Daniel M. Staines
European Bioinformatics Institute
20 Papers
103 Citations
Daniel M. Staines is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Ensembl & Ensembl Genomes. The author has an hindex of 18, co-authored 20 publications. Previous affiliations of Daniel M. Staines include Cold Spring Harbor Laboratory & University of Cambridge.
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Papers
Ensembl BioMarts: a hub for data retrieval across taxonomic space
Rhoda Kinsella,Andreas Kähäri,Syed Haider,Jorge Zamora,Glenn Proctor,Giulietta Spudich,Jeff Almeida-King,Daniel M. Staines,Paul S. Derwent,Arnaud Kerhornou,Paul J. Kersey,Paul Flicek +11 more
TL;DR: This article aims to give a comprehensive overview of the Ensembl and Ensemble Genomes BioMarts as well as some useful examples and a description of current data content and future objectives.
The BioMart community portal: an innovative alternative to large, centralized data repositories
Damian Smedley,Syed Haider,Steffen Durinck,Luca Pandini,Paolo Provero,Paolo Provero,James E. Allen,Olivier Arnaiz,Mohammad Awedh,Richard Baldock,Giulia Barbiera,Philippe Bardou,Tim Beck,Andrew Blake,Merideth Bonierbale,Anthony J. Brookes,Gabriele Bucci,Iwan Buetti,Sarah W. Burge,Cédric Cabau,Joseph W. Carlson,Claude Chelala,Charalambos Chrysostomou,Davide Cittaro,Olivier Collin,Raul Cordova,Rosalind J. Cutts,Erik Dassi,Alex Di Genova,Anis Djari,Anthony Esposito,Heather Estrella,Eduardo Eyras,Eduardo Eyras,Julio Fernandez-Banet,Simon A. Forbes,Robert C. Free,Takatomo Fujisawa,Emanuela Gadaleta,Jose Manuel Garcia-Manteiga,David Goodstein,Kristian Gray,José Afonso Guerra-Assunção,Bernard Haggarty,Dong Jin Han,Byung Woo Han,Todd W. Harris,Jayson Harshbarger,Robert K. Hastings,Richard D. Hayes,Claire Hoede,Shen Hu,Zhi-Liang Hu,Lucie N. Hutchins,Zhengyan Kan,Hideya Kawaji,Aminah Keliet,Arnaud Kerhornou,Sunghoon Kim,Rhoda Kinsella,Christophe Klopp,Lei Kong,Daniel Lawson,Dejan Lazarevic,Ji Hyun Lee,Thomas Letellier,Chuan-Yun Li,Pietro Liò,Chu Jun Liu,Jie Luo,Alejandro Maass,Jérôme Mariette,Thomas Maurel,Stefania Merella,Azza M. Mohamed,François Moreews,Ibounyamine Nabihoudine,Nelson Ndegwa,Céline Noirot,Cristian Perez-Llamas,Michael Primig,Alessandro Quattrone,Hadi Quesneville,Davide Rambaldi,James M. Reecy,Michela Riba,Steven Rosanoff,Amna A. Saddiq,Elisa Salas,Olivier Sallou,Rebecca Shepherd,Reinhard Simon,Linda Sperling,William Spooner,Daniel M. Staines,Delphine Steinbach,Kevin R. Stone,Elia Stupka,Jon W. Teague,Abu Z. Dayem Ullah,Jun Wang,Doreen Ware,Marie Wong-Erasmus,Ken Youens-Clark,Amonida Zadissa,Shi Jian Zhang,Arek Kasprzyk,Arek Kasprzyk +107 more
TL;DR: The latest version of the BioMart Community Portal comes with many new databases that have been created by the ever-growing community and comes with better support and extensibility for data analysis and visualization tools.
