Aylwyn Scally

Aylwyn Scally

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Aylwyn Scally

Publications by authors named "Aylwyn Scally"

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Genomes reveal marked differences in the adaptive evolution between orangutan species.

Authors:
Maja P Mattle-Greminger Tugce Bilgin Sonay Alexander Nater Marc Pybus Tariq Desai Guillem de Valles Ferran Casals Aylwyn Scally Jaume Bertranpetit Tomas Marques-Bonet Carel P van Schaik Maria Anisimova Michael Krützen

Genome Biol 2018 11 15;19(1):193. Epub 2018 Nov 15.

Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1562-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237011PMC
November 2018

Detecting archaic introgression using an unadmixed outgroup.

Authors:
Laurits Skov Ruoyun Hui Vladimir Shchur Asger Hobolth Aylwyn Scally Mikkel Heide Schierup Richard Durbin

PLoS Genet 2018 09 18;14(9):e1007641. Epub 2018 Sep 18.

Department of Genetics, University of Cambridge, Cambridge United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1007641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161914PMC
September 2018

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

Authors:
Eleanor M L Scerri Mark G Thomas Andrea Manica Philipp Gunz Jay T Stock Chris Stringer Matt Grove Huw S Groucutt Axel Timmermann G Philip Rightmire Francesco d'Errico Christian A Tryon Nick A Drake Alison S Brooks Robin W Dennell Richard Durbin Brenna M Henn Julia Lee-Thorp Peter deMenocal Michael D Petraglia Jessica C Thompson Aylwyn Scally Lounès Chikhi

Trends Ecol Evol 2018 08 11;33(8):582-594. Epub 2018 Jul 11.

Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France; Instituto Gulbenkian de Ciência, P-2780-156, Oeiras, Portugal.

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http://dx.doi.org/10.1016/j.tree.2018.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092560PMC
August 2018

High-quality genomes reveal new differences between the great apes.

Authors:
Aylwyn Scally

Nature 2018 07;559(7714):336-338

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http://dx.doi.org/10.1038/d41586-018-05679-9DOI Listing
July 2018

Ancient human parallel lineages within North America contributed to a coastal expansion.

Authors:
C L Scheib Hongjie Li Tariq Desai Vivian Link Christopher Kendall Genevieve Dewar Peter William Griffith Alexander Mörseburg John R Johnson Amiee Potter Susan L Kerr Phillip Endicott John Lindo Marc Haber Yali Xue Chris Tyler-Smith Manjinder S Sandhu Joseph G Lorenz Tori D Randall Zuzana Faltyskova Luca Pagani Petr Danecek Tamsin C O'Connell Patricia Martz Alan S Boraas Brian F Byrd Alan Leventhal Rosemary Cambra Ronald Williamson Louis Lesage Brian Holguin Ernestine Ygnacio-De Soto JohnTommy Rosas Mait Metspalu Jay T Stock Andrea Manica Aylwyn Scally Daniel Wegmann Ripan S Malhi Toomas Kivisild

Science 2018 06;360(6392):1024-1027

Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK.

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http://dx.doi.org/10.1126/science.aar6851DOI Listing
June 2018

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.

Authors:
Alexander Nater Maja P Mattle-Greminger Anton Nurcahyo Matthew G Nowak Marc de Manuel Tariq Desai Colin Groves Marc Pybus Tugce Bilgin Sonay Christian Roos Adriano R Lameira Serge A Wich James Askew Marina Davila-Ross Gabriella Fredriksson Guillem de Valles Ferran Casals Javier Prado-Martinez Benoit Goossens Ernst J Verschoor Kristin S Warren Ian Singleton David A Marques Joko Pamungkas Dyah Perwitasari-Farajallah Puji Rianti Augustine Tuuga Ivo G Gut Marta Gut Pablo Orozco-terWengel Carel P van Schaik Jaume Bertranpetit Maria Anisimova Aylwyn Scally Tomas Marques-Bonet Erik Meijaard Michael Krützen

Curr Biol 2017 Nov 2;27(22):3487-3498.e10. Epub 2017 Nov 2.

Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.09.047DOI Listing
November 2017

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.

Authors:
Alexander Nater Maja P Mattle-Greminger Anton Nurcahyo Matthew G Nowak Marc de Manuel Tariq Desai Colin Groves Marc Pybus Tugce Bilgin Sonay Christian Roos Adriano R Lameira Serge A Wich James Askew Marina Davila-Ross Gabriella Fredriksson Guillem de Valles Ferran Casals Javier Prado-Martinez Benoit Goossens Ernst J Verschoor Kristin S Warren Ian Singleton David A Marques Joko Pamungkas Dyah Perwitasari-Farajallah Puji Rianti Augustine Tuuga Ivo G Gut Marta Gut Pablo Orozco-terWengel Carel P van Schaik Jaume Bertranpetit Maria Anisimova Aylwyn Scally Tomas Marques-Bonet Erik Meijaard Michael Krützen

Curr Biol 2017 11;27(22):3576-3577

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http://dx.doi.org/10.1016/j.cub.2017.11.020DOI Listing
November 2017

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes.

