Richard Durbin

Richard Durbin

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Richard Durbin

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Haplotype-aware graph indexes.

Bioinformatics 2019 Jul 26. Epub 2019 Jul 26.

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

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http://dx.doi.org/10.1093/bioinformatics/btz575DOI Listing
July 2019

Crumble: reference free lossy compression of sequence quality values.

Bioinformatics 2019 Jan;35(2):337-339

DNA Pipelines, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330002PMC
January 2019

Detecting archaic introgression using an unadmixed outgroup.

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?

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

A graph-based approach to diploid genome assembly.

Bioinformatics 2018 07;34(13):i105-i114

Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany.

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https://academic.oup.com/bioinformatics/article/34/13/i105/5
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http://dx.doi.org/10.1093/bioinformatics/bty279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022571PMC
July 2018

No evidence for maintenance of a sympatric species barrier by chromosomal inversions.

Evol Lett 2017 Aug 14;1(3):138-154. Epub 2017 Jun 14.

Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ United Kingdom.

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http://dx.doi.org/10.1002/evl3.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6122123PMC
August 2017

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Authors:
Ioanna Tachmazidou Dániel Süveges Josine L Min Graham R S Ritchie Julia Steinberg Klaudia Walter Valentina Iotchkova Jeremy Schwartzentruber Jie Huang Yasin Memari Shane McCarthy Andrew A Crawford Cristina Bombieri Massimiliano Cocca Aliki-Eleni Farmaki Tom R Gaunt Pekka Jousilahti Marjolein N Kooijman Benjamin Lehne Giovanni Malerba Satu Männistö Angela Matchan Carolina Medina-Gomez Sarah J Metrustry Abhishek Nag Ioanna Ntalla Lavinia Paternoster Nigel W Rayner Cinzia Sala William R Scott Hashem A Shihab Lorraine Southam Beate St Pourcain Michela Traglia Katerina Trajanoska Gialuigi Zaza Weihua Zhang María S Artigas Narinder Bansal Marianne Benn Zhongsheng Chen Petr Danecek Wei-Yu Lin Adam Locke Jian'an Luan Alisa K Manning Antonella Mulas Carlo Sidore Anne Tybjaerg-Hansen Anette Varbo Magdalena Zoledziewska Chris Finan Konstantinos Hatzikotoulas Audrey E Hendricks John P Kemp Alireza Moayyeri Kalliope Panoutsopoulou Michal Szpak Scott G Wilson Michael Boehnke Francesco Cucca Emanuele Di Angelantonio Claudia Langenberg Cecilia Lindgren Mark I McCarthy Andrew P Morris Børge G Nordestgaard Robert A Scott Martin D Tobin Nicholas J Wareham Paul Burton John C Chambers George Davey Smith George Dedoussis Janine F Felix Oscar H Franco Giovanni Gambaro Paolo Gasparini Christopher J Hammond Albert Hofman Vincent W V Jaddoe Marcus Kleber Jaspal S Kooner Markus Perola Caroline Relton Susan M Ring Fernando Rivadeneira Veikko Salomaa Timothy D Spector Oliver Stegle Daniela Toniolo André G Uitterlinden Inês Barroso Celia M T Greenwood John R B Perry Brian R Walker Adam S Butterworth Yali Xue Richard Durbin Kerrin S Small Nicole Soranzo Nicholas J Timpson Eleftheria Zeggini

Am J Hum Genet 2017 Jun 25;100(6):865-884. Epub 2017 May 25.

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

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http://dx.doi.org/10.1016/j.ajhg.2017.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473732PMC
June 2017

A reference panel of 64,976 haplotypes for genotype imputation.