Gene ontology annotations and resources
Judith A. Blake,Mary E. Dolan,H. Drabkin,David P. Hill,Li N,D. Sitnikov,Susan M. Bridges,Shane C. Burgess,Teresia Buza,Fiona M. McCarthy,Divyaswetha Peddinti,Lakshmi Pillai,Seth Carbon,Heiko Dietze,Amelia Ireland,Suzanna E. Lewis,Christopher J. Mungall,Pascale Gaudet,Chrisholm Rl,Petra Fey,Warren A. Kibbe,S. Basu,Deborah A. Siegele,B. K. McIntosh,Daniel P. Renfro,Adrienne E. Zweifel,James C. Hu,Nicholas H. Brown,Susan Tweedie,Yasmin Alam-Faruque,Rolf Apweiler,A. Auchinchloss,Kristian B. Axelsen,Benoit Bely,M. C. Blatter,Bonilla C,Bouguerleret L,Emmanuel Boutet,Lionel Breuza,Alan Bridge,W. M. Chan,Gayatri Chavali,Elisabeth Coudert,E. Dimmer,Anne Estreicher,L Famiglietti,Marc Feuermann,Arnaud Gos,Nadine Gruaz-Gumowski,Hieta R,Hinz C,Chantal Hulo,Rachael P. Huntley,J. James,Florence Jungo,Guillaume Keller,Kati Laiho,Duncan Legge,P. Lemercier,Damien Lieberherr,Michele Magrane,Maria Jesus Martin,Patrick Masson,Mutowo-Muellenet P,Claire O'Donovan,Ivo Pedruzzi,Klemens Pichler,Diego Poggioli,Porras Millán P,Sylvain Poux,Catherine Rivoire,Bernd Roechert,Tony Sawford,Michel Schneider,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Ioannis Xenarios,Foulgar R,Jane Lomax,Paola Roncaglia,Varsha K. Khodiyar,Ruth C. Lovering,Philippa J. Talmud,Marcus C. Chibucos,Giglio Mg,Hsin-Yu Chang,Sarah Hunter,Craig McAnulla,Alex L. Mitchell,Sangrador A,Stephan R,Midori A. Harris,Stephen G. Oliver,Kim Rutherford,Wood,Jürg Bähler,Antonia Lock,Paul J. Kersey,McDowall Dm,Daniel M. Staines,Melinda R. Dwinell,Mary Shimoyama,Stan Laulederkind,Tom Hayman,Shur-Jen Wang,Timothy F. Lowry,P D'Eustachio,Lisa Matthews,Rama Balakrishnan,Gail Binkley,J. M. Cherry,Maria C. Costanzo,Selina S. Dwight,Engel,Dianna G. Fisk,Benjamin C. Hitz,Eurie L. Hong,Kalpana Karra,Miyasato,Robert S. Nash,Julie Park,Marek S. Skrzypek,Shuai Weng,Edith D. Wong,Tanya Z. Berardini,Eva Huala,Huaiyu Mi,Paul Thomas,Juancarlos Chan,Ranjana Kishore,Paul W. Sternberg,Van Auken K,Doug Howe,Monte Westerfield +134 more
TL;DR: The Gene Ontology (GO) Consortium is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies and has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology.
Ensembl Genomes 2016: more genomes, more complexity
Paul J. Kersey,James E. Allen,Irina M. Armean,Sanjay Boddu,Bruce J. Bolt,Denise Carvalho-Silva,Mikkel B. Christensen,Paul Davis,Lee J. Falin,Christoph Grabmueller,Jay C. Humphrey,Arnaud Kerhornou,Julia Khobova,Naveen K. Aranganathan,Nicholas Langridge,Ernesto Lowy,Mark D. McDowall,Uma Maheswari,Michael Nuhn,Chuang Kee Ong,Bert Overduin,Michael Paulini,Helder Pedro,Emily Perry,Giulietta Spudich,Electra Tapanari,Brandon Walts,Gareth Williams,Marcela K. Tello-Ruiz,Joshua C. Stein,Sharon Wei,Doreen Ware,Dan Bolser,Kevin L. Howe,Eugene Kulesha,Daniel Lawson,Gareth Maslen,Daniel M. Staines +37 more
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes, with a focus on recent developments, including the development of new analyses and views to represent polyploid genomes and the continued up-scaling of the resource.
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Paul J. Kersey,James E. Allen,Alexis Allot,Matthieu Barba,Sanjay Boddu,Bruce J. Bolt,Denise Carvalho-Silva,Mikkel B. Christensen,Paul Davis,Christoph Grabmueller,Navin Kumar,Zicheng Liu,Thomas Maurel,Ben Moore,Mark D. McDowall,Uma Maheswari,Guy Naamati,Victoria L. Newman,Chuang Kee Ong,Michael Paulini,Helder Pedro,Emily Perry,Matthew Russell,Helen Sparrow,Electra Tapanari,Kieron Taylor,Alessandro Vullo,Gareth Williams,Amonida Zadissia,Andrew Olson,Joshua C. Stein,Sharon Wei,Marcela K. Tello-Ruiz,Doreen Ware,Doreen Ware,Aurelien Luciani,Simon C. Potter,Robert D. Finn,Martin Urban,Kim E. Hammond-Kosack,Dan Bolser,Nishadi De Silva,Kevin L. Howe,Nicholas Langridge,Gareth Maslen,Daniel M. Staines,Andrew D. Yates +46 more
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes resource, with a focus on recent developments and expansions, including the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data.
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