D
David J. Lynn
Researcher at Flinders University
Publications - 105
Citations - 8431
David J. Lynn is an academic researcher from Flinders University. The author has contributed to research in topics: Gene & Innate immune system. The author has an hindex of 38, co-authored 98 publications receiving 7151 citations. Previous affiliations of David J. Lynn include University College Dublin & University of South Australia.
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Journal ArticleDOI
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
Christine G. Elsik,Christine G. Elsik,Christine G. Elsik,Ross L. Tellam,Kim C. Worley,Kim C. Worley,Richard A. Gibbs,Donna M. Muzny,George M. Weinstock,George M. Weinstock,David L. Adelson,Evan E. Eichler,Evan E. Eichler,Laura Elnitski,Roderic Guigó,Debora L. Hamernik,Steve M. Kappes,Harris A. Lewin,David J. Lynn,Frank W. Nicholas,Alexandre Reymond,Monique Rijnkels,Loren C. Skow,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Lawrence B. Schook,James E. Womack,Tyler Alioto,Stylianos E. Antonarakis,Alex Astashyn,Charles E. Chappie,Hsiu Chuan Chen,Jacqueline Chrast,Francisco Câmara,Olga Ermolaeva,Charlotte N. Henrichsen,Wratko Hlavina,Yuri Kapustin,Boris Kiryutin,Paul Kitts,Felix Kokocinski,Melissa J. Landrum,Donna Maglott,Kim D. Pruitt,Victor Sapojnikov,Stephen M. J. Searle,Victor V. Solovyev,Alexandre Souvorov,Catherine Ucla,Carine Wyss,Juan Manuel Anzola,Daniel Gerlach,Daniel Gerlach,Eran Elhaik,Eran Elhaik,Dan Graur,Justin T. Reese,Robert C. Edgar,John C. McEwan,Gemma Marie Payne,Joy M. Raison,Thomas Junier,Thomas Junier,Evgenia V. Kriventseva,Eduardo Eyras,Mireya Plass,Ravikiran Donthu,Denis M. Larkin,James M. Reecy,Mary Qu Yang,Lin Chen,Ze Cheng,Carol G. Chitko-McKown,George E. Liu,Lakshmi K. Matukumalli,Lakshmi K. Matukumalli,Jiuzhou Song,Bin Zhu,Daniel G. Bradley,Fiona S. L. Brinkman,Lilian P.L. Lau,Matthew D. Whiteside,Angela K. Walker,Thomas T. Wheeler,Theresa Casey,J. Bruce German,J. Bruce German,Danielle G. Lemay,Nauman J. Maqbool,A.J. Molenaar,Seongwon Seo,Paul Stothard,Cynthia L. Baldwin,R. Baxter,Candice L. Brinkmeyer-Larigford,Wendy C. Brown,Christopher P. Childers,Timothy Connelley,Shirley A. Ellis,Krista L. Fritz,Elizabeth Glass,Carolyn T.A. Herzig,Antti Livanainen,Kevin K. Lahmers,Anna K. Bennett,C. Michael Dickens,James G. R. Gilbert,Darren E. Hagen,Hanni Salih,Jan Aerts,Alexandre Rodrigues Caetano,Brian P. Dalrymple,José Fernando Garcia,Clare A. Gill,Stefan Hiendleder,Erdogan Memili,D.M. Spurlock,John L. Williams,Lee Alexander,Michael J. Brownstein,Le Luo Guan,Robert A. Holt,Steven J.M. Jones,Marco A. Marra,Richard A. Moore,Stephen S. Moore,Andrew J. Roberts,Masaaki Taniguchi,Masaaki Taniguchi,Richard C. Waterman,Joseph Chacko,Mimi M. Chandrabose,Andy Cree,Marvin Diep Dao,Huyen Dinh,Ramatu Ayiesha Gabisi,Sandra Hines,Jennifer Hume,Shalini N. Jhangiani,Vandita Joshi,Christie Kovar,Lora Lewis,Yin Shin Liu,John Lopez,Margaret Morgan,Ngoc Nguyen,Geoffrey Okwuonu,San Juana Ruiz,Jireh Santibanez,Rita A. Wright,Christian J. Buhay,Yan Ding,Shannon Dugan-Rocha,Judith Herdandez,Michael Holder,Aniko Sabo,Amy Egan,Jason Goodell,Katarzyna Wilczek-Boney,Gerald R. Fowler,Matthew Hitchens,Ryan J. Lozado,Charles Moen,David Steffen,James T. Warren,Jingkun