Publications by authors named "Andreas Heger"

55Publications

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial.

EBioMedicine 2018 May 10;31:133-142. Epub 2018 Apr 10.

Wellcome Centre for Human Genetics (WHG), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2018.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013786PMC
May 2018

Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations.

Genome Biol 2018 04 10;19(1):50. Epub 2018 Apr 10.

University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.

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http://dx.doi.org/10.1186/s13059-018-1422-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891941PMC
April 2018

Familial childhood-onset progressive cerebellar syndrome associated with the mutation.

Neurol Genet 2017 Apr 27;3(2):e145. Epub 2017 Mar 27.

Department of Neurosciences (F.J.), King's College Hospital, London; MRC Centre for Neuromuscular Diseases and Department of Molecular Neuroscience (F.J., H.H., M.G.H.), UCL Institute of Neurology; MRC Computational Genomics Analysis and Training Programme (K.F., D.S., A.H.), University of Oxford; Central Manchester University Hospitals (H.K.); and NIHR UCLH Biomedical Research Centre (S.M.S.), Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, UK.

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http://dx.doi.org/10.1212/NXG.0000000000000145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367920PMC
April 2017

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.

Genome Res 2017 03 18;27(3):491-499. Epub 2017 Jan 18.

Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom.

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http://dx.doi.org/10.1101/gr.209601.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340976PMC
March 2017

11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to Western diet.

J Endocrinol 2017 02 24;232(2):273-283. Epub 2016 Nov 24.

University/BHF Centre for Cardiovascular ScienceQueen's Medical Research Institute, Edinburgh, UK

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http://dx.doi.org/10.1530/JOE-16-0578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5184774PMC
February 2017

Long noncoding RNAs in B-cell development and activation.

Blood 2016 08 5;128(7):e10-9. Epub 2016 Jul 5.

The Francis Crick Institute, London, United Kingdom; Imperial College, London, United Kingdom.

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http://www.bloodjournal.org/lookup/doi/10.1182/blood-2015-11
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http://dx.doi.org/10.1182/blood-2015-11-680843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000579PMC
August 2016

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia.

Genome Res 2014 Dec 15;24(12):1918-31. Epub 2014 Sep 15.

Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland; Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1101/gr.171645.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248310PMC
December 2014

IRF5:RelA interaction targets inflammatory genes in macrophages.

Cell Rep 2014 Sep 21;8(5):1308-17. Epub 2014 Aug 21.

Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.07.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471814PMC
September 2014

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

Nat Commun 2014 Jun 9;5:3979. Epub 2014 Jun 9.

1] Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, BA2 7AY Bath, UK [2] Respiratory Research Group, University Hospital of South Manchester, University of Manchester, Southmoor Road, Manchester M23 9LY, UK [3] Airways Disease, National Heart and Lung Institute, Imperial College, London SW3 6LY, UK.

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http://dx.doi.org/10.1038/ncomms4979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061460PMC
June 2014

Sequencing depth and coverage: key considerations in genomic analyses.

Nat Rev Genet 2014 Feb;15(2):121-32

Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.

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http://dx.doi.org/10.1038/nrg3642DOI Listing
February 2014

Pfam: the protein families database.

Nucleic Acids Res 2014 Jan 27;42(Database issue):D222-30. Epub 2013 Nov 27.

HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1093/nar/gkt1223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965110PMC
January 2014

Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.

Eur Urol 2014 Jul 14;66(1):32-9. Epub 2013 Aug 14.

Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK; Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2013.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062940PMC
July 2014

GAT: a simulation framework for testing the association of genomic intervals.

Bioinformatics 2013 Aug 18;29(16):2046-8. Epub 2013 Jun 18.

MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722528PMC
August 2013

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

Elife 2013 Feb 26;2:e00348. Epub 2013 Feb 26.

Department of Biochemistry , University of Oxford , Oxford , United Kingdom ; Weatherall Institute of Molecular Medicine, University of Oxford , Oxford , United Kingdom.

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http://dx.doi.org/10.7554/eLife.00348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583005PMC
February 2013

The Pfam protein families database.

