作者：Pablo Moreno (1)
Stephan Beisken (1)
Bhavana Harsha (1)
Venkatesh Muthukrishnan (1)
Ilinca Tudose (1)
Adriano Dekker (1)
Stefanie Dornfeldt (2)
Franziska Taruttis (2) (3)
Ivo Grosse (4) (5)
Janna Hastings (1)
Steffen Neumann (2)
Christoph Steinbeck (1)

1. Cheminformatics and Metabolism ; European Molecular Biology Laboratory - European Bioinformatics Institute ; Cambridge ; UK
2. Dept. of Stress- and Developmental Biology ; Leibniz Institute of Plant Biochemistry ; Halle ; Germany
3. Dept. of Statistical Bioinformatics ; Institute for Functional Genomics ; University of Regensburg ; Halle ; Germany
4. Institute of Computer Science ; Martin Luther University Halle-Wittenberg ; Halle ; Germany
5. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig ; Leipzig ; Germany

关键词：Ontology ; Enrichment ; Small molecules

刊名：BMC Bioinformatics

出版年：2015

作者：Leif Andersson (1) (2)
Alan L Archibald (3)
Cynthia D Bottema (4)
Rudiger Brauning (5)
Shane C Burgess (6)
Dave W Burt (3)
Eduardo Casas (7)
Hans H Cheng (8)
Laura Clarke (9)
Christine Couldrey (10)
Brian P Dalrymple (11)
Christine G Elsik (12)
Sylvain Foissac (13)
Elisabetta Giuffra (14)
Martien A Groenen (15)
Ben J Hayes (16) (17) (18)
LuSheng S Huang (19)
Hassan Khatib (20)
James W Kijas (11)
Heebal Kim (21)
Joan K Lunney (22)
Fiona M McCarthy (23)
John C McEwan (24)
Stephen Moore (25)
Bindu Nanduri (26)
Cedric Notredame (27)
Yniv Palti (28)
Graham S Plastow (29)
James M Reecy (30)
Gary A Rohrer (31)
Elena Sarropoulou (32)
Carl J Schmidt (33)
Jeffrey Silverstein (34)
Ross L Tellam (35)
Michele Tixier-Boichard (14)
Gwenola Tosser-Klopp (13)
Christopher K Tuggle (30)
Johanna Vilkki (36)
Stephen N White (37) (38)
Shuhong Zhao (39)
Huaijun Zhou (40)
The FAANG Consortium

