Mandy Sanders

Mandy Sanders

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Mandy Sanders

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Global genome diversity of the complex.

Authors:
Susanne U Franssen Caroline Durrant Olivia Stark Bettina Moser Tim Downing Hideo Imamura Jean-Claude Dujardin Mandy J Sanders Isabel Mauricio Michael A Miles Lionel F Schnur Charles L Jaffe Abdelmajeed Nasereddin Henk Schallig Matthew Yeo Tapan Bhattacharyya Mohammad Z Alam Matthew Berriman Thierry Wirth Gabriele Schönian James A Cotton

Elife 2020 Mar 25;9. Epub 2020 Mar 25.

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

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http://dx.doi.org/10.7554/eLife.51243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105377PMC
March 2020

Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent.

Authors:
Malgorzata A Domagalska Hideo Imamura Mandy Sanders Frederik Van den Broeck Narayan Raj Bhattarai Manu Vanaerschot Ilse Maes Erika D'Haenens Keshav Rai Suman Rijal Matthew Berriman James A Cotton Jean-Claude Dujardin

PLoS Negl Trop Dis 2019 12 12;13(12):e0007900. Epub 2019 Dec 12.

Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium.

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http://dx.doi.org/10.1371/journal.pntd.0007900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6932831PMC
December 2019

Evolutionary analysis of the most polymorphic gene family in malaria.

Authors:
Thomas D Otto Sammy A Assefa Ulrike Böhme Mandy J Sanders Dominic Kwiatkowski Matt Berriman Chris Newbold

Wellcome Open Res 2019 3;4:193. Epub 2019 Dec 3.

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

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http://dx.doi.org/10.12688/wellcomeopenres.15590.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001760PMC
December 2019

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania.

Authors:
Megan A Sloan Karen Brooks Thomas D Otto Mandy J Sanders James A Cotton Petros Ligoxygakis

PLoS Genet 2019 11 11;15(11):e1008452. Epub 2019 Nov 11.

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1008452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872171PMC
November 2019

Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania.

Authors:
Ehud Inbar Jahangheer Shaik Stefano A Iantorno Audrey Romano Chukwunonso O Nzelu Katherine Owens Mandy J Sanders Deborah Dobson James A Cotton Michael E Grigg Stephen M Beverley David Sacks

PLoS Genet 2019 05 15;15(5):e1008042. Epub 2019 May 15.

Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1008042
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http://dx.doi.org/10.1371/journal.pgen.1008042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519804PMC
May 2019

Progression of the canonical reference malaria parasite genome from 2002-2019.

Authors:
Ulrike Böhme Thomas D Otto Mandy Sanders Chris I Newbold Matthew Berriman

Wellcome Open Res 2019 28;4:58. Epub 2019 May 28.

Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.15194.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484455PMC
May 2019

Repeated clinical malaria episodes are associated with modification of the immune system in children.

Authors:
Yaw Bediako Rhys Adams Adam J Reid John Joseph Valletta Francis M Ndungu Jan Sodenkamp Jedidah Mwacharo Joyce Mwongeli Ngoi Domtila Kimani Oscar Kai Juliana Wambua George Nyangweso Etienne P de Villiers Mandy Sanders Magda Ewa Lotkowska Jing-Wen Lin Sarah Manni John W G Addy Mario Recker Chris Newbold Matthew Berriman Philip Bejon Kevin Marsh Jean Langhorne

BMC Med 2019 03 13;17(1):60. Epub 2019 Mar 13.

Francis Crick Institute, London, UK.

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http://dx.doi.org/10.1186/s12916-019-1292-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415347PMC
March 2019

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern.

Authors:
Jing-Wen Lin Adam J Reid Deirdre Cunningham Ulrike Böhme Irene Tumwine Sara Keller-Mclaughlin Mandy Sanders Matthew Berriman Jean Langhorne

Wellcome Open Res 2018 6;3:142. Epub 2018 Dec 6.

Malaria Immunology laboratory, Francis Crick Institute, London, NW1 1AT, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.14797.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6259598PMC
December 2018

Pre-clinical evaluation of a -based whole-sporozoite malaria vaccine candidate.

Authors:
António M Mendes Isaie J Reuling Carolina M Andrade Thomas D Otto Marta Machado Filipa Teixeira Joana Pissarra Nataniel Gonçalves-Rosa Dolores Bonaparte João Sinfrónio Mandy Sanders Chris J Janse Shahid M Khan Chris I Newbold Matthew Berriman Cynthia K Lee Yimin Wu Christian F Ockenhouse Robert W Sauerwein Miguel Prudêncio

NPJ Vaccines 2018 27;3:54. Epub 2018 Nov 27.

1Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.

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http://www.nature.com/articles/s41541-018-0091-3
Publisher Site
http://dx.doi.org/10.1038/s41541-018-0091-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258718PMC
November 2018

Variant antigen repertoires in populations and experimental infections can be profiled from deep sequence data using universal protein motifs.

Authors:
Sara Silva Pereira Aitor Casas-Sánchez Lee R Haines Moses Ogugo Kihara Absolomon Mandy Sanders Steve Kemp Álvaro Acosta-Serrano Harry Noyes Matthew Berriman Andrew P Jackson

Genome Res 2018 09 13;28(9):1383-1394. Epub 2018 Jul 13.

Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom.

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http://dx.doi.org/10.1101/gr.234146.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120623PMC
September 2018

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent.

Authors:
Bart Cuypers Maya Berg Hideo Imamura Franck Dumetz Géraldine De Muylder Malgorzata A Domagalska Suman Rijal Narayan Raj Bhattarai Ilse Maes Mandy Sanders James A Cotton Pieter Meysman Kris Laukens Jean-Claude Dujardin

Infect Genet Evol 2018 08 19;62:170-178. Epub 2018 Apr 19.

Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.meegid.2018.04.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6261844PMC
August 2018

Genetic Diversity of Cryptosporidium hominis in a Bangladeshi Community as Revealed by Whole-Genome Sequencing.