Zhang,Readman Chiu,Jacqueline E. Schein,K. James Durbin,K. James Durbin,Paul Havlak,Paul Havlak,Huaiyang Jiang,Yue Liu,Xiang Qin,Yanru Ren,Yufeng Shen,Yufeng Shen,Henry Song,Stephanie Bell,Clay Davis,Angela Jolivet Johnson,Sandra L. Lee,Lynne V. Nazareth,Bella Mayurkumar Patel,Ling Ling Pu,Selina Vattathil,Rex Lee Williams,Stacey M. Curry,Cerissa Hamilton,Erica Sodergren,Erica Sodergren,David A. Wheeler,Wes Barris,Gary L. Bennett,André Eggen,Ronnie D. Green,Gregory P. Harhay,Matthew Hobbs,Oliver C. Jann,John W. Keele,Matthew Peter Kent,Sigbjam Lien,Stephanie D. McKay,Sean McWilliam,Abhirami Ratnakumar,Robert D. Schnabel,Timothy P. L. Smith,Warren M. Snelling,Tad S. Sonstegard,Roger T. Stone,Yoshikazu Sugimoto,Akiko Takasuga,Jeremy F. Taylor,Curtis P. Van Tassell,Michael D. MacNeil,A.R.R. Abatepaulo,Colette A. Abbey,Virpi Ahola,Lassudara G. Almeida,Ariel Fernando Amadio,Elen Anatriello,Suria M. Bahadue,Fernando H. Biase,Clayton R. Boldt,Jeffery A. Carroll,W. A. Carvalho,Eliane P. Cervelatti,Elsa Chacko,Jennifer E. Chapin,Ye Cheng,Jung-Woo Choi,Adam J. Colley,Tatiana A. DeCampos,Marcos De Donato,Isabel Kinney Ferreira de Miranda Santos,Carlo José Freire de Oliveira,Heather M Deobald,Eve Devinoy,Kaitlin E. Donohue,Peter Dove,Annett Eberlein,Carolyn Fitzsimmons,Alessandra Mara Franzin,Gustavo Garcia,Sem Genini,Cody J. Gladney,Jason R. Grant,Marion L. Greaser,Jonathan A. Green,Darryl L. Hadsell,Hatam A. Hakimov,Rob Halgren,Jennifer Harrow,E. Hart,N. Hastings,Marta Hernández,Zhi-Liang Hu,Antti Iivanainen,Aaron Ingham,Terhi Iso-Touru,Catherine Jamis,Kirsty Jensen,Dimos Kapetis,Tovah Kerr,Sari S. Khalil,Hasan Khatib,D. Kolbehdari,D. Kolbehdari,Cham G. Kumar,Dinesh Kumar,Richard J. Leach,Justin C. Lee,Changxi Li,Krystin M. Logan,Roberto Malinverni,E. Marques,William F. Martin,Natália F. Martins,Sandra Regina Maruyama,Raffaele Mazza,Kim L. McLean,Juan F. Medrano,Barbara T. Moreno,Daniela D. Moré,Carl T. Muntean,Hari Prasad Nandakumar,Marcelo Fábio Gouveia Nogueira,Ingrid Olsaker,Sameer D. Pant,Francesca Panzitta,Rosemeire Conceição Parra Pastor,Mario Andres Poli,Nathan Poslusny,Satyanarayana Rachagani,Shoba Ranganathan,Shoba Ranganathan,Andrej Razpet,Penny K. Riggs,Gonzalo Rincon,Nelida Rodriguez-Osorio,Nelida Rodriguez-Osorio,Sandra L. Rodriguez-Zas,Natasha E. Romero,Anne G. Rosenwald,Lillian Sando,Sheila M. Schmutz,Libing Shen,Laura Sherman,Bruce R. Southey,Ylva Strandberg Lutzow,Jonathan V. Sweedler,Imke Tammen,Bhanu Prakash V.L. Telugu,Jennifer M. Urbanski,Yuri Tani Utsunomiya,Chris P. Verschoor,Ashley J. Waardenberg,Zhiquan Wang,Robert Ward,Rosemarie Weikard,Thomas H. Welsh,Stephen N. White,Stephen N. White,Laurens G. Wilming,Kris R. Wunderlich,Jianqi Yang,Feng-Qi Zhao +328 more
TL;DR: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage and provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Journal ArticleDOI
InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
Karin Breuer,Amir Foroushani,Matthew R. Laird,Carol Chen,Anastasia Sribnaia,Raymond Lo,Geoffrey L. Winsor,Robert E. W. Hancock,Fiona S. L. Brinkman,David J. Lynn +9 more
TL;DR: The recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism, and a range of improvements to the integrated bioinformatics solutions are reported.
