Evgeny M Zdobnov

Evgeny M Zdobnov

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Evgeny M Zdobnov

Publications by authors named "Evgeny M Zdobnov"

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BUSCO: Assessing Genome Assembly and Annotation Completeness.

Methods Mol Biol 2019 ;1962:227-245

Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.

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http://dx.doi.org/10.1007/978-1-4939-9173-0_14DOI Listing
August 2019

Using BUSCO to Assess Insect Genomic Resources.

Methods Mol Biol 2019 ;1858:59-74

University of Geneva and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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http://dx.doi.org/10.1007/978-1-4939-8775-7_6DOI Listing
July 2019

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties.

Environ Microbiol 2019 Jul 17. Epub 2019 Jul 17.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

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http://dx.doi.org/10.1111/1462-2920.14746DOI Listing
July 2019

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Genome Biol 2019 04 2;20(1):64. Epub 2019 Apr 2.

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

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http://dx.doi.org/10.1186/s13059-019-1660-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444547PMC
April 2019

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.

Nucleic Acids Res 2019 Jan;47(D1):D807-D811

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gky1053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323947PMC
January 2019

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.

Environ Microbiol 2018 06 7;20(6):2288-2300. Epub 2018 Aug 7.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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http://dx.doi.org/10.1111/1462-2920.14276DOI Listing
June 2018

BUSCO applications from quality assessments to gene prediction and phylogenomics.

Mol Biol Evol 2017 Dec 6. Epub 2017 Dec 6.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland.

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https://academic.oup.com/mbe/article/35/3/543/4705839
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http://dx.doi.org/10.1093/molbev/msx319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850278PMC
December 2017

Metagenomics analysis of red blood cell and fresh-frozen plasma units.

Transfusion 2017 07 11;57(7):1787-1800. Epub 2017 May 11.

Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.

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http://dx.doi.org/10.1111/trf.14148DOI Listing
July 2017

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

Nucleic Acids Res 2017 01 28;45(D1):D744-D749. Epub 2016 Nov 28.

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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http://dx.doi.org/10.1093/nar/gkw1119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210582PMC
January 2017

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

Genome Biol 2016 11 11;17(1):227. Epub 2016 Nov 11.

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

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http://dx.doi.org/10.1186/s13059-016-1088-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105290PMC
November 2016

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

Nat Commun 2016 Feb 2;7:10165. Epub 2016 Feb 2.

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

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http://dx.doi.org/10.1038/ncomms10165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740739PMC
February 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

CEGA--a catalog of conserved elements from genomic alignments.

Nucleic Acids Res 2016 Jan 2;44(D1):D96-100. Epub 2015 Nov 2.

Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv1163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702837PMC
January 2016

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Bioinformatics 2015 Oct 9;31(19):3210-2. Epub 2015 Jun 9.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv351DOI Listing
October 2015

Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report.

Lancet Infect Dis 2015 Sep 19;15(9):1034-1040. Epub 2015 Jul 19.

Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Laboratory of Virology and Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland.

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http://dx.doi.org/10.1016/S1473-3099(15)00229-7DOI Listing
September 2015

The genomes of two key bumblebee species with primitive eusocial organization.