Authors:
Carol A Gilchrist James A Cotton Cecelia Burkey Tuhinur Arju Allissia Gilmartin Ye Lin Emtiaz Ahmed Kevin Steiner Masud Alam Shahnawaz Ahmed Guy Robinson Sultan Uz Zaman Mamun Kabir Mandy Sanders Rachel M Chalmers Tahmeed Ahmed Jennie Z Ma Rashidul Haque Abu S G Faruque Matthew Berriman William A Petri

J Infect Dis 2018 06;218(2):259-264

Department of Medicine, University of Virginia, Charlottesville.

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http://dx.doi.org/10.1093/infdis/jiy121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009673PMC
June 2018

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

Authors:
Thomas D Otto Aude Gilabert Thomas Crellen Ulrike Böhme Céline Arnathau Mandy Sanders Samuel O Oyola Alain Prince Okouga Larson Boundenga Eric Willaume Barthélémy Ngoubangoye Nancy Diamella Moukodoum Christophe Paupy Patrick Durand Virginie Rougeron Benjamin Ollomo François Renaud Chris Newbold Matthew Berriman Franck Prugnolle

Nat Microbiol 2018 06 21;3(6):687-697. Epub 2018 May 21.

Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD224-UM, Montpellier, France.

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http://dx.doi.org/10.1038/s41564-018-0162-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985962PMC
June 2018

Long read assemblies of geographically dispersed isolates reveal highly structured subtelomeres.

Authors:
Thomas D Otto Ulrike Böhme Mandy Sanders Adam Reid Ellen I Bruske Craig W Duffy Pete C Bull Richard D Pearson Abdirahman Abdi Sandra Dimonte Lindsay B Stewart Susana Campino Mihir Kekre William L Hamilton Antoine Claessens Sarah K Volkman Daouda Ndiaye Alfred Amambua-Ngwa Mahamadou Diakite Rick M Fairhurst David J Conway Matthias Franck Chris I Newbold Matt Berriman

Wellcome Open Res 2018 3;3:52. Epub 2018 May 3.

Wellcome Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.14571.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964635PMC
May 2018

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals.

Authors:
Ulrike Böhme Thomas D Otto James A Cotton Sascha Steinbiss Mandy Sanders Samuel O Oyola Antoine Nicot Sylvain Gandon Kailash P Patra Colin Herd Ellen Bushell Katarzyna K Modrzynska Oliver Billker Joseph M Vinetz Ana Rivero Chris I Newbold Matthew Berriman

Genome Res 2018 04 2;28(4):547-560. Epub 2018 Mar 2.

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

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http://dx.doi.org/10.1101/gr.218123.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880244PMC
April 2018

and reference genomes highlight genome structure and gene evolution in the subgenus.

Authors:
Simone Coughlan Ali Shirley Taylor Eoghan Feane Mandy Sanders Gabriele Schonian James A Cotton Tim Downing

R Soc Open Sci 2018 Apr 25;5(4):172212. Epub 2018 Apr 25.

School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Republic of Ireland.

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http://dx.doi.org/10.1098/rsos.172212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5936940PMC
April 2018

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.

Authors:
Adam J Reid Arthur M Talman Hayley M Bennett Ana R Gomes Mandy J Sanders Christopher J R Illingworth Oliver Billker Matthew Berriman Mara Kn Lawniczak

Elife 2018 03 27;7. Epub 2018 Mar 27.

Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom.

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http://dx.doi.org/10.7554/eLife.33105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871331PMC
March 2018

Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival.

Authors:
Arie Zackay James A Cotton Mandy Sanders Asrat Hailu Abedelmajeed Nasereddin Alon Warburg Charles L Jaffe

PLoS Genet 2018 01 9;14(1):e1007133. Epub 2018 Jan 9.

Dept Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious & Tropical Diseases, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.

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http://dx.doi.org/10.1371/journal.pgen.1007133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777657PMC
January 2018

Gene Expression in Is Regulated Predominantly by Gene Dosage.

Authors:
Stefano A Iantorno Caroline Durrant Asis Khan Mandy J Sanders Stephen M Beverley Wesley C Warren Matthew Berriman David L Sacks James A Cotton Michael E Grigg

mBio 2017 09 12;8(5). Epub 2017 Sep 12.

Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/mBio.01393-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596349PMC
September 2017

Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine.

Authors:
Gavin G Rutledge Ian Marr G Khai Lin Huang Sarah Auburn Jutta Marfurt Mandy Sanders Nicholas J White Matthew Berriman Chris I Newbold Nicholas M Anstey Thomas D Otto Ric N Price

Emerg Infect Dis 2017 08 15;23(8):1300-1307. Epub 2017 Aug 15.

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http://dx.doi.org/10.3201/eid2308.161582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547787PMC
August 2017

An improved genome assembly reveals an unexpected methyltransferase gene expansion.

Authors:
Erica M Pasini Ulrike Böhme Gavin G Rutledge Annemarie Voorberg-Van der Wel Mandy Sanders Matt Berriman Clemens Hm Kocken Thomas Dan Otto

Wellcome Open Res 2017 16;2:42. Epub 2017 Jun 16.

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

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http://dx.doi.org/10.12688/wellcomeopenres.11864.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500898PMC
June 2017

Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes.

Authors:
Annelies Mondelaers Maria P Sanchez-Cañete Sarah Hendrickx Eline Eberhardt Raquel Garcia-Hernandez Laurence Lachaud James Cotton Mandy Sanders Bart Cuypers Hideo Imamura Jean-Claude Dujardin Peter Delputte Paul Cos Guy Caljon Francisco Gamarro Santiago Castanys Louis Maes

PLoS One 2016 28;11(4):e0154101. Epub 2016 Apr 28.

Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154101PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849676PMC
March 2017

-Independent Treatment Failure in Four Imported Cases of Plasmodium falciparum Malaria Treated with Artemether-Lumefantrine in the United Kingdom.

Authors:
Colin J Sutherland Paul Lansdell Mandy Sanders Julian Muwanguzi Donelly A van Schalkwyk Harparkash Kaur Debbie Nolder Julie Tucker Hayley M Bennett Thomas D Otto Matthew Berriman Trupti A Patel Roderick Lynn Effrossyni Gkrania-Klotsas Peter L Chiodini

Antimicrob Agents Chemother 2017 03 23;61(3). Epub 2017 Feb 23.

Public Health England Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.1128/AAC.02382-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328508PMC
March 2017

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania.

