J
Jim Stalker
Researcher at Wellcome Trust Sanger Institute
Publications - 35
Citations - 9710
Jim Stalker is an academic researcher from Wellcome Trust Sanger Institute. The author has contributed to research in topics: Malaria & Genome. The author has an hindex of 21, co-authored 35 publications receiving 8603 citations.
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Journal ArticleDOI
Spread of Artemisinin Resistance in Plasmodium falciparum Malaria
Elizabeth A. Ashley,Mehul Dhorda,Rick M. Fairhurst,Chanaki Amaratunga,Pharath Lim,Seila Suon,Sokunthea Sreng,Jennifer M. Anderson,Mao S,Sam B,Chantha Sopha,Char Meng Chuor,Chea Nguon,Siv Sovannaroth,Sasithon Pukrittayakamee,Podjanee Jittamala,Kesinee Chotivanich,K Chutasmit,C Suchatsoonthorn,R Runcharoen,Tran Tinh Hien,Nguyen Thuy-Nhien,Thanh Nv,Nguyen Hoan Phu,Ye Htut,Han Kt,Kyin Hla Aye,Olugbenga A. Mokuolu,Rasaq Olaosebikan,Olaleke Oluwasegun Folaranmi,Mayfong Mayxay,Maniphone Khanthavong,Bouasy Hongvanthong,Paul N. Newton,M A Onyamboko,Caterina I. Fanello,Antoinette Tshefu,Neelima Mishra,Neena Valecha,Aung Pyae Phyo,François Nosten,Yi P,Rupam Tripura,Steffen Borrmann,Mahfudh Bashraheil,Judy Peshu,M A Faiz,Aniruddha Ghose,M A Hossain,Rasheda Samad,M. R. Rahman,Manal Hasan,Ashraful Islam,Olivo Miotto,Roberto Amato,Bronwyn MacInnis,Jim Stalker,Dominic P. Kwiatkowski,Zbynek Bozdech,Atthanee Jeeyapant,Phaik Yeong Cheah,Tharisara Sakulthaew,Jeremy Chalk,Benjamas Intharabut,Kamolrat Silamut,Lee Sj,Benchawan Vihokhern,Chanon Kunasol,Mallika Imwong,Joel Tarning,Taylor Wj,Shunmay Yeung,Charles J. Woodrow,Jennifer A. Flegg,Debashish Das,Jennifer L. Smith,Meera Venkatesan,Christopher V. Plowe,Kasia Stepniewska,Philippe J Guerin,Arjen M. Dondorp,Nicholas P. J. Day,Nicholas J. White +82 more
TL;DR: Prolonged courses of artemisinin-based combination therapies are currently efficacious in areas where standard 3-day treatments are failing, and the incidence of pretreatment and post-treatment gametocytemia was higher among patients with slow parasite clearance, suggesting greater potential for transmission.
Journal ArticleDOI
The Ensembl genome database project
Tim Hubbard,Daniel Barker,Ewan Birney,Graham Cameron,Yuan Chen,Louise Clark,Tony Cox,James Cuff,Val Curwen,Thomas A. Down,Richard Durbin,Eduardo Eyras,James G. R. Gilbert,Martin Hammond,Lukasz Huminiecki,Arek Kasprzyk,Heikki Lehväslaiho,Philip Lijnzaad,Craig Melsopp,Emmanuel Mongin,Roger Pettett,Matthew Pocock,Simon C. Potter,Alistair G. Rust,Esther Schmidt,Stephen M. J. Searle,Guy Slater,James Smith,William Spooner,Arne Stabenau,Jim Stalker,Elia Stupka,Abel Ureta-Vidal,Imre Vastrik,Michele Clamp +34 more
TL;DR: The Ensembl database project provides a bioinformatics framework to organise biology around the sequences of large genomes and is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources.