Authors:
Vagheesh M Narasimhan Raheleh Rahbari Aylwyn Scally Arthur Wuster Dan Mason Yali Xue John Wright Richard C Trembath Eamonn R Maher David A van Heel Adam Auton Matthew E Hurles Chris Tyler-Smith Richard Durbin

Nat Commun 2017 08 21;8(1):303. Epub 2017 Aug 21.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1038/s41467-017-00323-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566399PMC
August 2017

Global clues to the nature of genomic mutations in humans.

Authors:
Aylwyn Scally

Elife 2017 05 17;6. Epub 2017 May 17.

Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.7554/eLife.27605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435459PMC
May 2017

Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data.

Authors:
Cathal Seoighe Aylwyn Scally

PLoS Genet 2017 01 17;13(1):e1006549. Epub 2017 Jan 17.

Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1006549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283766PMC
January 2017

The mutation rate in human evolution and demographic inference.

Authors:
Aylwyn Scally

Curr Opin Genet Dev 2016 Dec 31;41:36-43. Epub 2016 Aug 31.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.07.008DOI Listing
December 2016

Chimpanzee genomic diversity reveals ancient admixture with bonobos.

Authors:
Marc de Manuel Martin Kuhlwilm Peter Frandsen Vitor C Sousa Tariq Desai Javier Prado-Martinez Jessica Hernandez-Rodriguez Isabelle Dupanloup Oscar Lao Pille Hallast Joshua M Schmidt José María Heredia-Genestar Andrea Benazzo Guido Barbujani Benjamin M Peter Lukas F K Kuderna Ferran Casals Samuel Angedakin Mimi Arandjelovic Christophe Boesch Hjalmar Kühl Linda Vigilant Kevin Langergraber John Novembre Marta Gut Ivo Gut Arcadi Navarro Frands Carlsen Aida M Andrés Hans R Siegismund Aylwyn Scally Laurent Excoffier Chris Tyler-Smith Sergi Castellano Yali Xue Christina Hvilsom Tomas Marques-Bonet

Science 2016 10 27;354(6311):477-481. Epub 2016 Oct 27.

Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.

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http://dx.doi.org/10.1126/science.aag2602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546212PMC
October 2016

Mutation rates and the evolution of germline structure.

Authors:
Aylwyn Scally

Philos Trans R Soc Lond B Biol Sci 2016 07;371(1699)

Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK

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http://dx.doi.org/10.1098/rstb.2015.0137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920338PMC
July 2016

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

Authors:
Vagheesh Narasimhan Petr Danecek Aylwyn Scally Yali Xue Chris Tyler-Smith Richard Durbin

Bioinformatics 2016 06 30;32(11):1749-51. Epub 2016 Jan 30.

Wellcome Trust Sanger Institute, Hinxton and.

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http://dx.doi.org/10.1093/bioinformatics/btw044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892413PMC
June 2016

Rethinking the dispersal of Homo sapiens out of Africa.

Authors:
Huw S Groucutt Michael D Petraglia Geoff Bailey Eleanor M L Scerri Ash Parton Laine Clark-Balzan Richard P Jennings Laura Lewis James Blinkhorn Nick A Drake Paul S Breeze Robyn H Inglis Maud H Devès Matthew Meredith-Williams Nicole Boivin Mark G Thomas Aylwyn Scally

Evol Anthropol 2015 Jul-Aug;24(4):149-64

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http://dx.doi.org/10.1002/evan.21455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715448PMC
May 2016

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

Authors:
Luca Pagani Stephan Schiffels Deepti Gurdasani Petr Danecek Aylwyn Scally Yuan Chen Yali Xue Marc Haber Rosemary Ekong Tamiru Oljira Ephrem Mekonnen Donata Luiselli Neil Bradman Endashaw Bekele Pierre Zalloua Richard Durbin Toomas Kivisild Chris Tyler-Smith

Am J Hum Genet 2015 Jun 28;96(6):986-91. Epub 2015 May 28.