Authors:
Shane McCarthy Sayantan Das Warren Kretzschmar Olivier Delaneau Andrew R Wood Alexander Teumer Hyun Min Kang Christian Fuchsberger Petr Danecek Kevin Sharp Yang Luo Carlo Sidore Alan Kwong Nicholas Timpson Seppo Koskinen Scott Vrieze Laura J Scott He Zhang Anubha Mahajan Jan Veldink Ulrike Peters Carlos Pato Cornelia M van Duijn Christopher E Gillies Ilaria Gandin Massimo Mezzavilla Arthur Gilly Massimiliano Cocca Michela Traglia Andrea Angius Jeffrey C Barrett Dorrett Boomsma Kari Branham Gerome Breen Chad M Brummett Fabio Busonero Harry Campbell Andrew Chan Sai Chen Emily Chew Francis S Collins Laura J Corbin George Davey Smith George Dedoussis Marcus Dorr Aliki-Eleni Farmaki Luigi Ferrucci Lukas Forer Ross M Fraser Stacey Gabriel Shawn Levy Leif Groop Tabitha Harrison Andrew Hattersley Oddgeir L Holmen Kristian Hveem Matthias Kretzler James C Lee Matt McGue Thomas Meitinger David Melzer Josine L Min Karen L Mohlke John B Vincent Matthias Nauck Deborah Nickerson Aarno Palotie Michele Pato Nicola Pirastu Melvin McInnis J Brent Richards Cinzia Sala Veikko Salomaa David Schlessinger Sebastian Schoenherr P Eline Slagboom Kerrin Small Timothy Spector Dwight Stambolian Marcus Tuke Jaakko Tuomilehto Leonard H Van den Berg Wouter Van Rheenen Uwe Volker Cisca Wijmenga Daniela Toniolo Eleftheria Zeggini Paolo Gasparini Matthew G Sampson James F Wilson Timothy Frayling Paul I W de Bakker Morris A Swertz Steven McCarroll Charles Kooperberg Annelot Dekker David Altshuler Cristen Willer William Iacono Samuli Ripatti Nicole Soranzo Klaudia Walter Anand Swaroop Francesco Cucca Carl A Anderson Richard M Myers Michael Boehnke Mark I McCarthy Richard Durbin

Nat Genet 2016 10 22;48(10):1279-83. Epub 2016 Aug 22.

Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.3643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388176PMC
October 2016

A genomic history of Aboriginal Australia.

Nature 2016 Oct 21;538(7624):207-214. Epub 2016 Sep 21.

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

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http://dx.doi.org/10.1038/nature18299DOI Listing
October 2016

A high-content platform to characterise human induced pluripotent stem cell lines.

Methods 2016 Mar 25;96:85-96. Epub 2015 Nov 25.

HipSci Cell Phenotyping, Centre for Stem Cells and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.11.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773406PMC
March 2016