Journal ArticleDOI
Mouse genomic variation and its effect on phenotypes and gene regulation
Thomas M. Keane,Leo Goodstadt,Petr Danecek,Michael A. White,Kim Wong,Binnaz Yalcin,Andreas Heger,Avigail Agam,Avigail Agam,Guy Slater,Martin Goodson,Nick Furlotte,Eleazar Eskin,Christoffer Nellåker,Helen Whitley,James Cleak,Deborah Janowitz,Deborah Janowitz,Polinka Hernandez-Pliego,Andrew Edwards,T G Belgard,Peter L. Oliver,Rebecca E. McIntyre,Amarjit Bhomra,Jérôme Nicod,Xiangchao Gan,Wei Yuan,L van der Weyden,Charles A. Steward,Sendu Bala,Jim Stalker,Richard Mott,Richard Durbin,Ian J. Jackson,Anne Czechanski,José Afonso Guerra-Assunção,Leah Rae Donahue,Laura G. Reinholdt,Bret A. Payseur,Chris P. Ponting,Ewan Birney,Jonathan Flint,David J. Adams +42 more
TL;DR: These sequences provide a starting point for a new era in the functional analysis of a key model organism and show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus.
Journal ArticleDOI
Mapping copy number variation by population-scale genome sequencing
Ryan E. Mills,Klaudia Walter,Chip Stewart,Robert E. Handsaker,Ken Chen,Can Alkan,Alexej Abyzov,Seungtai Yoon,Kai Ye,R. Keira Cheetham,Asif T. Chinwalla,Donald F. Conrad,Yutao Fu,Fabian Grubert,Iman Hajirasouliha,Fereydoun Hormozdiari,Lilia M. Iakoucheva,Zamin Iqbal,Shuli Kang,Jeffrey M. Kidd,Miriam K. Konkel,Joshua M. Korn,Ekta Khurana,Deniz Kural,Hugo Y. K. Lam,Jing Leng,Ruiqiang Li,Yingrui Li,Chang-Yun Lin,Ruibang Luo,Xinmeng Jasmine Mu,James Nemesh,Heather E. Peckham,Tobias Rausch,Aylwyn Scally,Xinghua Shi,Michael Strömberg,Adrian M. Sütz,Alexander E. Urban,Jerilyn A. Walker,Jiantao Wu,Yujun Zhang,Zhengdong D. Zhang,Mark A. Batzer,Li Ding,Gabor T. Marth,Gil McVean,Jonathan Sebat,Michael Snyder,Jun Wang,Jun Wang,Kenny Ye,Evan E. Eichler,Mark Gerstein,Matthew E. Hurles,Charles Lee,Steven A. McCarroll,Steven A. McCarroll,Jan O. Korbel,Francis S. Collins,D. L. Altshuler,Richard Durbin,Gonçalo R. Abecasis,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,F. M. De La Vega,Peter Donnelly,Michael Egholm,Paul Flicek,S. Gabriel,Richard A. Gibbs,Bartha Maria Knoppers,Eric S. Lander,Hans Lehrach,Elaine R. Mardis,Gilean McVean,Deborah A. Nickerson,Leena Peltonen,Alan J. Schafer,Stephen T. Sherry,Richard K. Wilson,David Rio Deiros,Michael L. Metzker,Donna Muzny,Jeffrey S. Reid,D Wheeler,Jingxiang Li,Min Jian,Guoqing Li,Huiqing Liang,Geng Tian,Bo Wang,Wei Wang,Huanming Yang,Xiuqing Zhang,Huisong Zheng,Lauren Ambrogio,Toby Bloom,Kristian Cibulskis,T. J. Fennell,David B. Jaffe,Erica Shefler,Carrie Sougnez,Niall Anthony Gormley,Sean Humphray,Zoya Kingsbury,P. Koko-Gonzales,Jennifer Stone,Kevin McKernan,Gianna Costa,Jeffrey K. Ichikawa,Cheng-Sheng Lee,Ralf