1. Science for Life Laboratory Uppsala ; Department of Medical Biochemistry and Microbiology ; Uppsala University ; Uppsala ; SE 751 23 ; Sweden
2. Department of Animal Breeding and Genetics ; Swedish University of Agricultural Sciences ; Uppsala ; SE-750 07 ; Sweden
3. The Roslin Institute and Royal (Dick) School of Veterinary Studies ; University of Edinburgh ; Edinburgh ; EH25 9RG ; UK
4. School of Animal and Veterinary Sciences ; The University of Adelaide ; Roseworthy ; SA ; 5371 ; Australia
5. Invermay Agricultural Centre ; AgResearch Limited ; Mosgiel ; 9053 ; New Zealand
6. College of Agriculture and Life Sciences ; University of Arizona ; Tucson ; AZ ; 85719 ; USA
7. National Animal Disease Center ; United States Department of Agriculture ; Agricultural Research Service ; Ames ; IA ; 50010 ; USA
8. Avian Disease and Oncology Laboratory ; United States Department of Agriculture ; Agricultural Research Service ; East Lansing ; MI ; 48823 ; USA
9. European Molecular Biology Laboratory European Bioinformatics Institute ; Hinxton ; Cambridge ; CB10 1SD ; UK
10. Livestock Improvement Corporation ; Hamilton ; 3284 ; New Zealand
11. Agriculture Flagship ; Commonwealth Scientific and Industrial Research Organisation ; St Lucia ; 4067 ; Brisbane ; Australia
12. Division of Animal Sciences ; University of Missouri ; Columbia ; MO ; 65211 ; USA
13. UMR1388 G茅n茅tique ; Physiologie et Syst猫mes d鈥橢levage (GenPhySE) ; French National Institute for Agricultural Research (INRA) ; F-31326 ; Castanet-Tolosan ; France
14. UMR1313 G茅n茅tique Animale et Biologie Int茅grative (GABI) ; French National Institute for Agricultural Research (INRA) ; F-78352 ; Jouy-en-Josas ; France
15. Animal Breeding and Genomics Centre ; Wageningen University ; 6708聽PB ; Wageningen ; The Netherlands
16. Biosciences Research Division ; Department of Environment and Primary Industries Victoria ; Bundoora ; 3083 ; Australia
17. Dairy Futures Cooperative Research Centre ; Bundoora ; 3083 ; VIC ; Australia
18. La Trobe University ; Bundoora ; 3086 ; VIC ; Australia
19. Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China ; Jiangxi Agricultural University ; Jiangxi ; 330029 ; People鈥檚 Republic of China
20. Department of Animal Sciences ; University of Wisconsin-Madison ; Madison ; WI ; 53706 ; USA
21. Department of Agricultural Biotechnology ; Seoul National University ; Seoul ; Republic of Korea
22. Animal Parasitic Diseases Laboratory ; United States Department of Agriculture ; Agricultural Research Service ; Beltsville ; MD ; 20705 ; USA
23. School of Animal and Comparative Biomedical Sciences ; University of Arizona ; Tucson ; AZ ; 85721 ; USA
24. Animal Productivity Group ; AgResearch Limited ; Mosgiel ; 9053 ; New Zealand
25. Centre for Animal Science ; Queensland Alliance for Agriculture & Food Innovation ; University of Queensland ; St Lucia ; QLD ; 4067 ; Australia
26. Department of Basic Sciences ; College of Veterinary Medicine and Institute for Genomics ; Biocomputing and Biotechnology ; Mississippi State University ; Mississippi ; MS ; 39762 ; USA
27. Comparative Bioinformatics ; Centre for Genomic Regulation (CRG) ; Dr. Aiguader 88 ; 08003 ; Barcelona ; Spain
28. National Center for Cool and Cold Water Aquaculture ; United States Department of Agriculture ; Agricultural Research Service ; Kearneysville ; WV ; 25430 ; USA
29. Livestock Gentec Centre ; Department of Agricultural ; Food and Nutritional Science ; University of Alberta ; Edmonton ; Alberta ; T6G 2C8 ; Canada
30. Department of Animal Science ; Iowa State University ; Ames ; IA ; 50011 ; USA
31. US Meat Animal Research Center ; United States Department of Agriculture ; Agricultural Research Service ; Clay Center ; NE ; 68933 ; USA
32. Institute of Marine Biology ; Biotechnology and Aquaculture ; Hellenic Centre for Marine Research ; 71003 ; Heraklion ; Greece
33. Department of Animal and Food Sciences ; University of Delaware ; Newark ; DE ; 19716 ; USA
34. Animal Production and Protection ; United States Department of Agriculture ; Agricultural Research Service Aquaculture ; Beltsville ; MD ; 20705 ; USA
35. CSIRO Agriculture ; Commonwealth Scientific and Industrial Research Organisation ; St Lucia ; 4067 ; Australia
36. Green Technology ; Natural Resources Institute Finland ; 31600 ; Jokioinen ; Finland
37. Animal Disease Research Unit ; United States Department of Agriculture ; Agricultural Research Service ; Pullman ; WA ; 99164-6630 ; USA
38. Department of Veterinary Microbiology and Pathology ; Washington State University ; Pullman ; WA ; 99164-7040 ; USA
39. Key Laboratory of Agricultural Animal Genetics ; Breeding and Reproduction of Ministry of Education of China ; Huazhong Agricultural University ; Wuhan ; Hubei ; 430070 ; People鈥檚 Republic of China
40. Department of Animal Science ; University of California ; Davis ; CA ; 95616 ; USA

刊名：Genome Biology

出版年：2015

作者：Isidro Cortes-Ciriano (1)
Daniel S Murrell (2)
Gerard JP van Westen (3)
Andreas Bender (2)
Th茅r猫se E Malliavin (1)

1. D茅partement de Biologie Structurale et Chimie ; Institut Pasteur ; Unit茅 de Bioinformatique Structurale ; CNRS UMR 3825 ; 25 ; rue du Dr Roux ; Paris ; 75015 ; France
2. Centre for Molecular Science Informatics ; Department of Chemistry ; University of Cambridge ; Cambridge ; UK
3. European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus ; Hinxton ; Cambridge ; CB10 1SD ; UK