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Authors:
Hou-Feng Zheng Vincenzo Forgetta Yi-Hsiang Hsu Karol Estrada Alberto Rosello-Diez Paul J Leo Chitra L Dahia Kyung Hyun Park-Min Jonathan H Tobias Charles Kooperberg Aaron Kleinman Unnur Styrkarsdottir Ching-Ti Liu Charlotta Uggla Daniel S Evans Carrie M Nielson Klaudia Walter Ulrika Pettersson-Kymmer Shane McCarthy Joel Eriksson Tony Kwan Mila Jhamai Katerina Trajanoska Yasin Memari Josine Min Jie Huang Petr Danecek Beth Wilmot Rui Li Wen-Chi Chou Lauren E Mokry Alireza Moayyeri Melina Claussnitzer Chia-Ho Cheng Warren Cheung Carolina Medina-Gómez Bing Ge Shu-Huang Chen Kwangbom Choi Ling Oei James Fraser Robert Kraaij Matthew A Hibbs Celia L Gregson Denis Paquette Albert Hofman Carl Wibom Gregory J Tranah Mhairi Marshall Brooke B Gardiner Katie Cremin Paul Auer Li Hsu Sue Ring Joyce Y Tung Gudmar Thorleifsson Anke W Enneman Natasja M van Schoor Lisette C P G M de Groot Nathalie van der Velde Beatrice Melin John P Kemp Claus Christiansen Adrian Sayers Yanhua Zhou Sophie Calderari Jeroen van Rooij Chris Carlson Ulrike Peters Soizik Berlivet Josée Dostie Andre G Uitterlinden Stephen R Williams Charles Farber Daniel Grinberg Andrea Z LaCroix Jeff Haessler Daniel I Chasman Franco Giulianini Lynda M Rose Paul M Ridker John A Eisman Tuan V Nguyen Jacqueline R Center Xavier Nogues Natalia Garcia-Giralt Lenore L Launer Vilmunder Gudnason Dan Mellström Liesbeth Vandenput Najaf Amin Cornelia M van Duijn Magnus K Karlsson Östen Ljunggren Olle Svensson Göran Hallmans François Rousseau Sylvie Giroux Johanne Bussière Pascal P Arp Fjorda Koromani Richard L Prince Joshua R Lewis Bente L Langdahl A Pernille Hermann Jens-Erik B Jensen Stephen Kaptoge Kay-Tee Khaw Jonathan Reeve Melissa M Formosa Angela Xuereb-Anastasi Kristina Åkesson Fiona E McGuigan Gaurav Garg Jose M Olmos Maria T Zarrabeitia Jose A Riancho Stuart H Ralston Nerea Alonso Xi Jiang David Goltzman Tomi Pastinen Elin Grundberg Dominique Gauguier Eric S Orwoll David Karasik George Davey-Smith Albert V Smith Kristin Siggeirsdottir Tamara B Harris M Carola Zillikens Joyce B J van Meurs Unnur Thorsteinsdottir Matthew T Maurano Nicholas J Timpson Nicole Soranzo Richard Durbin Scott G Wilson Evangelia E Ntzani Matthew A Brown Kari Stefansson David A Hinds Tim Spector L Adrienne Cupples Claes Ohlsson Celia M T Greenwood Rebecca D Jackson David W Rowe Cynthia A Loomis David M Evans Cheryl L Ackert-Bicknell Alexandra L Joyner Emma L Duncan Douglas P Kiel Fernando Rivadeneira J Brent Richards

Nature 2015 Oct 14;526(7571):112-7. Epub 2015 Sep 14.

Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada.

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http://dx.doi.org/10.1038/nature14878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714PMC
October 2015

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Authors:
Maanasa Raghavan Matthias Steinrücken Kelley Harris Stephan Schiffels Simon Rasmussen Michael DeGiorgio Anders Albrechtsen Cristina Valdiosera María C Ávila-Arcos Anna-Sapfo Malaspinas Anders Eriksson Ida Moltke Mait Metspalu Julian R Homburger Jeff Wall Omar E Cornejo J Víctor Moreno-Mayar Thorfinn S Korneliussen Tracey Pierre Morten Rasmussen Paula F Campos Peter de Barros Damgaard Morten E Allentoft John Lindo Ene Metspalu Ricardo Rodríguez-Varela Josefina Mansilla Celeste Henrickson Andaine Seguin-Orlando Helena Malmström Thomas Stafford Suyash S Shringarpure Andrés Moreno-Estrada Monika Karmin Kristiina Tambets Anders Bergström Yali Xue Vera Warmuth Andrew D Friend Joy Singarayer Paul Valdes Francois Balloux Ilán Leboreiro Jose Luis Vera Hector Rangel-Villalobos Davide Pettener Donata Luiselli Loren G Davis Evelyne Heyer Christoph P E Zollikofer Marcia S Ponce de León Colin I Smith Vaughan Grimes Kelly-Anne Pike Michael Deal Benjamin T Fuller Bernardo Arriaza Vivien Standen Maria F Luz Francois Ricaut Niede Guidon Ludmila Osipova Mikhail I Voevoda Olga L Posukh Oleg Balanovsky Maria Lavryashina Yuri Bogunov Elza Khusnutdinova Marina Gubina Elena Balanovska Sardana Fedorova Sergey Litvinov Boris Malyarchuk Miroslava Derenko M J Mosher David Archer Jerome Cybulski Barbara Petzelt Joycelynn Mitchell Rosita Worl Paul J Norman Peter Parham Brian M Kemp Toomas Kivisild Chris Tyler-Smith Manjinder S Sandhu Michael Crawford Richard Villems David Glenn Smith Michael R Waters Ted Goebel John R Johnson Ripan S Malhi Mattias Jakobsson David J Meltzer Andrea Manica Richard Durbin Carlos D Bustamante Yun S Song Rasmus Nielsen Eske Willerslev

Science 2015 Aug 21;349(6250):aab3884. Epub 2015 Jul 21.