Authors:
Simone Coughlan Peter Mulhair Mandy Sanders Gabriele Schonian James A Cotton Tim Downing

Sci Rep 2017 03 3;7:43747. Epub 2017 Mar 3.

School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Ireland.

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http://dx.doi.org/10.1038/srep43747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335649PMC
March 2017

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.

Authors:
Gavin G Rutledge Ulrike Böhme Mandy Sanders Adam J Reid James A Cotton Oumou Maiga-Ascofare Abdoulaye A Djimdé Tobias O Apinjoh Lucas Amenga-Etego Magnus Manske John W Barnwell François Renaud Benjamin Ollomo Franck Prugnolle Nicholas M Anstey Sarah Auburn Ric N Price James S McCarthy Dominic P Kwiatkowski Chris I Newbold Matthew Berriman Thomas D Otto

Nature 2017 02 25;542(7639):101-104. Epub 2017 Jan 25.

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

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http://dx.doi.org/10.1038/nature21038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326575PMC
February 2017

Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection.

Authors:
Thibaut Brugat Adam James Reid Jingwen Lin Deirdre Cunningham Irene Tumwine Garikai Kushinga Sarah McLaughlin Philip Spence Ulrike Böhme Mandy Sanders Solomon Conteh Ellen Bushell Tom Metcalf Oliver Billker Patrick E Duffy Chris Newbold Matthew Berriman Jean Langhorne

Nat Microbiol 2017 Feb 6;2:16276. Epub 2017 Feb 6.

The Francis Crick institute, London NW1 1AT, UK.

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http://dx.doi.org/10.1038/nmicrobiol.2016.276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373435PMC
February 2017

Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil.

Authors:
Hugo O Valdivia Laila V Almeida Bruno M Roatt João Luís Reis-Cunha Agnes Antônia Sampaio Pereira Celia Gontijo Ricardo Toshio Fujiwara Alexandre B Reis Mandy J Sanders James A Cotton Daniella C Bartholomeu

Sci Rep 2017 01 16;7:40804. Epub 2017 Jan 16.

Universidade Federal de Minas Gerais, Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.

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http://dx.doi.org/10.1038/srep40804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238499PMC
January 2017

A new reference sequence with improved assembly of the subtelomeres reveals an abundance of genes.

Authors:
Sarah Auburn Ulrike Böhme Sascha Steinbiss Hidayat Trimarsanto Jessica Hostetler Mandy Sanders Qi Gao Francois Nosten Chris I Newbold Matthew Berriman Ric N Price Thomas D Otto

Wellcome Open Res 2016 Nov 15;1. Epub 2016 Nov 15.

Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.9876.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172418PMC
November 2016

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax.

Authors:
Andrew P Jackson Sophie Goyard Dong Xia Bernardo J Foth Mandy Sanders Jonathan M Wastling Paola Minoprio Matthew Berriman

PLoS Negl Trop Dis 2015 12;9(8):e0003975. Epub 2015 Aug 12.

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

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http://dx.doi.org/10.1371/journal.pntd.0003975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534299PMC
April 2016

Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

Authors:
Hideo Imamura Tim Downing Frederik Van den Broeck Mandy J Sanders Suman Rijal Shyam Sundar An Mannaert Manu Vanaerschot Maya Berg Géraldine De Muylder Franck Dumetz Bart Cuypers Ilse Maes Malgorzata Domagalska Saskia Decuypere Keshav Rai Surendra Uranw Narayan Raj Bhattarai Basudha Khanal Vijay Kumar Prajapati Smriti Sharma Olivia Stark Gabriele Schönian Harry P De Koning Luca Settimo Benoit Vanhollebeke Syamal Roy Bart Ostyn Marleen Boelaert Louis Maes Matthew Berriman Jean-Claude Dujardin James A Cotton

Elife 2016 Mar 22;5. Epub 2016 Mar 22.

Wellcome Trust Sanger Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.7554/eLife.12613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772PMC
March 2016

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.

Authors:
Andrew P Jackson Thomas D Otto Martin Aslett Stuart D Armstrong Frederic Bringaud Alexander Schlacht Catherine Hartley Mandy Sanders Jonathan M Wastling Joel B Dacks Alvaro Acosta-Serrano Mark C Field Michael L Ginger Matthew Berriman

Curr Biol 2016 Jan 24;26(2):161-172. Epub 2015 Dec 24.

Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1016/j.cub.2015.11.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728078PMC
January 2016

A genome wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya.

Authors:
Jason P Wendler John Okombo Roberto Amato Olivo Miotto Steven M Kiara Leah Mwai Lewa Pole John O'Brien Magnus Manske Dan Alcock Eleanor Drury Mandy Sanders Samuel O Oyola Cinzia Malangone Dushyanth Jyothi Alistair Miles Kirk A Rockett Bronwyn L MacInnis Kevin Marsh Philip Bejon Alexis Nzila Dominic P Kwiatkowski

PLoS One 2014 8;9(5):e96486. Epub 2014 May 8.

Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096486PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014544PMC
October 2015

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Authors:
Adam J Reid Damer P Blake Hifzur R Ansari Karen Billington Hilary P Browne Josephine Bryant Matt Dunn Stacy S Hung Fumiya Kawahara Diego Miranda-Saavedra Tareq B Malas Tobias Mourier Hardeep Naghra Mridul Nair Thomas D Otto Neil D Rawlings Pierre Rivailler Alejandro Sanchez-Flores Mandy Sanders Chandra Subramaniam Yea-Ling Tay Yong Woo Xikun Wu Bart Barrell Paul H Dear Christian Doerig Arthur Gruber Alasdair C Ivens John Parkinson Marie-Adèle Rajandream Martin W Shirley Kiew-Lian Wan Matthew Berriman Fiona M Tomley Arnab Pain

Genome Res 2014 Oct 11;24(10):1676-85. Epub 2014 Jul 11.

Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia;

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http://dx.doi.org/10.1101/gr.168955.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199364PMC
October 2014

A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

Authors:
Thomas D Otto Ulrike Böhme Andrew P Jackson Martin Hunt Blandine Franke-Fayard Wieteke A M Hoeijmakers Agnieszka A Religa Lauren Robertson Mandy Sanders Solabomi A Ogun Deirdre Cunningham Annette Erhart Oliver Billker Shahid M Khan Hendrik G Stunnenberg Jean Langhorne Anthony A Holder Andrew P Waters Chris I Newbold Arnab Pain Matthew Berriman Chris J Janse

BMC Biol 2014 Oct 30;12:86. Epub 2014 Oct 30.

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http://dx.doi.org/10.1186/s12915-014-0086-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242472PMC
October 2014

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

Authors:
Thomas D Otto Julian C Rayner Ulrike Böhme Arnab Pain Natasha Spottiswoode Mandy Sanders Michael Quail Benjamin Ollomo François Renaud Alan W Thomas Franck Prugnolle David J Conway Chris Newbold Matthew Berriman

Nat Commun 2014 Sep 9;5:4754. Epub 2014 Sep 9.

1] Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK [2].

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http://dx.doi.org/10.1038/ncomms5754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166903PMC
September 2014

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

Authors:
Andrew P Jackson Thomas D Otto Alistair Darby Abhinay Ramaprasad Dong Xia Ignacio Eduardo Echaide Marisa Farber Sunayna Gahlot John Gamble Dinesh Gupta Yask Gupta Louise Jackson Laurence Malandrin Tareq B Malas Ehab Moussa Mridul Nair Adam J Reid Mandy Sanders Jyotsna Sharma Alan Tracey Mike A Quail William Weir Jonathan M Wastling Neil Hall Peter Willadsen Klaus Lingelbach Brian Shiels Andy Tait Matt Berriman David R Allred Arnab Pain

Nucleic Acids Res 2014 Jun 5;42(11):7113-31. Epub 2014 May 5.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gku322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066756PMC
June 2014

Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

Authors:
Matthew B Rogers Tim Downing Barbara A Smith Hideo Imamura Mandy Sanders Milena Svobodova Petr Volf Matthew Berriman James A Cotton Deborah F Smith

PLoS Genet 2014 Jan 16;10(1):e1004092. Epub 2014 Jan 16.

Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894156PMC
January 2014

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.

Authors:
Olivo Miotto Jacob Almagro-Garcia Magnus Manske Bronwyn Macinnis Susana Campino Kirk A Rockett Chanaki Amaratunga Pharath Lim Seila Suon Sokunthea Sreng Jennifer M Anderson Socheat Duong Chea Nguon Char Meng Chuor David Saunders Youry Se Chantap Lon Mark M Fukuda Lucas Amenga-Etego Abraham V O Hodgson Victor Asoala Mallika Imwong Shannon Takala-Harrison François Nosten Xin-Zhuan Su Pascal Ringwald Frédéric Ariey Christiane Dolecek Tran Tinh Hien Maciej F Boni Cao Quang Thai Alfred Amambua-Ngwa David J Conway Abdoulaye A Djimdé Ogobara K Doumbo Issaka Zongo Jean-Bosco Ouedraogo Daniel Alcock Eleanor Drury Sarah Auburn Oliver Koch Mandy Sanders Christina Hubbart Gareth Maslen Valentin Ruano-Rubio Dushyanth Jyothi Alistair Miles John O'Brien Chris Gamble Samuel O Oyola Julian C Rayner Chris I Newbold Matthew Berriman Chris C A Spencer Gilean McVean Nicholas P Day Nicholas J White Delia Bethell Arjen M Dondorp Christopher V Plowe Rick M Fairhurst Dominic P Kwiatkowski

Nat Genet 2013 Jun 28;45(6):648-55. Epub 2013 Apr 28.

Medical Research Council MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/ng.2624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807790PMC
June 2013

Vector transmission regulates immune control of Plasmodium virulence.

Authors:
Philip J Spence William Jarra Prisca Lévy Adam J Reid Lia Chappell Thibaut Brugat Mandy Sanders Matthew Berriman Jean Langhorne

Nature 2013 Jun 29;498(7453):228-31. Epub 2013 May 29.

Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1038/nature12231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784817PMC
June 2013

Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates.

Authors:
Jue Ning Thomas D Otto Claudia Pfander Frank Schwach Mathieu Brochet Ellen Bushell David Goulding Mandy Sanders Paul A Lefebvre Jimin Pei Nick V Grishin Gary Vanderlaan Oliver Billker William J Snell

Genes Dev 2013 May;27(10):1198-215

Department of Cell Biology, University of Texas Southwestern Medical School, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1101/gad.212746.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672651PMC
May 2013

REAPR: a universal tool for genome assembly evaluation.

Authors:
Martin Hunt Taisei Kikuchi Mandy Sanders Chris Newbold Matthew Berriman Thomas D Otto

Genome Biol 2013 May 27;14(5):R47. Epub 2013 May 27.

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http://dx.doi.org/10.1186/gb-2013-14-5-r47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798757PMC
May 2013

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.

Authors:
Adam James Reid Sarah J Vermont James A Cotton David Harris Grant A Hill-Cawthorne Stephanie Könen-Waisman Sophia M Latham Tobias Mourier Rebecca Norton Michael A Quail Mandy Sanders Dhanasekaran Shanmugam Amandeep Sohal James D Wasmuth Brian Brunk Michael E Grigg Jonathan C Howard John Parkinson David S Roos Alexander J Trees Matthew Berriman Arnab Pain Jonathan M Wastling

PLoS Pathog 2012 22;8(3):e1002567. Epub 2012 Mar 22.

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

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http://dx.doi.org/10.1371/journal.ppat.1002567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310773PMC
July 2012

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.

