Between 2013 and 2014, Biodalliance development was support by the BBSRC Tools and Resources Development Fund.
Creator and lead developer of Biodalliance. Developed Dazzle, one of the first implementation of a DAS server built on the BioJava library, which he co-founded in 2000 (Holland et al, 2008). He has also worked on sequence analysis and epigenetics, and believes that we need more scientific software that is a pleasure to use.
Has expertise in designing and writing usable software, both academic research tools (Piipari et al, 2010) and commercial applications.
Bugfinder General and feature proposer for Dalliance. Has been an advocate of DAS since its beginning, encouraging its adoption by Ensembl (Hubbard et al, 2002) and the efamily and biosapiens projects, under which Andreas Prlic developed the SPICE DAS client (Prlic et al, 2005) and the DAS registry (Prlic et al, 2007). He has had an interest in methods for layering annotation onto protein structures in a distributed way since the early days of the SCOP database (Hubbard, et al, 1995)
Special thanks to all our users, especially those who've provided feedback about early versions of Dalliance:
Guillermo Carbajosa, Nicole Cheung, Claire Chewapreecha, Alex Down, Mike Gilchrist, Jing Su, Vardhman Rakyan, Jonathan Warren
Dalliance: interactive genome viewing on the web.
Down TA, Piipari M, Hubbard TJ
Bioinformatics (2011) 27:889-890
PUBMED: 21252075;
ukPMC: 3051325
iMotifs: an integrated sequence motif visualization and
analysis environment.
Piipari M, Down TA, Saini H, Enright A and Hubbard TJP
Bioinformatics (2010) vol. 26 (6) pp. 843-4
PUBMED: 20106815;
ukPMC: 2832821
iMotifs: an integrated sequence motif visualization and
analysis environment.
Piipari M, Down TA, Saini H, Enright A and Hubbard TJP
Bioinformatics (2010) vol. 26 (6) pp. 843-4
PUBMED: 20106815;
ukPMC: 2832821
Integrating biological data - the Distributed Annotation System.
Jenkinson A, Albrecht M, Birney E, Blankenburg H, Down T, Finn R, Hermjakob H, Hubbard TJP, Jimenez R, Jones P, Kahari A, Kulesha E, Macias J, Reeves G and Prlic A
BMC Bioinformatics (2008) vol. 9 Suppl 8 pp. S3
PUBMED: 18673527;
ukPMC: 2500094
BioJava: an open-source framework for bioinformatics.
Holland RCG, Down TA, Pocock M, Prlic A, Huen D, James K, Foisy S, Drager A, Yates A, Heuer M, Schreiber MJ
Bioinformatics (2008) vol. 24 (18) pp. 2096-7
PUBMED: 18689808;
ukPMC: 2530884
Integrating sequence and structural biology with DAS.
Prlic A, Down TA, Kulesha E, Finn RD, Kahari A, Hubbard TJP
Bioinformatics (2007) vol. 8 pp. 333
PUBMED: 17850653;
ukPMC: 2031907
Adding some SPICE to DAS.
Prlic A, Down TA, Hubbard TJP
Bioinformatics (2005) vol. 21 Suppl 2 pp. ii40-1
PUBMED: 16204122;
ukPMC: 2656757
The Ensembl genome database project.
Hubbard TJP, Barker D, Birney E, Cameron G, Chen Y, Clark L,
Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J,
Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P,
Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E,
Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E,
Ureta-Vidal A, Vastrik I, Clamp M.
Nucleic Acids Res (2002) vol. 30 (1) pp. 38-41
PUBMED: 11752248;
ukPMC: 99161
SCOP: a structural classification of proteins database.
Hubbard TJP, Murzin AG, Brenner SE, Chothia C
Nucleic Acids Res (1997) vol. 25 (1) pp. 236-9
PUBMED: 9016544;
ukPMC: 146380