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

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http://dx.doi.org/10.1126/science.aab3884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733658PMC
August 2015

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.

Nat Genet 2015 Jan 1;47(1):88-91. Epub 2014 Dec 1.

1] Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland. [2] Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland. [3] Swiss Institute of Bioinformatics, Geneva, Switzerland.

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http://dx.doi.org/10.1038/ng.3162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643454PMC
January 2015

Estimation of epistatic variance components and heritability in founder populations and crosses.

Genetics 2014 Dec 17;198(4):1405-16. Epub 2014 Oct 17.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1534/genetics.114.170795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256760PMC
December 2014

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

PLoS Genet 2014 Nov 20;10(11):e1004798. Epub 2014 Nov 20.

The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238955PMC
November 2014

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

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

Inferring human population size and separation history from multiple genome sequences.

Nat Genet 2014 Aug 22;46(8):919-25. Epub 2014 Jun 22.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.3015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116295PMC
August 2014

Distribution and medical impact of loss-of-function variants in the Finnish founder population.

PLoS Genet 2014 Jul 31;10(7):e1004494. Epub 2014 Jul 31.

Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117444PMC
July 2014

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

Authors:
Richard Durbin

Bioinformatics 2014 May 9;30(9):1266-72. Epub 2014 Jan 9.

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

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http://dx.doi.org/10.1093/bioinformatics/btu014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998136PMC
May 2014

Estimating telomere length from whole genome sequence data.

Nucleic Acids Res 2014 May 7;42(9):e75. Epub 2014 Mar 7.

Genome Informatics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK

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http://dx.doi.org/10.1093/nar/gku181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027178PMC
May 2014

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

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

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
Publisher Site
http://dx.doi.org/10.1038/nrg3295DOI Listing
October 2012

Efficient de novo assembly of large genomes using compressed data structures.

Genome Res 2012 Mar 7;22(3):549-56. Epub 2011 Dec 7.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://genome.cshlp.org/content/22/3/549.full.pdf
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http://genome.cshlp.org/content/suppl/2011/12/12/gr.126953.1
Web Search
http://genome.cshlp.org/cgi/doi/10.1101/gr.126953.111
Publisher Site
http://dx.doi.org/10.1101/gr.126953.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290790PMC
March 2012

WormBase: Annotating many nematode genomes.

Worm 2012 Jan;1(1):15-21

European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge UK.

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http://dx.doi.org/10.4161/worm.19574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670165PMC
January 2012

Identity-by-descent-based phasing and imputation in founder populations using graphical models.

Genet Epidemiol 2011 Dec 17;35(8):853-60. Epub 2011 Oct 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/gepi.20635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368215PMC
December 2011

Inference of human population history from individual whole-genome sequences.

Nature 2011 Jul 13;475(7357):493-6. Epub 2011 Jul 13.

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

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http://www.nature.com/articles/nature10231
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http://dx.doi.org/10.1038/nature10231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154645PMC
July 2011

Dindel: accurate indel calls from short-read data.

Genome Res 2011 Jun 27;21(6):961-73. Epub 2010 Oct 27.

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, United Kingdom.

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http://dx.doi.org/10.1101/gr.112326.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106329PMC
June 2011

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.

Genome Res 2011 Jun 27;21(6):952-60. Epub 2010 Oct 27.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1101/gr.113084.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106328PMC
June 2011

Joint genetic analysis of gene expression data with inferred cellular phenotypes.

PLoS Genet 2011 Jan 20;7(1):e1001276. Epub 2011 Jan 20.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1001276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024309PMC
January 2011

Efficient construction of an assembly string graph using the FM-index.

Bioinformatics 2010 Jun;26(12):i367-73

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

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http://dx.doi.org/10.1093/bioinformatics/btq217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881401PMC
June 2010