Publications by authors named "Daniel L Halligan"

32Publications

Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer.

Authors:
Marie-Claire Wagle Joseph Castillo Shrividhya Srinivasan Thomas Holcomb Kobe C Yuen Edward E Kadel Sanjeev Mariathasan Daniel L Halligan Adrian R Carr Max Bylesjo Paul R McAdam Sarah Lynagh Koen M Marien Mark Kockx Yannick Waumans Shih-Min A Huang Mark R Lackner Zineb Mounir

Cancer Immunol Res 2020 07 22;8(7):844-850. Epub 2020 Apr 22.

Oncology Biomarker Development, Genentech, Inc., South San Francisco, California.

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July 2020

Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts.

Authors:
Katherine E Hutchinson Susan E Yost Ching-Wei Chang Radia Marie Johnson Adrian R Carr Paul R McAdam Daniel L Halligan Chun-Chieh Chang Daniel Schmolze Jackson Liang Yuan Yuan

Clin Cancer Res 2020 02 14;26(3):657-668. Epub 2019 Oct 14.

Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, California.

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February 2020

Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors.

Authors:
Andrew C Kidd Michael McGettrick Selina Tsim Daniel L Halligan Max Bylesjo Kevin G Blyth

BMJ Open Respir Res 2018 30;5(1):e000240. Epub 2018 Jan 30.

Pleural Disease Unit, Queen Elizabeth University Hospital, Glasgow, UK.

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January 2018

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.

Authors:
Sanjeev Mariathasan Shannon J Turley Dorothee Nickles Alessandra Castiglioni Kobe Yuen Yulei Wang Edward E Kadel Hartmut Koeppen Jillian L Astarita Rafael Cubas Suchit Jhunjhunwala Romain Banchereau Yagai Yang Yinghui Guan Cecile Chalouni James Ziai Yasin Şenbabaoğlu Stephen Santoro Daniel Sheinson Jeffrey Hung Jennifer M Giltnane Andrew A Pierce Kathryn Mesh Steve Lianoglou Johannes Riegler Richard A D Carano Pontus Eriksson Mattias Höglund Loan Somarriba Daniel L Halligan Michiel S van der Heijden Yohann Loriot Jonathan E Rosenberg Lawrence Fong Ira Mellman Daniel S Chen Marjorie Green Christina Derleth Gregg D Fine Priti S Hegde Richard Bourgon Thomas Powles

Nature 2018 02 14;554(7693):544-548. Epub 2018 Feb 14.

Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.

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February 2018

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

Authors:
R Axel W Wiberg Daniel L Halligan Rob W Ness Anamaria Necsulea Henrik Kaessmann Peter D Keightley

Genome Biol Evol 2015 Aug 12;7(8):2432-44. Epub 2015 Aug 12.

Institute of Evolutionary Biology, University of Edinburgh, United Kingdom.

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August 2015

Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.

Authors:
Eva E Deinum Daniel L Halligan Rob W Ness Yao-Hua Zhang Lin Cong Jian-Xu Zhang Peter D Keightley

Mol Biol Evol 2015 Oct 1;32(10):2547-58. Epub 2015 Jun 1.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

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October 2015

Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements.

Authors:
Gabriel Santpere Elena Carnero-Montoro Natalia Petit François Serra Christina Hvilsom Jordi Rambla Jose Maria Heredia-Genestar Daniel L Halligan Hernan Dopazo Arcadi Navarro Elena Bosch

Genome Biol Evol 2015 May 14;7(6):1490-505. Epub 2015 May 14.

Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain

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May 2015

The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster.

Authors:
José L Campos Daniel L Halligan Penelope R Haddrill Brian Charlesworth

Mol Biol Evol 2014 Apr 30;31(4):1010-28. Epub 2014 Jan 30.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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April 2014

Faster-X adaptive protein evolution in house mice.

Authors:
Athanasios Kousathanas Daniel L Halligan Peter D Keightley

Genetics 2014 Apr 20;196(4):1131-43. Epub 2013 Dec 20.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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April 2014

Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Authors:
Daniel L Halligan Athanasios Kousathanas Rob W Ness Bettina Harr Lél Eöry Thomas M Keane David J Adams Peter D Keightley

PLoS Genet 2013 5;9(12):e1003995. Epub 2013 Dec 5.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.

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August 2014

Processing genome scale tabular data with wormtable.

Authors:
Jerome Kelleher Rob W Ness Daniel L Halligan

BMC Bioinformatics 2013 Dec 5;14:356. Epub 2013 Dec 5.

University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.

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December 2013

Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family.