Sudbrak,Tatjana Borodina,Andreas Dahl,Alexey N. Davydov,P. Marquardt,Florian Mertes,Wilfried Nietfeld,Philip Rosenstiel,Stuart L. Schreiber,Alexey Soldatov,Bernd Timmermann,M. Tolzmann,Jason P. Affourtit,D. Ashworth,S. Attiya,M. Bachorski,E. Buglione,A. Burke,A. Caprio,Christopher Celone,S. Clark,D. Conners,B. Desany,L. Gu,L. Guccione,K. Kao,A. Kebbel,J. Knowlton,M. Labrecque,L. McDade,Craig Elder Mealmaker,M. Minderman,A. Nawrocki,Faheem Niazi,K. Pareja,Ramenani Ravi K,D. Riches,W. Song,Cynthia L. Turcotte,S. Wang,David J. Dooling,Linnea Fulton,Robert S. Fulton,George M. Weinstock,James O. Burton,David M. Carter,Carol Churcher,Alison J. Coffey,Anthony J. Cox,A. Palotie,Michael A. Quail,Tara Skelly,Jim Stalker,Harold Swerdlow,Dan Turner,A. De Witte,S. Giles,Matthew N. Bainbridge,Danny Challis,Aniko Sabo,Fuli Yu,Jin Yu,Xiaodong Fang,Xiaosen Guo,Shuaishuai Tai,Honglong Wu,Xiaole Zheng,Yan Zhou,E. P. Garrison,Weichun Huang,Amit Indap,Wan-Ping Lee,Wen Fung Leong,Aaron R. Quinlan,Alistair Ward,Mark J. Daly,Mark A. DePristo,A. D. Ball,Eric Banks,Brian L. Browning,Kiran V. Garimella,Sharon R. Grossman,Megan Hanna,Christopher Hartl,Andrew Kernytsky,J. M. Korn,Heng Li,Jared Maguire,Aaron McKenna,James Nemesh,Anthony A. Philippakis,Ryan Poplin,Amanda J. Price,Manual Rivas,Pardis C. Sabeti,Stephen F. Schaffner,Ilya Shlyakhter,David Neil Cooper,Edward V. Ball,Matthew Mort,Adam Phillips,Peter D. Stenson,Vladimir Makarov,Carlos Bustamante,Adam R. Boyko,Jeremiah D. Degenhardt,Simon Gravel,Ryan N. Gutenkunst,Mark Kaganovich,Alon Keinan,Philippe Lacroute,Xin Ma,Alex Reynolds,Laura Clarke,Fiona Cunningham,Javier Herrero,S. Keenen,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Raffaella Smith,Vadim Zalunin,Xiangqun Zheng-Bradley,Adrian M. Stütz,Michael Bauer,Tony Cox,Michael A. Eberle,Terena James,Scott Kahn,Lucinda Murray,Fiona Hyland,Jonathan M. Manning,Stephen F. McLaughlin,Onur Sakarya,Yongming A. Sun,Eric F. Tsung,M. Albrecht,Vyacheslav Amstislavskiy,Ralf Herwig,Dmitri Parkhomchuk,Richa Agarwala,H. M. Khouri,Aleksandr Morgulis,Justin Paschall,Lon Phan,Kirill Rotmistrovsky,Robert Sanders,Martin Shumway,Chunlin Xiao,Adam Auton,Gerton Lunter,Jonathan Marchini,Loukas Moutsianas,Simon Myers,Afidalina Tumian,Jo Knight,Roger Winer,David Craig,Stephen M. Beckstrom-Sternberg,Alexis Christoforides,Ahmet Kurdoglu,John V. Pearson,Shripad Sinari,Waibhav Tembe,David Haussler,Angie S. Hinrichs,Sol Katzman,Andrew D. Kern,Robert M. Kuhn,Molly Przeworski,Ryan D. Hernandez,Bryan Howie,Joanna L. Kelley,S. C. Melton,Paige Anderson,Thomas W. Blackwell,Wei Chen,William O.C.M. Cookson,Jun Ding,Hyun Min Kang,Mark Lathrop,Liming Liang,Miriam F. Moffatt,Paul Scheet,C Sidore,Xiaowei