关键词：Proteochemometrics ; Cyclooxygenases ; Chemogenomics ; QSAR ; Ensemble modeling ; Applicability domain

刊名：Journal of Cheminformatics

出版年：2015

作者：Frank T Bergmann (1)
Richard Adams (2)
Stuart Moodie (3) (4)
Jonathan Cooper (5)
Mihai Glont (3)
Martin Golebiewski (6)
Michael Hucka (7)
Camille Laibe (3)
Andrew K Miller (8)
David P Nickerson (8)
Brett G Olivier (9)
Nicolas Rodriguez (10)
Herbert M Sauro (11)
Martin Scharm (12)
Stian Soiland-Reyes (13)
Dagmar Waltemath (12)
Florent Yvon (3)
Nicolas Le Nov猫re (10) (3)

1. Modelling of Biological Processes ; BioQUANT/COS ; University of Heidelberg ; INF 267 ; Heidelberg ; 69120 ; Germany
2. ResearchSpace ; 24 Fountainhall Road ; Edinburgh ; EH9 2LW ; UK
3. European Molecular Biology Laboratory ; European Bioinformatics Institute (EMBL-EBI) ; Wellcome Trust Genome Campus ; Hinxton ; Cambridge ; CB10 1SD ; UK
4. Current affiliation ; Eight Pillars Ltd ; 19 Redford Walk ; Edinburgh ; EH13 0AG ; UK
5. Department of Computer Science ; University of Oxford ; Wolfson Building ; Parks Road ; Oxford ; OX1 3QD ; UK
6. HITS gGmbH ; Schloss-Wolfsbrunnenweg 35 ; D-69118 ; Heidelberg ; Germany
7. Computing and Mathematical sciences ; California Institute of Technology ; Pasadena ; CA ; 91125 ; USA
8. Auckland Bioengineering Institute ; University of Auckland ; Private Bag 92019 ; Auckland Mail Centre ; Auckland ; 1142 ; New Zealand
9. Systems Bioinformatics ; VU University Amsterdam ; Amsterdam ; 1081 HV ; The Netherlands
10. Babraham Institute ; Babraham Research Campus ; Cambridge ; CB22 3AT ; UK
11. Department of Bioengineering ; University of Washington ; Seattle ; 98195 ; WA ; USA
12. Systems Biology and Bioinformatics ; University of Rostock ; Ulmenstrasse 69 ; Rostock ; 18057 ; Germany
13. School of Computer Science ; The University of Manchester ; Oxford Road ; Manchester ; M13 9PL ; UK

关键词：Data format ; Archive ; Computational modeling ; Reproducible research ; Reproducible science

刊名：BMC Bioinformatics

出版年：2014

作者：Andrew C Nelson (1) (6)
Stephen J Cutty (1)
Marie Niini (2)
Derek L Stemple (3)
Paul Flicek (4)
Corinne Houart (2)
Ashley EE Bruce (5)
Fiona C Wardle (1)

1. Randall Division of Cell and Molecular Biophysics ; New Hunt鈥檚 House ; King鈥檚 College London ; Guy鈥檚 Campus ; London ; SE1 1UL ; UK
6. Current address ; Sir William Dunn School of Pathology ; South Parks Road ; Oxford ; OX1 3RE ; UK
2. MRC Centre for Developmental Neurobiology ; New Hunt鈥檚 House ; King鈥檚 College London ; Guy鈥檚 Campus ; London ; SE1 1UL ; UK
3. Wellcome Trust Sanger Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridge ; CB10 1HH ; UK
4. European Molecular Biology Laboratory ; European Bioinformatics Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridge ; CB10 1SD ; UK
5. Department of Cell and Systems Biology ; University of Toronto ; 25 Harbord Street ; Toronto ; ON ; M5S 3G5 ; Canada

关键词：Nodal ; Smad2 ; Eomesodermin ; Foxh1 ; Neural ; Transcriptional regulation

刊名：BMC Biology

出版年：2014

作者：Jose A Egea (1)
David Henriques (2) (3)
Thomas Cokelaer (3)
Alejandro F Villaverde (2)
Aidan MacNamara (3)
Diana-Patricia Danciu (3)
Julio R Banga (2)
Julio Saez-Rodriguez (3)