Nucleic Acids Res 2012 Jan 29;40(Database issue):D290-301. Epub 2011 Nov 29.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkr1065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245129PMC
January 2012

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Molecular evolution of genes in avian genomes.

Genome Biol 2010 23;11(6):R68. Epub 2010 Jun 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, S-752 36, Sweden.

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http://dx.doi.org/10.1186/gb-2010-11-6-r68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911116PMC
November 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata.

Mol Biol Evol 2010 Aug 17;27(8):1923-34. Epub 2010 Mar 17.

Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msq080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889628PMC
August 2010

The Pfam protein families database.

Nucleic Acids Res 2010 Jan 17;38(Database issue):D211-22. Epub 2009 Nov 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkp985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889PMC
January 2010

Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.

Mol Biol Evol 2009 Aug 20;26(8):1715-21. Epub 2009 Apr 20.

Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, UK.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msp080DOI Listing
August 2009

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

BMC Evol Biol 2008 Feb 12;8:46. Epub 2008 Feb 12.

Department of Medical Genetics, University of Washington, Seattle, USA and Division of Human Biology, Fred Hutchinson CancerResearch Center, Seattle, USA.

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http://www.springerlink.com/index/h858267t6575k611.pdf
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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-8-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291036PMC
February 2008

Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

Genome Res 2008 Feb 11;18(2):298-309. Epub 2007 Dec 11.

MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://dx.doi.org/10.1101/gr.6725608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203628PMC
February 2008

Variable strength of translational selection among 12 Drosophila species.

Genetics 2007 Nov;177(3):1337-48

MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://dx.doi.org/10.1534/genetics.107.070466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147958PMC
November 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

Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes.

Genome Res 2007 Dec 7;17(12):1837-49. Epub 2007 Nov 7.

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.6249707
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http://dx.doi.org/10.1101/gr.6249707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099592PMC
December 2007

PairsDB atlas of protein sequence space.

Nucleic Acids Res 2008 Jan 5;36(Database issue):D276-80. Epub 2007 Nov 5.

MRC Functional Genetics Unit, University of Oxford, UK.

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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/gkm879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238971PMC
January 2008

OPTIC: orthologous and paralogous transcripts in clades.

Nucleic Acids Res 2008 Jan 11;36(Database issue):D267-70. Epub 2007 Oct 11.

Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK.

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http://dx.doi.org/10.1093/nar/gkm852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238935PMC
January 2008

The global trace graph, a novel paradigm for searching protein sequence databases.

Bioinformatics 2007 Sep 6;23(18):2361-7. Epub 2007 Sep 6.

Institute of Biotechnology, P.O. Box 56 (Viikinkaari 5), FI-00014 University of Helsinki, Finland.

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http://bioinformatics.oxfordjournals.org/content/23/18/2361.
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btm358DOI Listing
September 2007

An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes.

Genome Res 2007 Jul 10;17(7):969-81. Epub 2007 May 10.

MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Oxford, UK.

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http://dx.doi.org/10.1101/gr.6093907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899124PMC
July 2007