Zhan,Sebastian Zöllner,Philip Awadalla,Ferran Casals,Youssef Idaghdour,Jon Keebler,Eric A. Stone,Martine Zilversmit,Lynn B. Jorde,Jinchuan Xing,Gozde Aksay,Suleyman Cenk Sahinalp,Peter H. Sudmant,Daniel C. Koboldt,Michael D. McLellan,John W. Wallis,Michael C. Wendl,Qunyuan Zhang,Cornelis A. Albers,Qasim Ayub,Senduran Balasubramaniam,Jeffrey C. Barrett,Yuan Chen,Petr Danecek,Emmanouil T. Dermitzakis,Min Hu,Ni Huang,Han-Jun Jin,Luke Jostins,Thomas M. Keane,Si Quang Le,Susan Lindsay,Quan Long,Daniel G. MacArthur,Stephen B. Montgomery,Leopold Parts,Chris Tyler-Smith,Shankar Balasubramanian,Robert D. Bjornson,Jiang Du,Lukas Habegger,Rajini R Haraksingh,Justin Jee,H. Y. Lam,J. Jeng,Zhaolei Zhang,E. Bank,S. Yoon,J. Kidd,C. Coafra,Huyen Dinh,Christie Kovar,Sandra J. Lee,Lynne V. Nazareth,Jane Wilkinson,H. M. Khouri,Carol Scott,Neda Gharani,Jane Kaye,Alastair Kent,T. Li,Amy L. McGuire,Pilar N. Ossorio,Charles N. Rotimi,Yeyang Su,Lorraine Toji,Lisa D Brooks,Adam Felsenfeld,Jean E. McEwen,Assya Abdallah,C. R. Juenger,N. C. Clemm,Audrey Duncanson,Eric D. Green,Mark S. Guyer,Jessica L. Peterson +374 more
TL;DR: A map of unbalanced SVs is constructed based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations, and serves as a resource for sequencing-based association studies.
The UK10K project identifies rare variants in health and disease
Klaudia Walter,Josine L. Min,Jie Huang,Lucy Crooks,Yasin Memari,Shane A. McCarthy,John R. B. Perry,ChangJiang Xu,Marta Futema,Daniel Lawson,Valentina Iotchkova,Stephan Schiffels,Audrey E. Hendricks,Petr Danecek,Rui Li,James A B Floyd,Louise V. Wain,Inês Barroso,Steve E. Humphries,Matthew E. Hurles,Eleftheria Zeggini,Jeffrey C. Barrett,Vincent Plagnol,J. Brent Richards,Celia M. T. Greenwood,Nicholas J. Timpson,Richard Durbin,Nicole Soranzo,Senduran Bala,Peter Clapham,Guy Coates,Tony Cox,Allan Daly,Yuanping Du,Sarah Edkins,Peter R. Ellis,Paul Flicek,Xiaosen Guo,Xueqin Guo,Liren Huang,David K. Jackson,Christopher J. Joyce,Thomas Keane,Anja Kolb-Kokocinski,Cordelia Langford,Yingrui Li,Jieqin Liang,Hong Lin,Ryan Liu,John Maslen,Dawn Muddyman,Michael A. Quail,Jim Stalker,Jianping Sun,Jing Tian,Guangbiao Wang,Jun Wang,Yu Wang,Kim Wong,Pingbo Zhang,Ewan Birney,Chris Boustred,Lu Chen,Gail Clement,Massimiliano Cocca,George Davey Smith,Ian N.M. Day,Aaron G. Day-Williams,Thomas A. Down,Ian Dunham,David M. Evans,Tom R. Gaunt,Matthias Geihs,Deborah J. Hart,Bryan Howie,Tim Hubbard,Pirro G. Hysi,Yalda Jamshidi,Konrad J. Karczewski,John P. Kemp,Genevieve Lachance,Monkol Lek,Margarida C. Lopes,Daniel G. MacArthur,Jonathan Marchini,Massimo Mangino,Iain Mathieson,Sarah Metrustry,Alireza Moayyeri,Kate Northstone,Kalliope Panoutsopoulou,Lavinia