1. Department of Applied Mathematics and Statistics ; Universidad Polit茅cnica de Cartagena ; 30202 ; Cartagena ; Spain
2. (Bio)Process Engineering Group ; Spanish National Research Council ; IIM-CSIC ; 36208 ; Vigo ; Spain
3. European Molecular Biology Laboratory ; European Bioinformatics Institute ; Wellcome Trust Genome Campus ; Cambridge ; CB10 1SD ; UK

刊名：BMC Bioinformatics

出版年：2014

作者：Anna Sheydina (49) (50)
Ruth Y Eberhardt (51) (52)
Daniel J Rigden (53)
Yuanyuan Chang (49) (50)
Zhanwen Li (50)
Christian C Zmasek (50)
Herbert L Axelrod (49) (54)
Adam Godzik (49) (50) (55)

49. Joint Center for Structural Genomics ; 10550 North Torrey Pines Road ; BCC-206 ; La Jolla ; California ; 92037 ; USA
50. Bioinformatics and Systems Biology Program ; Sanford-Burnham Medical Research Institute ; La Jolla ; CA ; 92037 ; USA
51. Wellcome Trust Sanger Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridgeshire ; CB10 1SA ; UK
52. European Molecular Biology Laboratory ; European Bioinformatics Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridgeshire ; CB10 1SD ; UK
53. Institute of Integrative Biology ; University of Liverpool ; Crown Street ; Liverpool ; L69 7ZB ; UK
54. Stanford Synchrotron Radiation Lightsource ; Menlo Park ; CA ; 94025 ; USA
55. Center for Research in Biological Systems ; University of California ; 9500 Gilman Dr ; La Jolla ; CA ; 92093-0446 ; USA

关键词：Glycoside hydrolase ; Carbohydrate metabolism ; 3D structure ; Protein family ; Protein function prediction ; Domain of unknown function ; DUF

刊名：BMC Bioinformatics

出版年：2014

作者：Patricia Sebastian-Leon (1)
Enrique Vidal (1) (2) (3)
Pablo Minguez (1) (4)
Ana Conesa (1)
Sonia Tarazona (1)
Alicia Amadoz (1)
Carmen Armero (5)
Francisco Salavert (1) (2)
Antonio Vidal-Puig (6)
David Montaner (1)
Joaqu铆n Dopazo (1) (2) (7)

1. Department of Computational Genomics ; Centro de Investigaci贸n Pr铆ncipe Felipe (CIPF) ; Avda. Autopista del Saler ; 16 ; 46012 ; Valencia ; Spain
2. BIER ; CIBER de Enfermedades Raras (CIBERER) ; Valencia ; 46012 ; Spain
3. Present Address ; Cancer Epigenetics and Biology Program (PEBC) ; Bellvitge Biomedical Research Institute (IDIBELL) ; L鈥橦ospitalet de Llobregat ; Barcelona ; Spain
4. Present Address ; Structural and Computational Biology ; European Molecular Biology Laboratory ; Heidelberg ; 69117 ; Germany
5. Department of Statistics and Operations Research ; University of Valencia ; Valencia ; 46100 ; Spain
6. Institute of Metabolic Science - Metabolic Research Laboratories and Department of Clinical Biochemistry ; University of Cambridge ; Addenbrooke鈥檚 Hospital ; Cambridge ; CB2 0QQ ; UK
7. Functional Genomics Node ; (INB) at CIPF ; Valencia ; Spain

关键词：Signaling pathways ; Probabilistic model ; Disease mechanism ; Precision medicine ; Disease mechanism ; Cancer ; Fanconi anemia ; Obesity ; Stem cells

刊名：BMC Systems Biology

出版年：2014

作者：Janna Hastings (17)
Kenneth Haug (17)
Christoph Steinbeck (17)

17. Cheminformatics and Metabolism ; European Molecular Biology Laboratory 鈥?European Bioinformatics Institute ; Wellcome Trust Genome Campus ; CB10 1SD ; Hinxton ; UK

关键词：Software engineering ; Best practices

刊名：GigaScience

出版年：2014

作者：Kalai Vanii Jayaseelan (22)
Christoph Steinbeck (22)

22. Cheminformatics and Metabolism ; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) ; Wellcome Trust Genome Campus ; Hinxton ; Cambridge ; CB10 1SD ; UK

关键词：Computer ; assisted structure elucidation ; Metabolomics ; Natural product ; likeness

刊名：BMC Bioinformatics

出版年：2014