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:
Kerstin Lindblad-Toh Claire M Wade Tarjei S Mikkelsen Elinor K Karlsson David B Jaffe Michael Kamal Michele Clamp Jean L Chang Edward J Kulbokas Michael C Zody Evan Mauceli Xiaohui Xie Matthew Breen Robert K Wayne Elaine A Ostrander Chris P Ponting Francis Galibert Douglas R Smith Pieter J DeJong Ewen Kirkness Pablo Alvarez Tara Biagi William Brockman Jonathan Butler Chee-Wye Chin April Cook James Cuff Mark J Daly David DeCaprio Sante Gnerre Manfred Grabherr Manolis Kellis Michael Kleber Carolyne Bardeleben Leo Goodstadt Andreas Heger Christophe Hitte Lisa Kim Klaus-Peter Koepfli Heidi G Parker John P Pollinger Stephen M J Searle Nathan B Sutter Rachael Thomas Caleb Webber Jennifer Baldwin Adal Abebe Amr Abouelleil Lynne Aftuck Mostafa Ait-Zahra Tyler Aldredge Nicole Allen Peter An Scott Anderson Claudel Antoine Harindra Arachchi Ali Aslam Laura Ayotte Pasang Bachantsang Andrew Barry Tashi Bayul Mostafa Benamara Aaron Berlin Daniel Bessette Berta Blitshteyn Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Adam Brown Patrick Cahill Nadia Calixte Jody Camarata Yama Cheshatsang Jeffrey Chu Mieke Citroen Alville Collymore Patrick Cooke Tenzin Dawoe Riza Daza Karin Decktor Stuart DeGray Norbu Dhargay Kimberly Dooley Kathleen Dooley Passang Dorje Kunsang Dorjee Lester Dorris Noah Duffey Alan Dupes Osebhajajeme Egbiremolen Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Patricia Ferreira Sheila Fisher Mike FitzGerald Karen Foley Chelsea Foley Alicia Franke Dennis Friedrich Diane Gage Manuel Garber Gary Gearin Georgia Giannoukos Tina Goode Audra Goyette Joseph Graham Edward Grandbois Kunsang Gyaltsen Nabil Hafez Daniel Hagopian Birhane Hagos Jennifer Hall Claire Healy Ryan Hegarty Tracey Honan Andrea Horn Nathan Houde Leanne Hughes Leigh Hunnicutt M Husby Benjamin Jester Charlien Jones Asha Kamat Ben Kanga Cristyn Kells Dmitry Khazanovich Alix Chinh Kieu Peter Kisner Mayank Kumar Krista Lance Thomas Landers Marcia Lara William Lee Jean-Pierre Leger Niall Lennon Lisa Leuper Sarah LeVine Jinlei Liu Xiaohong Liu Yeshi Lokyitsang Tashi Lokyitsang Annie Lui Jan Macdonald John Major Richard Marabella Kebede Maru Charles Matthews Susan McDonough Teena Mehta James Meldrim Alexandre Melnikov Louis Meneus Atanas Mihalev Tanya Mihova Karen Miller Rachel Mittelman Valentine Mlenga Leonidas Mulrain Glen Munson Adam Navidi Jerome Naylor Tuyen Nguyen Nga Nguyen Cindy Nguyen Thu Nguyen Robert Nicol Nyima Norbu Choe Norbu Nathaniel Novod Tenchoe Nyima Peter Olandt Barry O'Neill Keith O'Neill Sahal Osman Lucien Oyono Christopher Patti Danielle Perrin Pema Phunkhang Fritz Pierre Margaret Priest Anthony Rachupka Sujaa Raghuraman Rayale Rameau Verneda Ray Christina Raymond Filip Rege Cecil Rise Julie Rogers Peter Rogov Julie Sahalie Sampath Settipalli Theodore Sharpe Terrance Shea Mechele Sheehan Ngawang Sherpa Jianying Shi Diana Shih Jessie Sloan Cherylyn Smith Todd Sparrow John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Sabrina Stone Sean Sykes Pierre Tchuinga Pema Tenzing Senait Tesfaye Dawa Thoulutsang Yama Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Vijay Venkataraman Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Shuli Yang Xiaoping Yang Geneva Young Qing Yu Joanne Zainoun Lisa Zembek Andrew Zimmer Eric S Lander

Nature 2005 Dec;438(7069):803-19

Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.

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http://www.nature.com/articles/nature04338
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http://dx.doi.org/10.1038/nature04338DOI Listing
December 2005

Accurate detection of very sparse sequence motifs.

J Comput Biol 2004 ;11(5):843-57

Institute of Biotechnology, University of Helsinki, Finland.

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http://dx.doi.org/10.1089/cmb.2004.11.843DOI Listing
March 2005

ADDA: a domain database with global coverage of the protein universe.

Nucleic Acids Res 2005 Jan;33(Database issue):D188-91

Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gki096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540050PMC
January 2005

Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins.

Bioinformatics 2003 ;19 Suppl 1:i130-7

Institute of Biotechnology, P.O. Box 56, 00014 University of Helsinki Finland.

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http://dx.doi.org/10.1093/bioinformatics/btg1017DOI Listing
October 2004

Exhaustive enumeration of protein domain families.

J Mol Biol 2003 May;328(3):749-67

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/s0022-2836(03)00269-9DOI Listing
May 2003