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

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http://dx.doi.org/10.1016/j.ajhg.2015.04.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457944PMC
June 2015

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

Authors:
Yali Xue Javier Prado-Martinez Peter H Sudmant Vagheesh Narasimhan Qasim Ayub Michal Szpak Peter Frandsen Yuan Chen Bryndis Yngvadottir David N Cooper Marc de Manuel Jessica Hernandez-Rodriguez Irene Lobon Hans R Siegismund Luca Pagani Michael A Quail Christina Hvilsom Antoine Mudakikwa Evan E Eichler Michael R Cranfield Tomas Marques-Bonet Chris Tyler-Smith Aylwyn Scally

Science 2015 Apr 9;348(6231):242-245. Epub 2015 Apr 9.

Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.

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http://dx.doi.org/10.1126/science.aaa3952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668944PMC
April 2015

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

Authors:
Aylwyn Scally Bryndis Yngvadottir Yali Xue Qasim Ayub Richard Durbin Chris Tyler-Smith

PLoS One 2013 4;8(6):e65066. Epub 2013 Jun 4.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065066PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672199PMC
September 2014

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Authors:
Thomas Mailund Anders E Halager Michael Westergaard Julien Y Dutheil Kasper Munch Lars N Andersen Gerton Lunter Kay Prüfer Aylwyn Scally Asger Hobolth Mikkel H Schierup

PLoS Genet 2012 20;8(12):e1003125. Epub 2012 Dec 20.

Bioinformatics Research Center, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1371/journal.pgen.1003125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527290PMC
May 2013

Revising the human mutation rate: implications for understanding human evolution.

Authors:
Aylwyn Scally Richard Durbin

Nat Rev Genet 2012 10 11;13(10):745-53. Epub 2012 Sep 11.

Wellcome Trust Sanger Institute, Hinxton, UK.

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http://www.nature.com/articles/nrg3295
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http://dx.doi.org/10.1038/nrg3295DOI Listing
October 2012

Insights into hominid evolution from the gorilla genome sequence.

Authors:
Aylwyn Scally Julien Y Dutheil LaDeana W Hillier Gregory E Jordan Ian Goodhead Javier Herrero Asger Hobolth Tuuli Lappalainen Thomas Mailund Tomas Marques-Bonet Shane McCarthy Stephen H Montgomery Petra C Schwalie Y Amy Tang Michelle C Ward Yali Xue Bryndis Yngvadottir Can Alkan Lars N Andersen Qasim Ayub Edward V Ball Kathryn Beal Brenda J Bradley Yuan Chen Chris M Clee Stephen Fitzgerald Tina A Graves Yong Gu Paul Heath Andreas Heger Emre Karakoc Anja Kolb-Kokocinski Gavin K Laird Gerton Lunter Stephen Meader Matthew Mort James C Mullikin Kasper Munch Timothy D O'Connor Andrew D Phillips Javier Prado-Martinez Anthony S Rogers Saba Sajjadian Dominic Schmidt Katy Shaw Jared T Simpson Peter D Stenson Daniel J Turner Linda Vigilant Albert J Vilella Weldon Whitener Baoli Zhu David N Cooper Pieter de Jong Emmanouil T Dermitzakis Evan E Eichler Paul Flicek Nick Goldman Nicholas I Mundy Zemin Ning Duncan T Odom Chris P Ponting Michael A Quail Oliver A Ryder Stephen M Searle Wesley C Warren Richard K Wilson Mikkel H Schierup Jane Rogers Chris Tyler-Smith Richard Durbin

Nature 2012 Mar 7;483(7388):169-75. Epub 2012 Mar 7.

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

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http://dx.doi.org/10.1038/nature10842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303130PMC
March 2012

Mapping copy number variation by population-scale genome sequencing.

Authors:
Ryan E Mills Klaudia Walter Chip Stewart Robert E Handsaker Ken Chen Can Alkan Alexej Abyzov Seungtai Chris Yoon Kai Ye R Keira Cheetham Asif Chinwalla Donald F Conrad Yutao Fu Fabian Grubert Iman Hajirasouliha Fereydoun Hormozdiari Lilia M Iakoucheva Zamin Iqbal Shuli Kang Jeffrey M Kidd Miriam K Konkel Joshua Korn Ekta Khurana Deniz Kural Hugo Y K Lam Jing Leng Ruiqiang Li Yingrui Li Chang-Yun Lin Ruibang Luo Xinmeng Jasmine Mu James Nemesh Heather E Peckham Tobias Rausch Aylwyn Scally Xinghua Shi Michael P Stromberg Adrian M Stütz Alexander Eckehart Urban Jerilyn A Walker Jiantao Wu Yujun Zhang Zhengdong D Zhang Mark A Batzer Li Ding Gabor T Marth Gil McVean Jonathan Sebat Michael Snyder Jun Wang Kenny Ye Evan E Eichler Mark B Gerstein Matthew E Hurles Charles Lee Steven A McCarroll Jan O Korbel

Nature 2011 Feb;470(7332):59-65

Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nature09708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077050PMC
February 2011

A large genome center's improvements to the Illumina sequencing system.