Authors:
Ben M Sadd Seth M Barribeau Guy Bloch Dirk C de Graaf Peter Dearden Christine G Elsik Jürgen Gadau Cornelis J P Grimmelikhuijzen Martin Hasselmann Jeffrey D Lozier Hugh M Robertson Guy Smagghe Eckart Stolle Matthias Van Vaerenbergh Robert M Waterhouse Erich Bornberg-Bauer Steffen Klasberg Anna K Bennett Francisco Câmara Roderic Guigó Katharina Hoff Marco Mariotti Monica Munoz-Torres Terence Murphy Didac Santesmasses Gro V Amdam Matthew Beckers Martin Beye Matthias Biewer Márcia M G Bitondi Mark L Blaxter Andrew F G Bourke Mark J F Brown Severine D Buechel Rossanah Cameron Kaat Cappelle James C Carolan Olivier Christiaens Kate L Ciborowski David F Clarke Thomas J Colgan David H Collins Andrew G Cridge Tamas Dalmay Stephanie Dreier Louis du Plessis Elizabeth Duncan Silvio Erler Jay Evans Tiago Falcon Kevin Flores Flávia C P Freitas Taro Fuchikawa Tanja Gempe Klaus Hartfelder Frank Hauser Sophie Helbing Fernanda C Humann Frano Irvine Lars S Jermiin Claire E Johnson Reed M Johnson Andrew K Jones Tatsuhiko Kadowaki Jonathan H Kidner Vasco Koch Arian Köhler F Bernhard Kraus H Michael G Lattorff Megan Leask Gabrielle A Lockett Eamonn B Mallon David S Marco Antonio Monika Marxer Ivan Meeus Robin F A Moritz Ajay Nair Kathrin Näpflin Inga Nissen Jinzhi Niu Francis M F Nunes John G Oakeshott Amy Osborne Marianne Otte Daniel G Pinheiro Nina Rossié Olav Rueppell Carolina G Santos Regula Schmid-Hempel Björn D Schmitt Christina Schulte Zilá L P Simões Michelle P M Soares Luc Swevers Eva C Winnebeck Florian Wolschin Na Yu Evgeny M Zdobnov Peshtewani K Aqrawi Kerstin P Blankenburg Marcus Coyle Liezl Francisco Alvaro G Hernandez Michael Holder Matthew E Hudson LaRonda Jackson Joy Jayaseelan Vandita Joshi Christie Kovar Sandra L Lee Robert Mata Tittu Mathew Irene F Newsham Robin Ngo Geoffrey Okwuonu Christopher Pham Ling-Ling Pu Nehad Saada Jireh Santibanez DeNard Simmons Rebecca Thornton Aarti Venkat Kimberly K O Walden Yuan-Qing Wu Griet Debyser Bart Devreese Claire Asher Julie Blommaert Ariel D Chipman Lars Chittka Bertrand Fouks Jisheng Liu Meaghan P O'Neill Seirian Sumner Daniela Puiu Jiaxin Qu Steven L Salzberg Steven E Scherer Donna M Muzny Stephen Richards Gene E Robinson Richard A Gibbs Paul Schmid-Hempel Kim C Worley

Genome Biol 2015 Apr 24;16:76. Epub 2015 Apr 24.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13059-015-0623-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414376PMC
April 2015

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

Curr Biol 2015 Mar 5;25(5):613-20. Epub 2015 Feb 5.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2014.12.057DOI Listing
March 2015

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Nucleic Acids Res 2015 Jan 26;43(Database issue):D250-6. Epub 2014 Nov 26.

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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http://dx.doi.org/10.1093/nar/gku1220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383991PMC
January 2015

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 2015

Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

Am J Hum Genet 2014 Dec;95(6):660-74

Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259975PMC
December 2014

Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.

J Clin Microbiol 2014 Sep 9;52(9):3351-61. Epub 2014 Jul 9.

Division of Infectious Diseases, Laboratory of Virology and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva, Switzerland Department of Medicine, University of Geneva Medical School, Geneva, Switzerland.

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http://jcm.asm.org/lookup/doi/10.1128/JCM.01389-14
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http://dx.doi.org/10.1128/JCM.01389-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313162PMC
September 2014

Repression of arginase-2 expression in dendritic cells by microRNA-155 is critical for promoting T cell proliferation.

J Immunol 2014 Aug 9;193(4):1690-700. Epub 2014 Jul 9.

Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; and

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1301913
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http://dx.doi.org/10.4049/jimmunol.1301913DOI Listing
August 2014

miRmap web: Comprehensive microRNA target prediction online.