Authors:
Peter D Keightley Rob W Ness Daniel L Halligan Penelope R Haddrill

Genetics 2014 Jan 8;196(1):313-20. Epub 2013 Nov 8.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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January 2014

Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.

Authors:
Peter D Keightley Daniel L Halligan

Genetics 2011 Aug 19;188(4):931-40. Epub 2011 May 19.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.

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August 2011

Positive and negative selection in murine ultraconserved noncoding elements.

Authors:
Daniel L Halligan Fiona Oliver Jack Guthrie Kathryn C Stemshorn Bettina Harr Peter D Keightley

Mol Biol Evol 2011 Sep 8;28(9):2651-60. Epub 2011 Apr 8.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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September 2011

Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation.

Authors:
Peter D Keightley Lél Eöry Daniel L Halligan Mark Kirkpatrick

Genetics 2011 Apr 1;187(4):1153-61. Epub 2011 Feb 1.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.

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April 2011

Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.

Authors:
Athanasios Kousathanas Fiona Oliver Daniel L Halligan Peter D Keightley

Mol Biol Evol 2011 Mar 8;28(3):1183-91. Epub 2010 Nov 8.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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March 2011

Evidence for pervasive adaptive protein evolution in wild mice.

Authors:
Daniel L Halligan Fiona Oliver Adam Eyre-Walker Bettina Harr Peter D Keightley

PLoS Genet 2010 Jan 22;6(1):e1000825. Epub 2010 Jan 22.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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January 2010

Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.

Authors:
Sophie Marion de Procé Daniel L Halligan Peter D Keightley Brian Charlesworth

J Mol Evol 2009 Dec 27;69(6):601-11. Epub 2009 Oct 27.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK.

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December 2009

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.

Authors:
Lél Eory Daniel L Halligan Peter D Keightley

Mol Biol Evol 2010 Jan;27(1):177-92

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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January 2010

Analysis and implications of mutational variation.

Authors:
Peter D Keightley Daniel L Halligan

Genetica 2009 Jun 29;136(2):359-69. Epub 2008 Jul 29.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK.

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June 2009

Effects of spontaneous mutation accumulation on sex ratio traits in a parasitoid wasp.

Authors:
Bart A Pannebakker Daniel L Halligan K Tracy Reynolds Gavin A Ballantyne David M Shuker Nick H Barton Stuart A West

Evolution 2008 Aug 3;62(8):1921-35. Epub 2008 Jun 3.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.

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August 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.

Authors:
Jun Wang Peter D Keightley Daniel L Halligan

J Mol Evol 2007 Dec 25;65(6):627-39. Epub 2007 Sep 25.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.

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December 2007

Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over.

Authors:
Penelope R Haddrill Daniel L Halligan Dimitris Tomaras Brian Charlesworth

Genome Biol 2007 ;8(2):R18

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK.

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July 2007

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila.

Authors:
Cathy Haag-Liautard Mark Dorris Xulio Maside Steven Macaskill Daniel L Halligan David Houle Brian Charlesworth Peter D Keightley

Nature 2007 Jan;445(7123):82-5

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.

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January 2007

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison.

Authors:
Daniel L Halligan Peter D Keightley

Genome Res 2006 Jul 2;16(7):875-84. Epub 2006 Jun 2.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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July 2006

Natural selection drives extremely rapid evolution in antiviral RNAi genes.

Authors:
Darren J Obbard Francis M Jiggins Daniel L Halligan Tom J Little

Curr Biol 2006 Mar;16(6):580-5

Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, United Kingdom.

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March 2006

Evolutionary constraints in conserved nongenic sequences of mammals.

Authors:
Peter D Keightley Gregory V Kryukov Shamil Sunyaev Daniel L Halligan Daniel J Gaffney

Genome Res 2005 Oct;15(10):1373-8

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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October 2005

Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.

Authors:
Penelope R Haddrill Brian Charlesworth Daniel L Halligan Peter Andolfatto

Genome Biol 2005 27;6(8):R67. Epub 2005 Jul 27.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.

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July 2006

Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines.

Authors:
Daniel L Halligan Andrew D Peters Peter D Keightley

Genet Res 2003 Dec;82(3):191-205

Institute of Cell, Animal and Population Biology, University of Edinburgh, UK.

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December 2003

Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.

Authors:
Daniel L Halligan Adam Eyre-Walker Peter Andolfatto Peter D Keightley

Genome Res 2004 Feb;14(2):273-9

University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK.

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February 2004

How many lethal alleles?

Authors:
Daniel L Halligan Peter D Keightley

Trends Genet 2003 Feb;19(2):57-9

Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT, Edinburgh, UK.

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February 2003