Authors:
Magnus Manske Olivo Miotto Susana Campino Sarah Auburn Jacob Almagro-Garcia Gareth Maslen Jack O'Brien Abdoulaye Djimde Ogobara Doumbo Issaka Zongo Jean-Bosco Ouedraogo Pascal Michon Ivo Mueller Peter Siba Alexis Nzila Steffen Borrmann Steven M Kiara Kevin Marsh Hongying Jiang Xin-Zhuan Su Chanaki Amaratunga Rick Fairhurst Duong Socheat Francois Nosten Mallika Imwong Nicholas J White Mandy Sanders Elisa Anastasi Dan Alcock Eleanor Drury Samuel Oyola Michael A Quail Daniel J Turner Valentin Ruano-Rubio Dushyanth Jyothi Lucas Amenga-Etego Christina Hubbart Anna Jeffreys Kate Rowlands Colin Sutherland Cally Roper Valentina Mangano David Modiano John C Tan Michael T Ferdig Alfred Amambua-Ngwa David J Conway Shannon Takala-Harrison Christopher V Plowe Julian C Rayner Kirk A Rockett Taane G Clark Chris I Newbold Matthew Berriman Bronwyn MacInnis Dominic P Kwiatkowski

Nature 2012 Jul;487(7407):375-9

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

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http://dx.doi.org/10.1038/nature11174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909PMC
July 2012

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Authors:
Claudio U Köser Matthew T G Holden Matthew J Ellington Edward J P Cartwright Nicholas M Brown Amanda L Ogilvy-Stuart Li Yang Hsu Claire Chewapreecha Nicholas J Croucher Simon R Harris Mandy Sanders Mark C Enright Gordon Dougan Stephen D Bentley Julian Parkhill Louise J Fraser Jason R Betley Ole B Schulz-Trieglaff Geoffrey P Smith Sharon J Peacock

N Engl J Med 2012 Jun;366(24):2267-75

University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1056/NEJMoa1109910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715836PMC
June 2012

Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids.

Authors:
Bruce Humphrey Nicholas R Thomson Christopher M Thomas Karen Brooks Mandy Sanders Anne A Delsol John M Roe Peter M Bennett Virve I Enne

BMC Microbiol 2012 Apr 4;12:53. Epub 2012 Apr 4.

Bristol Centre for Antimicrobial Research, Department of Cellular and Molecular Medicine, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.

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http://dx.doi.org/10.1186/1471-2180-12-53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347995PMC
April 2012

Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

Authors:
Helena M B Seth-Smith Maria C Fookes Chinyere K Okoro Stephen Baker Simon R Harris Paul Scott Derek Pickard Michael A Quail Carol Churcher Mandy Sanders Johan Harmse Gordon Dougan Julian Parkhill Nicholas R Thomson

J Bacteriol 2012 Mar 13;194(6):1494-504. Epub 2012 Jan 13.

Pathogen Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1128/JB.06403-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294861PMC
March 2012

Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.

Authors:
Andrew P Jackson Andrew Berry Martin Aslett Harriet C Allison Peter Burton Jana Vavrova-Anderson Robert Brown Hilary Browne Nicola Corton Heidi Hauser John Gamble Ruth Gilderthorp Lucio Marcello Jacqueline McQuillan Thomas D Otto Michael A Quail Mandy J Sanders Andries van Tonder Michael L Ginger Mark C Field J David Barry Christiane Hertz-Fowler Matthew Berriman

Proc Natl Acad Sci U S A 2012 Feb 13;109(9):3416-21. Epub 2012 Feb 13.

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

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http://dx.doi.org/10.1073/pnas.1117313109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295286PMC
February 2012

Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex.

Authors:
Tim Downing Olivia Stark Manu Vanaerschot Hideo Imamura Mandy Sanders Saskia Decuypere Simonne de Doncker Ilse Maes Suman Rijal Shyam Sundar Jean-Claude Dujardin Matthew Berriman Gabriele Schönian

Infect Genet Evol 2012 Jan 20;12(1):149-59. Epub 2011 Nov 20.

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

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http://dx.doi.org/10.1016/j.meegid.2011.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315668PMC
January 2012

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae.

Authors:
Bärbel Stecher Rémy Denzler Lisa Maier Florian Bernet Mandy J Sanders Derek J Pickard Manja Barthel Astrid M Westendorf Karen A Krogfelt Alan W Walker Martin Ackermann Ulrich Dobrindt Nicholas R Thomson Wolf-Dietrich Hardt

Proc Natl Acad Sci U S A 2012 Jan 9;109(4):1269-74. Epub 2012 Jan 9.

Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland.

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http://dx.doi.org/10.1073/pnas.1113246109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268327PMC
January 2012

Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients.

Authors:
Timothy Robinson Susana G Campino Sarah Auburn Samuel A Assefa Spencer D Polley Magnus Manske Bronwyn MacInnis Kirk A Rockett Gareth L Maslen Mandy Sanders Michael A Quail Peter L Chiodini Dominic P Kwiatkowski Taane G Clark Colin J Sutherland

PLoS One 2011 11;6(8):e23204. Epub 2011 Aug 11.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023204PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154926PMC
December 2011

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.

Authors:
Tim Downing Hideo Imamura Saskia Decuypere Taane G Clark Graham H Coombs James A Cotton James D Hilley Simonne de Doncker Ilse Maes Jeremy C Mottram Mike A Quail Suman Rijal Mandy Sanders Gabriele Schönian Olivia Stark Shyam Sundar Manu Vanaerschot Christiane Hertz-Fowler Jean-Claude Dujardin Matthew Berriman

Genome Res 2011 Dec 28;21(12):2143-56. Epub 2011 Oct 28.

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

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http://dx.doi.org/10.1101/gr.123430.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227103PMC
December 2011

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania.

Authors:
Matthew B Rogers James D Hilley Nicholas J Dickens Jon Wilkes Paul A Bates Daniel P Depledge David Harris Yerim Her Pawel Herzyk Hideo Imamura Thomas D Otto Mandy Sanders Kathy Seeger Jean-Claude Dujardin Matthew Berriman Deborah F Smith Christiane Hertz-Fowler Jeremy C Mottram

Genome Res 2011 Dec 28;21(12):2129-42. Epub 2011 Oct 28.

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

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http://dx.doi.org/10.1101/gr.122945.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227102PMC
December 2011

Salmonella bongori provides insights into the evolution of the Salmonellae.

Authors:
Maria Fookes Gunnar N Schroeder Gemma C Langridge Carlos J Blondel Caterina Mammina Thomas R Connor Helena Seth-Smith Georgios S Vernikos Keith S Robinson Mandy Sanders Nicola K Petty Robert A Kingsley Andreas J Bäumler Sean-Paul Nuccio Inés Contreras Carlos A Santiviago Duncan Maskell Paul Barrow Tom Humphrey Antonino Nastasi Mark Roberts Gad Frankel Julian Parkhill Gordon Dougan Nicholas R Thomson

PLoS Pathog 2011 Aug 18;7(8):e1002191. Epub 2011 Aug 18.