Nucleic Acids Res 2013 Jul 28;41(Web Server issue):W165-8. Epub 2013 May 28.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gkt430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692044PMC
July 2013

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.

Nucleic Acids Res 2013 Jan 24;41(Database issue):D358-65. Epub 2012 Nov 24.

Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gks1116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531149PMC
January 2013

MiRmap: comprehensive prediction of microRNA target repression strength.

Nucleic Acids Res 2012 Dec 2;40(22):11673-83. Epub 2012 Oct 2.

Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1093/nar/gks901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526310PMC
December 2012

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits.

BMC Evol Biol 2011 Nov 18;11:337. Epub 2011 Nov 18.

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1186/1471-2148-11-337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240667PMC
November 2011

Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi.

Genome Biol Evol 2011 9;3:75-86. Epub 2010 Dec 9.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evq083/
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http://dx.doi.org/10.1093/gbe/evq083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030422PMC
April 2011

The ecoresponsive genome of Daphnia pulex.

Science 2011 Feb;331(6017):555-61

Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.

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http://www3.nd.edu/~mpfrende/PDFs/Science-2011-Colbourne-555
Web Search
http://www.sciencemag.org/cgi/doi/10.1126/science.1197761
Publisher Site
http://dx.doi.org/10.1126/science.1197761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199PMC
February 2011

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.

Nucleic Acids Res 2011 Jan 23;39(Database issue):D283-8. Epub 2010 Oct 23.

Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gkq930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013786PMC
January 2011

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Science 2010 Oct;330(6000):86-8

Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1126/science.1191864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384PMC
October 2010

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

Bioinformatics 2010 Jul 13;26(13):1669-70. Epub 2010 May 13.

Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btq243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887050PMC
July 2010

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

Rhinovirus genome evolution during experimental human infection.

PLoS One 2010 May 11;5(5):e10588. Epub 2010 May 11.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010588PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868056PMC
May 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
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Science 2009 Apr;324(5926):522-8

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April 2009

Sertoli cell Dicer is essential for spermatogenesis in mice.

Dev Biol 2009 Feb 28;326(1):250-9. Epub 2008 Nov 28.

Department of Genetic Medicine and Development, University of Geneva Medical School, 1, rue Michel Servet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1016/j.ydbio.2008.11.011DOI Listing
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February 2009

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Nucleic Acids Res 2009 Jan 15;37(Database issue):D111-7. Epub 2008 Oct 15.

Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gkn707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686488PMC
January 2009

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates.

BMC Genomics 2009 Jan 12;10:17. Epub 2009 Jan 12.

Department of Applied Biological Sciences, School of Agricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan.

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http://dx.doi.org/10.1186/1471-2164-10-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656531PMC
January 2009

Quantification of ortholog losses in insects and vertebrates.

Genome Biol 2007 ;8(11):R242

Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258195PMC
August 2008

The cis-acting replication elements define human enterovirus and rhinovirus species.

RNA 2008 Aug 9;14(8):1568-78. Epub 2008 Jun 9.

Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 1211 Geneva 14, Switzerland.

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http://dx.doi.org/10.1261/rna.1031408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2491478PMC
August 2008

The genome of the model beetle and pest Tribolium castaneum.

Authors:
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Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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April 2008

Mapping of small RNAs in the human ENCODE regions.

Am J Hum Genet 2008 Apr;82(4):971-81

Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva 1211, Switzerland.

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http://dx.doi.org/10.1016/j.ajhg.2008.02.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427294PMC
April 2008

OrthoDB: the hierarchical catalog of eukaryotic orthologs.

Nucleic Acids Res 2008 Jan 18;36(Database issue):D271-5. Epub 2007 Oct 18.

Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel-Servet, Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gkm845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238902PMC
January 2008

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

BMC Genomics 2007 Jul 10;8:224. Epub 2007 Jul 10.

Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-8-224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949831PMC
July 2007

Genome sequence of Aedes aegypti, a major arbovirus vector.

Science 2007 Jun 17;316(5832):1718-23. Epub 2007 May 17.

Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1138878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868357PMC
June 2007

Quantification of insect genome divergence.

Trends Genet 2007 Jan 9;23(1):16-20. Epub 2006 Nov 9.

University of Geneva Medical School, Department of Genetic Medicine and Development, Geneva 1211, Switzerland.

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January 2007

AnoEST: toward A. gambiae functional genomics.

Genome Res 2005 Jun 17;15(6):893-9. Epub 2005 May 17.

European Molecular Biology Laboratory, D69117 Heidelberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142480PMC
June 2005

Consistency of genome-based methods in measuring Metazoan evolution.

FEBS Lett 2005 Jun 18;579(15):3355-61. Epub 2005 Apr 18.

EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

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June 2005

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

Nucleic Acids Res 2005 16;33(3):946-54. Epub 2005 Feb 16.

EMBL Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gki236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549403PMC
March 2005

Genome evolution reveals biochemical networks and functional modules.

Proc Natl Acad Sci U S A 2003 Dec 12;100(26):15428-33. Epub 2003 Dec 12.

European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1073/pnas.2136809100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307584PMC
December 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
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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.

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December 2002

The genome sequence of the malaria mosquito Anopheles gambiae.

Authors:
Robert A Holt G Mani Subramanian Aaron Halpern Granger G Sutton Rosane Charlab Deborah R Nusskern Patrick Wincker Andrew G Clark José M C Ribeiro Ron Wides Steven L Salzberg Brendan Loftus Mark Yandell William H Majoros Douglas B Rusch Zhongwu Lai Cheryl L Kraft Josep F Abril Veronique Anthouard Peter Arensburger Peter W Atkinson Holly Baden Veronique de Berardinis Danita Baldwin Vladimir Benes Jim Biedler Claudia Blass Randall Bolanos Didier Boscus Mary Barnstead Shuang Cai Angela Center Kabir Chaturverdi George K Christophides Mathew A Chrystal Michele Clamp Anibal Cravchik Val Curwen Ali Dana Art Delcher Ian Dew Cheryl A Evans Michael Flanigan Anne Grundschober-Freimoser Lisa Friedli Zhiping Gu Ping Guan Roderic Guigo Maureen E Hillenmeyer Susanne L Hladun James R Hogan Young S Hong Jeffrey Hoover Olivier Jaillon Zhaoxi Ke Chinnappa Kodira Elena Kokoza Anastasios Koutsos Ivica Letunic Alex Levitsky Yong Liang Jhy-Jhu Lin Neil F Lobo John R Lopez Joel A Malek Tina C McIntosh Stephan Meister Jason Miller Clark Mobarry Emmanuel Mongin Sean D Murphy David A O'Brochta Cynthia Pfannkoch Rong Qi Megan A Regier Karin Remington Hongguang Shao Maria V Sharakhova Cynthia D Sitter Jyoti Shetty Thomas J Smith Renee Strong Jingtao Sun Dana Thomasova Lucas Q Ton Pantelis Topalis Zhijian Tu Maria F Unger Brian Walenz Aihui Wang Jian Wang Mei Wang Xuelan Wang Kerry J Woodford Jennifer R Wortman Martin Wu Alison Yao Evgeny M Zdobnov Hongyu Zhang Qi Zhao Shaying Zhao Shiaoping C Zhu Igor Zhimulev Mario Coluzzi Alessandra della Torre Charles W Roth Christos Louis Francis Kalush Richard J Mural Eugene W Myers Mark D Adams Hamilton O Smith Samuel Broder Malcolm J Gardner Claire M Fraser Ewan Birney Peer Bork Paul T Brey J Craig Venter Jean Weissenbach Fotis C Kafatos Frank H Collins Stephen L Hoffman

Science 2002 Oct;298(5591):129-49

Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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October 2002

The EBI SRS server-new features.

Bioinformatics 2002 Aug;18(8):1149-50

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

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August 2002