Authors:
Michael A Quail Iwanka Kozarewa Frances Smith Aylwyn Scally Philip J Stephens Richard Durbin Harold Swerdlow Daniel J Turner

Nat Methods 2008 Dec;5(12):1005-10

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

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http://dx.doi.org/10.1038/nmeth.1270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610436PMC
December 2008

Accurate whole human genome sequencing using reversible terminator chemistry.

Authors:
David R Bentley Shankar Balasubramanian Harold P Swerdlow Geoffrey P Smith John Milton Clive G Brown Kevin P Hall Dirk J Evers Colin L Barnes Helen R Bignell Jonathan M Boutell Jason Bryant Richard J Carter R Keira Cheetham Anthony J Cox Darren J Ellis Michael R Flatbush Niall A Gormley Sean J Humphray Leslie J Irving Mirian S Karbelashvili Scott M Kirk Heng Li Xiaohai Liu Klaus S Maisinger Lisa J Murray Bojan Obradovic Tobias Ost Michael L Parkinson Mark R Pratt Isabelle M J Rasolonjatovo Mark T Reed Roberto Rigatti Chiara Rodighiero Mark T Ross Andrea Sabot Subramanian V Sankar Aylwyn Scally Gary P Schroth Mark E Smith Vincent P Smith Anastassia Spiridou Peta E Torrance Svilen S Tzonev Eric H Vermaas Klaudia Walter Xiaolin Wu Lu Zhang Mohammed D Alam Carole Anastasi Ify C Aniebo David M D Bailey Iain R Bancarz Saibal Banerjee Selena G Barbour Primo A Baybayan Vincent A Benoit Kevin F Benson Claire Bevis Phillip J Black Asha Boodhun Joe S Brennan John A Bridgham Rob C Brown Andrew A Brown Dale H Buermann Abass A Bundu James C Burrows Nigel P Carter Nestor Castillo Maria Chiara E Catenazzi Simon Chang R Neil Cooley Natasha R Crake Olubunmi O Dada Konstantinos D Diakoumakos Belen Dominguez-Fernandez David J Earnshaw Ugonna C Egbujor David W Elmore Sergey S Etchin Mark R Ewan Milan Fedurco Louise J Fraser Karin V Fuentes Fajardo W Scott Furey David George Kimberley J Gietzen Colin P Goddard George S Golda Philip A Granieri David E Green David L Gustafson Nancy F Hansen Kevin Harnish Christian D Haudenschild Narinder I Heyer Matthew M Hims Johnny T Ho Adrian M Horgan Katya Hoschler Steve Hurwitz Denis V Ivanov Maria Q Johnson Terena James T A Huw Jones Gyoung-Dong Kang Tzvetana H Kerelska Alan D Kersey Irina Khrebtukova Alex P Kindwall Zoya Kingsbury Paula I Kokko-Gonzales Anil Kumar Marc A Laurent Cynthia T Lawley Sarah E Lee Xavier Lee Arnold K Liao Jennifer A Loch Mitch Lok Shujun Luo Radhika M Mammen John W Martin Patrick G McCauley Paul McNitt Parul Mehta Keith W Moon Joe W Mullens Taksina Newington Zemin Ning Bee Ling Ng Sonia M Novo Michael J O'Neill Mark A Osborne Andrew Osnowski Omead Ostadan Lambros L Paraschos Lea Pickering Andrew C Pike Alger C Pike D Chris Pinkard Daniel P Pliskin Joe Podhasky Victor J Quijano Come Raczy Vicki H Rae Stephen R Rawlings Ana Chiva Rodriguez Phyllida M Roe John Rogers Maria C Rogert Bacigalupo Nikolai Romanov Anthony Romieu Rithy K Roth Natalie J Rourke Silke T Ruediger Eli Rusman Raquel M Sanches-Kuiper Martin R Schenker Josefina M Seoane Richard J Shaw Mitch K Shiver Steven W Short Ning L Sizto Johannes P Sluis Melanie A Smith Jean Ernest Sohna Sohna Eric J Spence Kim Stevens Neil Sutton Lukasz Szajkowski Carolyn L Tregidgo Gerardo Turcatti Stephanie Vandevondele Yuli Verhovsky Selene M Virk Suzanne Wakelin Gregory C Walcott Jingwen Wang Graham J Worsley Juying Yan Ling Yau Mike Zuerlein Jane Rogers James C Mullikin Matthew E Hurles Nick J McCooke John S West Frank L Oaks Peter L Lundberg David Klenerman Richard Durbin Anthony J Smith

Nature 2008 Nov;456(7218):53-9

Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK.

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http://dx.doi.org/10.1038/nature07517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791PMC
November 2008