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

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http://dx.doi.org/10.1371/journal.ppat.1002191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158058PMC
August 2011

The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.

Authors:
Michal Letek Patricia González Iain Macarthur Héctor Rodríguez Tom C Freeman Ana Valero-Rello Mónica Blanco Tom Buckley Inna Cherevach Ruth Fahey Alexia Hapeshi Jolyon Holdstock Desmond Leadon Jesús Navas Alain Ocampo Michael A Quail Mandy Sanders Mariela M Scortti John F Prescott Ursula Fogarty Wim G Meijer Julian Parkhill Stephen D Bentley José A Vázquez-Boland

PLoS Genet 2010 Sep 30;6(9):e1001145. Epub 2010 Sep 30.

Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1001145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947987PMC
September 2010

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

Authors:
Thomas D Otto Mandy Sanders Matthew Berriman Chris Newbold

Bioinformatics 2010 Jul 18;26(14):1704-7. Epub 2010 Jun 18.

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

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http://dx.doi.org/10.1093/bioinformatics/btq269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894513PMC
July 2010

Characterization of a novel wood mouse virus related to murid herpesvirus 4.

Authors:
David J Hughes Anja Kipar Steven G Milligan Charles Cunningham Mandy Sanders Michael A Quail Marie-Adele Rajandream Stacey Efstathiou Rory J Bowden Claude Chastel Malcolm Bennett Jeffery T Sample Bart Barrell Andrew J Davison James P Stewart

J Gen Virol 2010 Apr 25;91(Pt 4):867-79. Epub 2009 Nov 25.

School of Infection and Host Defence, University of Liverpool, Liverpool L69 3GA, UK.

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http://dx.doi.org/10.1099/vir.0.017327-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888160PMC
April 2010

The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

Authors:
Andrew P Jackson Mandy Sanders Andrew Berry Jacqueline McQuillan Martin A Aslett Michael A Quail Bridget Chukualim Paul Capewell Annette MacLeod Sara E Melville Wendy Gibson J David Barry Matthew Berriman Christiane Hertz-Fowler

PLoS Negl Trop Dis 2010 Apr 13;4(4):e658. Epub 2010 Apr 13.

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

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http://dx.plos.org/10.1371/journal.pntd.0000658
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http://dx.doi.org/10.1371/journal.pntd.0000658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854126PMC
April 2010

Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense.

Authors:
Jared R Helm Christiane Hertz-Fowler Martin Aslett Matthew Berriman Mandy Sanders Michael A Quail Marcelo B Soares Maria F Bonaldo Tatsuya Sakurai Noboru Inoue John E Donelson

Mol Biochem Parasitol 2009 Nov 25;168(1):34-42. Epub 2009 Jun 25.

Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.

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http://dx.doi.org/10.1016/j.molbiopara.2009.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741298PMC
November 2009

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.

Authors:
Matthew T G Holden Heidi Hauser Mandy Sanders Thi Hoa Ngo Inna Cherevach Ann Cronin Ian Goodhead Karen Mungall Michael A Quail Claire Price Ester Rabbinowitsch Sarah Sharp Nicholas J Croucher Tran Bich Chieu Nguyen Thi Hoang Mai To Song Diep Nguyen Tran Chinh Michael Kehoe James A Leigh Philip N Ward Christopher G Dowson Adrian M Whatmore Neil Chanter Pernille Iversen Marcelo Gottschalk Josh D Slater Hilde E Smith Brian G Spratt Jianguo Xu Changyun Ye Stephen Bentley Barclay G Barrell Constance Schultsz Duncan J Maskell Julian Parkhill

PLoS One 2009 Jul 15;4(7):e6072. Epub 2009 Jul 15.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006072PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705793PMC
July 2009

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.

Authors:
Iwanka Kozarewa Zemin Ning Michael A Quail Mandy J Sanders Matthew Berriman Daniel J Turner

Nat Methods 2009 Apr 15;6(4):291-5. Epub 2009 Mar 15.

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

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http://www.nature.com/articles/nmeth.1311
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http://dx.doi.org/10.1038/nmeth.1311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664327PMC
April 2009

Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens.

Authors:
Matthew T G Holden Zoe Heather Romain Paillot Karen F Steward Katy Webb Fern Ainslie Thibaud Jourdan Nathalie C Bason Nancy E Holroyd Karen Mungall Michael A Quail Mandy Sanders Mark Simmonds David Willey Karen Brooks David M Aanensen Brian G Spratt Keith A Jolley Martin C J Maiden Michael Kehoe Neil Chanter Stephen D Bentley Carl Robinson Duncan J Maskell Julian Parkhill Andrew S Waller

PLoS Pathog 2009 Mar 27;5(3):e1000346. Epub 2009 Mar 27.

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

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http://dx.doi.org/10.1371/journal.ppat.1000346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654543PMC
March 2009

Telomeric expression sites are highly conserved in Trypanosoma brucei.

Authors:
Christiane Hertz-Fowler Luisa M Figueiredo Michael A Quail Marion Becker Andrew Jackson Nathalie Bason Karen Brooks Carol Churcher Samah Fahkro Ian Goodhead Paul Heath Magdalena Kartvelishvili Karen Mungall David Harris Heidi Hauser Mandy Sanders David Saunders Kathy Seeger Sarah Sharp Jesse E Taylor Danielle Walker Brian White Rosanna Young George A M Cross Gloria Rudenko J David Barry Edward J Louis Matthew Berriman

PLoS One 2008 27;3(10):e3527. Epub 2008 Oct 27.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003527PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567434PMC
January 2009

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

Authors:
Nicholas R Thomson Debra J Clayton Daniel Windhorst Georgios Vernikos Susanne Davidson Carol Churcher Michael A Quail Mark Stevens Michael A Jones Michael Watson Andy Barron Abigail Layton Derek Pickard Robert A Kingsley Alex Bignell Louise Clark Barbara Harris Doug Ormond Zahra Abdellah Karen Brooks Inna Cherevach Tracey Chillingworth John Woodward Halina Norberczak Angela Lord Claire Arrowsmith Kay Jagels Sharon Moule Karen Mungall Mandy Sanders Sally Whitehead Jose A Chabalgoity Duncan Maskell Tom Humphrey Mark Roberts Paul A Barrow Gordon Dougan Julian Parkhill

Genome Res 2008 Oct 26;18(10):1624-37. Epub 2008 Jun 26.