Journal ArticleDOI
Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds
Richard A. Gibbs,Jeremy F. Taylor,Curtis P. Van Tassell,William Barendse,William Barendse,Kellye Eversole,Clare A. Gill,Ronnie D. Green,Debora L. Hamernik,Steven M. Kappes,Sigbjørn Lien,Lakshmi K. Matukumalli,Lakshmi K. Matukumalli,John C. McEwan,Lynne V. Nazareth,Robert D. Schnabel,George M. Weinstock,David A. Wheeler,Paolo Ajmone-Marsan,Paul Boettcher,Alexandre Rodrigues Caetano,José Fernando Garcia,José Fernando Garcia,Olivier Hanotte,Paola Mariani,Loren C. Skow,Tad S. Sonstegard,John L. Williams,John L. Williams,Boubacar Diallo,Lemecha Hailemariam,Mário Luiz Martinez,C. A. Morris,Luiz Otávio Campos da Silva,Richard J. Spelman,Woudyalew Mulatu,Keyan Zhao,Colette A. Abbey,Morris Agaba,Flábio R. Araújo,Rowan J. Bunch,Rowan J. Bunch,James O. Burton,C. Gorni,Hanotte Olivier,Blair E. Harrison,Blair E. Harrison,Bill Luff,Marco Antonio Machado,Joel Mwakaya,Graham Plastow,Warren Sim,Warren Sim,Timothy P. L. Smith,Merle B Thomas,Merle B Thomas,Alessio Valentini,Paul D. Williams,James E. Womack,John Woolliams,Yue Liu,Xiang Qin,Kim C. Worley,Chuan Gao,Huaiyang Jiang,Stephen S. Moore,Yanru Ren,Xingzhi Song,Carlos Bustamante,Ryan D. Hernandez,Donna M. Muzny,Shobha Patil,Anthony San Lucas,Qing Fu,Matthew Peter Kent,Richard Vega,Aruna Matukumalli,Sean McWilliam,Sean McWilliam,Gert Sclep,Katarzyna Bryc,Jung-Woo Choi,Hong Gao,John J. Grefenstette,Brenda M. Murdoch,Alessandra Stella,Rafael Villa-Angulo,Mark G. Wright,Jan Aerts,Jan Aerts,Oliver C. Jann,Riccardo Negrini,Michael E. Goddard,Michael E. Goddard,Ben J. Hayes,Daniel G. Bradley,Marcos V.B. da Silva,Marcos V.B. da Silva,Lilian P.L. Lau,George E. Liu,David J. Lynn,David J. Lynn,Francesca Panzitta,Ken G. Dodds +103 more
TL;DR: Data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation.
Journal ArticleDOI
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
Sandra Orchard,Samuel Kerrien,Sara Abbani,Bruno Aranda,Jignesh Bhate,Shelby L. Bidwell,Alan Bridge,Leonardo Briganti,Fiona S. L. Brinkman,Gianni Cesareni,Andrew Chatr-aryamontri,Andrew Chatr-aryamontri,Emilie Chautard,Emilie Chautard,Carol Chen,Marine Dumousseau,Johannes B. Goll,Robert E. W. Hancock,Linda Hannick,Igor Jurisica,Jyoti Khadake,David J. Lynn,Usha Mahadevan,Livia Perfetto,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Lukasz Salwinski,Volker Stümpflen,Mike Tyers,Mike Tyers,Peter Uetz,Ioannis Xenarios,Ioannis Xenarios,Henning Hermjakob +34 more
TL;DR: The International Molecular Exchange consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website.
Book
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
David J. Lynn,David J. Lynn,Geoffrey L. Winsor,Calvin Chan,Nicolas Richard,Matthew R. Laird,Aaron Barsky,Jennifer L. Gardy,Fiona M. Roche,Timothy H.W. Chan,Naisha Shah,Naisha Shah,Raymond Lo,Misbah Naseer,Jaimmie Que,Melissa Yau,Michael Acab,Dan Tulpan,Matthew D. Whiteside,Avinash Chikatamarla,Bernadette Mah,Tamara Munzner,Karsten Hokamp,Robert E. W. Hancock,Fiona S. L. Brinkman +24 more
TL;DR: InnateDB as mentioned in this paper is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human-and mouse interactomes.