Paternoster,Lydia Quaye,Susan M. Ring,Graham R. S. Ritchie,Hashem A. Shihab,So-Youn Shin,Kerrin S. Small,María Soler Artigas,Lorraine Southam,Tim D. Spector,Beate St Pourcain,Gabriela L. Surdulescu,Ioanna Tachmazidou,Martin D. Tobin,Ana M. Valdes,Peter M. Visscher,Kirsten J. Ward,Scott Wilson,Jian Yang,Feng Zhang,Hou-Feng Zheng,Richard Anney,Muhammad Ayub,Douglas Blackwood,Patrick Bolton,Gerome Breen,David A. Collier,Nicholas John Craddock,Sarah Curran,David Curtis,Louise Gallagher,Daniel H. Geschwind,Hugh Gurling,Peter Holmans,Irene Lee,Jouko Lönnqvist,Peter McGuffin,Andrew M. McIntosh,Andrew McKechanie,Andrew McQuillin,James Morris,Michael Conlon O'Donovan,Michael John Owen,Aarno Palotie,Jeremy R. Parr,Tiina Paunio,Olli Pietiläinen,Karola Rehnström,Sally I. Sharp,David Skuse,David St Clair,Jaana Suvisaari,James T.R. Walters,Hywel Williams,Elena G. Bochukova,Rebecca Bounds,Anna F. Dominiczak,I. Sadaf Farooqi,Julia M. Keogh,Gaëlle Marenne,Andrew D. Morris,Stephen O'Rahilly,David J. Porteous,Blair H. Smith,Eleanor Wheeler,Saeed Al Turki,Carl A. Anderson,Dinu Antony,PL Beales,Jamie Bentham,Shoumo Bhattacharya,Mattia Calissano,Keren J. Carss,Krishna Chatterjee,Sebahattin Cirak,Catherine Cosgrove,David R. FitzPatrick,A. Reghan Foley,Christopher S. Franklin,Detelina Grozeva,Hannah M. Mitchison,Francesco Muntoni,Alexandros Onoufriadis,Victoria E. R. Parker,Felicity Payne,F. Lucy Raymond,Nicola D. Roberts,David B. Savage,Peter J. Scambler,Miriam Schmidts,Nadia Schoenmakers,Robert K. Semple,Eva Goncalves Serra,Olivera Spasic-Boskovic,Elizabeth Stevens,Margriet van Kogelenberg,Parthiban Vijayarangakannan,Kathleen A. Williamson,Crispian Wilson,Tamieka Whyte,Antonio Ciampi,Karim Oualkacha,Martin Bobrow,Heather Griffin,Jane Kaye,Karen Kennedy,Alastair Kent,Carol Smee,R. Charlton,Rosemary Ekong,Farrah Khawaja,Luis R. Lopes,Nicola Migone,Stewart J. Payne,Rebecca C. Pollitt,Sue Povey,Cheryl K. Ridout,Rachel L. Robinson,Richard H Scott,Adam Shaw,Petros Syrris,Rohan Taylor,Anthony M. Vandersteen,Antoinette Amuzu,Juan P. Casas,John C. Chambers,George Dedoussis,Giovanni Gambaro,Paolo Gasparini,Aaron Isaacs,Jon Johnson,Marcus E. Kleber,Jaspal S. Kooner,Claudia Langenberg,Jian'an Luan,Giovanni Malerba,Winfried Maerz,Angela Matchan,Richard W Morris,Børge G. Nordestgaard,Marianne Benn,Robert A. Scott,Daniela Toniolo,Michela Traglia,Anne Tybjærg-Hansen,Cornelia M. van Duijn,Elisabeth M. van Leeuwen,Anette Varbo,Peter H. Whincup,Gianluigi Zaza,Weihua Zhang +241 more
TL;DR: The contribution of rare and low-frequency variants to human traits is largely unexplored as mentioned in this paper, but the contribution of these variants to the human traits has not yet been fully explored.