The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1101/gr.077404.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556274PMC
October 2008

Genome evolution of Wolbachia strain wPip from the Culex pipiens group.

Authors:
Lisa Klasson Thomas Walker Mohammed Sebaihia Mandy J Sanders Michael A Quail Angela Lord Susanne Sanders Julie Earl Scott L O'Neill Nicholas Thomson Steven P Sinkins Julian Parkhill

Mol Biol Evol 2008 Sep 12;25(9):1877-87. Epub 2008 Jun 12.

Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msn133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515876PMC
September 2008

Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids.

Authors:
Michal Letek Alain A Ocampo-Sosa Mandy Sanders Ursula Fogarty Tom Buckley Desmond P Leadon Patricia González Mariela Scortti Wim G Meijer Julian Parkhill Stephen Bentley José A Vázquez-Boland

J Bacteriol 2008 Sep 7;190(17):5797-805. Epub 2008 Jul 7.

Division of Microbial Pathogenesis, Centre for Infectious Diseases, Ashworth Laboratories, King's Buildings, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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http://jb.asm.org/cgi/doi/10.1128/JB.00468-08
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http://dx.doi.org/10.1128/JB.00468-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519538PMC
September 2008

The genome of Rhizobium leguminosarum has recognizable core and accessory components.

Authors:
J Peter W Young Lisa C Crossman Andrew W B Johnston Nicholas R Thomson Zara F Ghazoui Katherine H Hull Margaret Wexler Andrew R J Curson Jonathan D Todd Philip S Poole Tim H Mauchline Alison K East Michael A Quail Carol Churcher Claire Arrowsmith Inna Cherevach Tracey Chillingworth Kay Clarke Ann Cronin Paul Davis Audrey Fraser Zahra Hance Heidi Hauser Kay Jagels Sharon Moule Karen Mungall Halina Norbertczak Ester Rabbinowitsch Mandy Sanders Mark Simmonds Sally Whitehead Julian Parkhill

Genome Biol 2006 26;7(4):R34. Epub 2006 Apr 26.

Department of Biology, University of York, York, UK.

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http://dx.doi.org/10.1186/gb-2006-7-4-r34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557990PMC
April 2008

Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids.

Authors:
Carlos Revilla M Pilar Garcillán-Barcia Raúl Fernández-López Nicholas R Thomson Mandy Sanders Martin Cheung Christopher M Thomas Fernando de la Cruz

Antimicrob Agents Chemother 2008 Apr 11;52(4):1472-80. Epub 2008 Feb 11.

Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, 39011 Santander, Spain.

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http://dx.doi.org/10.1128/AAC.00982-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292564PMC
April 2008

Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group.

Authors:
Thomas Walker Lisa Klasson Mohammed Sebaihia Mandy J Sanders Nicholas R Thomson Julian Parkhill Steven P Sinkins

BMC Biol 2007 Sep 20;5:39. Epub 2007 Sep 20.

Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1186/1741-7007-5-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045654PMC
September 2007

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.

Authors:
Mohammed Sebaihia Michael W Peck Nigel P Minton Nicholas R Thomson Matthew T G Holden Wilfrid J Mitchell Andrew T Carter Stephen D Bentley David R Mason Lisa Crossman Catherine J Paul Alasdair Ivens Marjon H J Wells-Bennik Ian J Davis Ana M Cerdeño-Tárraga Carol Churcher Michael A Quail Tracey Chillingworth Theresa Feltwell Audrey Fraser Ian Goodhead Zahra Hance Kay Jagels Natasha Larke Mark Maddison Sharon Moule Karen Mungall Halina Norbertczak Ester Rabbinowitsch Mandy Sanders Mark Simmonds Brian White Sally Whithead Julian Parkhill

Genome Res 2007 Jul 22;17(7):1082-92. Epub 2007 May 22.

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

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http://dx.doi.org/10.1101/gr.6282807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899119PMC
July 2007

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

Authors:
Nicholas R Thomson Sarah Howard Brendan W Wren Matthew T G Holden Lisa Crossman Gregory L Challis Carol Churcher Karen Mungall Karen Brooks Tracey Chillingworth Theresa Feltwell Zahra Abdellah Heidi Hauser Kay Jagels Mark Maddison Sharon Moule Mandy Sanders Sally Whitehead Michael A Quail Gordon Dougan Julian Parkhill Michael B Prentice

PLoS Genet 2006 Dec;2(12):e206

The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.0020206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698947PMC
December 2006

The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate.

Authors:
Barbara Froehlich Julian Parkhill Mandy Sanders Michael A Quail June R Scott

J Bacteriol 2005 Sep;187(18):6509-16

Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.

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http://dx.doi.org/10.1128/JB.187.18.6509-6516.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236633PMC
September 2005

The genome of the African trypanosome Trypanosoma brucei.

Authors:
Matthew Berriman Elodie Ghedin Christiane Hertz-Fowler Gaëlle Blandin Hubert Renauld Daniella C Bartholomeu Nicola J Lennard Elisabet Caler Nancy E Hamlin Brian Haas Ulrike Böhme Linda Hannick Martin A Aslett Joshua Shallom Lucio Marcello Lihua Hou Bill Wickstead U Cecilia M Alsmark Claire Arrowsmith Rebecca J Atkin Andrew J Barron Frederic Bringaud Karen Brooks Mark Carrington Inna Cherevach Tracey-Jane Chillingworth Carol Churcher Louise N Clark Craig H Corton Ann Cronin Rob M Davies Jonathon Doggett Appolinaire Djikeng Tamara Feldblyum Mark C Field Audrey Fraser Ian Goodhead Zahra Hance David Harper Barbara R Harris Heidi Hauser Jessica Hostetler Al Ivens Kay Jagels David Johnson Justin Johnson Kristine Jones Arnaud X Kerhornou Hean Koo Natasha Larke Scott Landfear Christopher Larkin Vanessa Leech Alexandra Line Angela Lord Annette Macleod Paul J Mooney Sharon Moule David M A Martin Gareth W Morgan Karen Mungall Halina Norbertczak Doug Ormond Grace Pai Chris S Peacock Jeremy Peterson Michael A Quail Ester Rabbinowitsch Marie-Adele Rajandream Chris Reitter Steven L Salzberg Mandy Sanders Seth Schobel Sarah Sharp Mark Simmonds Anjana J Simpson Luke Tallon C Michael R Turner Andrew Tait Adrian R Tivey Susan Van Aken Danielle Walker David Wanless Shiliang Wang Brian White Owen White Sally Whitehead John Woodward Jennifer Wortman Mark D Adams T Martin Embley Keith Gull Elisabetta Ullu J David Barry Alan H Fairlamb Fred Opperdoes Barclay G Barrell John E Donelson Neil Hall Claire M Fraser Sara E Melville Najib M El-Sayed

