse David B Sattelle José de la Fuente Jose M Ribeiro Karine Megy Jyothi Thimmapuram Jason R Miller Brian P Walenz Sergey Koren Jessica B Hostetler Mathangi Thiagarajan Vinita S Joardar Linda I Hannick Shelby Bidwell Martin P Hammond Sarah Young Qiandong Zeng Jenica L Abrudan Francisca C Almeida Nieves Ayllón Ketaki Bhide Brooke W Bissinger Elena Bonzon-Kulichenko Steven D Buckingham Daniel R Caffrey Melissa J Caimano Vincent Croset Timothy Driscoll Don Gilbert Joseph J Gillespie Gloria I Giraldo-Calderón Jeffrey M Grabowski David Jiang Sayed M S Khalil Donghun Kim Katherine M Kocan Juraj Koči Richard J Kuhn Timothy J Kurtti Kristin Lees Emma G Lang Ryan C Kennedy Hyeogsun Kwon Rushika Perera Yumin Qi Justin D Radolf Joyce M Sakamoto Alejandro Sánchez-Gracia Maiara S Severo Neal Silverman Ladislav Šimo Marta Tojo Cristian Tornador Janice P Van Zee Jesús Vázquez Filipe G Vieira Margarita Villar Adam R Wespiser Yunlong Yang Jiwei Zhu Peter Arensburger Patricia V Pietrantonio Stephen C Barker Renfu Shao Evgeny M Zdobnov Frank Hauser Cornelis J P Grimmelikhuijzen Yoonseong Park Julio Rozas Richard Benton Joao H F Pedra David R Nelson Maria F Unger Jose M C Tubio Zhijian Tu Hugh M Robertson Martin Shumway Granger Sutton Jennifer R Wortman Daniel Lawson Stephen K Wikel Vishvanath M Nene Claire M Fraser Frank H Collins Bruce Birren Karen E Nelson Elisabet Caler Catherine A Hill

Nat Commun 2016 Feb 9;7:10507. Epub 2016 Feb 9.

Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA.

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http://dx.doi.org/10.1038/ncomms10507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748124PMC
February 2016

Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.

Mol Biol Evol 2016 Feb 17;33(2):478-91. Epub 2015 Nov 17.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.

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https://ristainolab.cals.ncsu.edu/files/2014/07/Mol-Biol-Evo
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http://mbe.oxfordjournals.org/lookup/doi/10.1093/molbev/msv2
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http://dx.doi.org/10.1093/molbev/msv241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866541PMC
February 2016

Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families.

Genome Biol Evol 2014 Jun 5;6(6):1454-65. Epub 2014 Jun 5.

Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain

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http://dx.doi.org/10.1093/gbe/evu117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079203PMC
June 2014

ngsTools: methods for population genetics analyses from next-generation sequencing data.

Bioinformatics 2014 May 23;30(10):1486-7. Epub 2014 Jan 23.

Department of Integrative Biology, Department of Statistics, University of California, Berkeley, CA 94720, USA and Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btu041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016704PMC
May 2014

Quantifying population genetic differentiation from next-generation sequencing data.

Genetics 2013 Nov 26;195(3):979-92. Epub 2013 Aug 26.

Department of Integrative Biology, University of California, Berkeley, California 94720.

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http://dx.doi.org/10.1534/genetics.113.154740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813878PMC
November 2013

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.

Genome Res 2013 Nov 15;23(11):1852-61. Epub 2013 Aug 15.

Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA;

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http://dx.doi.org/10.1101/gr.157388.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814885PMC
November 2013

Unique features of odorant-binding proteins of the parasitoid wasp Nasonia vitripennis revealed by genome annotation and comparative analyses.

PLoS One 2012 27;7(8):e43034. Epub 2012 Aug 27.

Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043034PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428353PMC
February 2013

Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system.

Genome Biol Evol 2011 28;3:476-90. Epub 2011 Apr 28.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evr033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134979PMC
November 2011

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Proc Natl Acad Sci U S A 2010 Jul 21;107(27):12168-73. Epub 2010 Jun 21.

J Craig Venter Institute, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1073/pnas.1003379107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901460PMC
July 2010

Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution.

Genome Biol 2007 ;8(11):R235

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av, Diagonal 645, Barcelona 08028, Spain.

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http://dx.doi.org/10.1186/gb-2007-8-11-r235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258175PMC
August 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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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007