Science 2005 Jul;309(5733):416-22

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

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http://dx.doi.org/10.1126/science.1112642DOI Listing
July 2005

The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.

Authors:
Nicholas R Thomson Corin Yeats Kenneth Bell Matthew T G Holden Stephen D Bentley Morag Livingstone Ana M Cerdeño-Tárraga Barbara Harris Jon Doggett Doug Ormond Karen Mungall Kay Clarke Theresa Feltwell Zahra Hance Mandy Sanders Michael A Quail Claire Price Bart G Barrell Julian Parkhill David Longbottom

Genome Res 2005 May 18;15(5):629-40. Epub 2005 Apr 18.

The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.3684805
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http://dx.doi.org/10.1101/gr.3684805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088291PMC
May 2005

Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses.

Authors:
Andrey V Karlyshev Olivia L Champion Carol Churcher Jean-Robert Brisson Harold C Jarrell Michel Gilbert Denis Brochu Frank St Michael Jianjun Li Warren W Wakarchuk Ian Goodhead Mandy Sanders Kim Stevens Brian White Julian Parkhill Brendan W Wren Christine M Szymanski

Mol Microbiol 2005 Jan;55(1):90-103

Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WCIE 7HT, UK.

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http://dx.doi.org/10.1111/j.1365-2958.2004.04374.xDOI Listing
January 2005

The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics.

Authors:
Matthew W Gilmour Nicholas R Thomson Mandy Sanders Julian Parkhill Diane E Taylor

Plasmid 2004 Nov;52(3):182-202

Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alta., Canada T6G 2R3.

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http://dx.doi.org/10.1016/j.plasmid.2004.06.006DOI Listing
November 2004

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

Authors:
Matthew T G Holden Richard W Titball Sharon J Peacock Ana M Cerdeño-Tárraga Timothy Atkins Lisa C Crossman Tyrone Pitt Carol Churcher Karen Mungall Stephen D Bentley Mohammed Sebaihia Nicholas R Thomson Nathalie Bason Ifor R Beacham Karen Brooks Katherine A Brown Nat F Brown Greg L Challis Inna Cherevach Tracy Chillingworth Ann Cronin Ben Crossett Paul Davis David DeShazer Theresa Feltwell Audrey Fraser Zahra Hance Heidi Hauser Simon Holroyd Kay Jagels Karen E Keith Mark Maddison Sharon Moule Claire Price Michael A Quail Ester Rabbinowitsch Kim Rutherford Mandy Sanders Mark Simmonds Sirirurg Songsivilai Kim Stevens Sarinna Tumapa Monkgol Vesaratchavest Sally Whitehead Corin Yeats Bart G Barrell Petra C F Oyston Julian Parkhill

Proc Natl Acad Sci U S A 2004 Sep 17;101(39):14240-5. Epub 2004 Sep 17.

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

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http://dx.doi.org/10.1073/pnas.0403302101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521101PMC
September 2004

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance.

Authors:
Matthew T G Holden Edward J Feil Jodi A Lindsay Sharon J Peacock Nicholas P J Day Mark C Enright Tim J Foster Catrin E Moore Laurence Hurst Rebecca Atkin Andrew Barron Nathalie Bason Stephen D Bentley Carol Chillingworth Tracey Chillingworth Carol Churcher Louise Clark Craig Corton Ann Cronin Jon Doggett Linda Dowd Theresa Feltwell Zahra Hance Barbara Harris Heidi Hauser Simon Holroyd Kay Jagels Keith D James Nicola Lennard Alexandra Line Rebecca Mayes Sharon Moule Karen Mungall Douglas Ormond Michael A Quail Ester Rabbinowitsch Kim Rutherford Mandy Sanders Sarah Sharp Mark Simmonds Kim Stevens Sally Whitehead Bart G Barrell Brian G Spratt Julian Parkhill

Proc Natl Acad Sci U S A 2004 Jun 22;101(26):9786-91. Epub 2004 Jun 22.

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

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http://dx.doi.org/10.1073/pnas.0402521101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC470752PMC
June 2004

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

Authors:
Julian Parkhill Mohammed Sebaihia Andrew Preston Lee D Murphy Nicholas Thomson David E Harris Matthew T G Holden Carol M Churcher Stephen D Bentley Karen L Mungall Ana M Cerdeño-Tárraga Louise Temple Keith James Barbara Harris Michael A Quail Mark Achtman Rebecca Atkin Steven Baker David Basham Nathalie Bason Inna Cherevach Tracey Chillingworth Matthew Collins Anne Cronin Paul Davis Jonathan Doggett Theresa Feltwell Arlette Goble Nancy Hamlin Heidi Hauser Simon Holroyd Kay Jagels Sampsa Leather Sharon Moule Halina Norberczak Susan O'Neil Doug Ormond Claire Price Ester Rabbinowitsch Simon Rutter Mandy Sanders David Saunders Katherine Seeger Sarah Sharp Mark Simmonds Jason Skelton Robert Squares Steven Squares Kim Stevens Louise Unwin Sally Whitehead Bart G Barrell Duncan J Maskell

Nat Genet 2003 Sep 10;35(1):32-40. Epub 2003 Aug 10.

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

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http://dx.doi.org/10.1038/ng1227DOI Listing
September 2003