The Ensembl genome database project. - Tim J. P. Hubbard; Daniel Barker; Ewan Birney; Graham Cameron; Yuan Chen 007; Laura Clarke; Tony Cox 001; James A. Cuff; Val Curwen; Thomas A. Down; Richard Durbin; Eduardo Eyras; et al. (Nucleic Acids Res., 2002)

ddbRNA: detection of conserved secondary structures in multiple alignments. - Diego di Bernardo; Thomas A. Down; Tim J. P. Hubbard (Bioinform., 2003)

Ensembl 2002: accommodating comparative genomics. - Michele E. Clamp; T. Daniel Andrews; Daniel Barker; Paul Bevan 001; Graham Cameron; Yuan Chen 007; Laura Clarke; Tony Cox 001; James A. Cuff; Val Curwen; Thomas A. Down; Richard Durbin; et al. (Nucleic Acids Res., 2003)

What can we learn from noncoding regions of similarity between genomes? - Thomas A. Down; Tim J. P. Hubbard (BMC Bioinform., 2004)

Ensembl 2004. - Ewan Birney; T. Daniel Andrews; Paul Bevan 001; Mario Cáccamo; Graham Cameron; Yuan Chen 007; Laura Clarke; Guy Coates; Tony Cox 001; James A. Cuff; Val Curwen; Tim Cutts; et al. (Nucleic Acids Res., 2004)

Adding Some SPICE to DAS. - Andreas Prlic; Thomas A. Down; Tim J. P. Hubbard (ECCB/JBI, 2005)

Dasty and UniProt DAS: a perfect pair for protein feature visualization. - Philip Jones; Nisha Vinod; Thomas A. Down; Andre Hackmann; Andreas Kähäri; Ernst Kretschmann; Antony F. Quinn; Daniela Wieser; Henning Hermjakob; Rolf Apweiler (Bioinform., 2005)

Ensembl 2005. - Tim J. P. Hubbard; D. Andrews; Mario Cáccamo; Graham Cameron; Yuan Chen 007; Michele E. Clamp; Laura Clarke; Guy Coates; Tony Cox 001; Fiona Cunningham; Val Curwen; Tim Cutts; et al. (Nucleic Acids Res., 2005)

The Distributed Annotation System for Integration of Biological Data. - Andreas Prlic; Ewan Birney; Tony Cox 001; Thomas A. Down; Robert D. Finn; Stefan Gräf; David K. Jackson; Andreas Kähäri; Eugene Kulesha; Roger Pettett; James A. Smith; Jim Stalker; et al. (DILS, 2006)

A machine learning strategy to identify candidate binding sites in human protein-coding sequence. - Thomas A. Down; Bernard Leong; Tim J. P. Hubbard (BMC Bioinform., 2006)

Ensembl 2006. - Ewan Birney; T. Daniel Andrews; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Tony Cox 001; Fiona Cunningham; Val Curwen; Tim Cutts; Thomas A. Down; Richard Durbin; et al. (Nucleic Acids Res., 2006)

Integrating sequence and structural biology with DAS. - Andreas Prlic; Thomas A. Down; Eugene Kulesha; Robert D. Finn; Andreas Kähäri; Tim J. P. Hubbard (BMC Bioinform., 2007)

Ensembl 2007. - Tim J. P. Hubbard; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2007)

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster. - Thomas A. Down; Casey M. Bergman; Jing Su; Tim J. P. Hubbard (PLoS Comput. Biol., 2007)

BioJava: an open-source framework for bioinformatics. - Richard C. G. Holland; Thomas A. Down; Matthew R. Pocock; Andreas Prlic; David S. Huen; Keith James; Sylvain Foisy; Andreas Dräger; Andy Yates; Michael L. Heuer; Mark J. Schreiber (Bioinform., 2008)

NestedMICA as an ab initio protein motif discovery tool. - Mutlu Dogruel; Thomas A. Down; Tim J. P. Hubbard (BMC Bioinform., 2008)

Integrating biological data - the Distributed Annotation System. - Andrew M. Jenkinson; Mario Albrecht; Ewan Birney; Hagen Blankenburg; Thomas A. Down; Robert D. Finn; Henning Hermjakob; Tim J. P. Hubbard; Rafael C. Jiménez; Philip Jones; Andreas Kähäri; Eugene Kulesha; et al. (BMC Bioinform., 2008)

Ensembl 2008. - Paul Flicek; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2008)

iMotifs: an integrated sequence motif visualization and analysis environment. - Matias Piipari; Thomas A. Down; Harpreet Kaur Saini; Anton J. Enright; Tim J. P. Hubbard (Bioinform., 2010)

Metamotifs - a generative model for building families of nucleotide position weight matrices. - Matias Piipari; Thomas A. Down; Tim J. P. Hubbard (BMC Bioinform., 2010)

Assessing Computational Methods of Cis-Regulatory Module Prediction. - Jing Su; Sarah A. Teichmann; Thomas A. Down (PLoS Comput. Biol., 2010)

Dalliance: interactive genome viewing on the web. - Thomas A. Down; Matias Piipari; Tim J. P. Hubbard (Bioinform., 2011)

An interactive genome browser of association results from the UK10K cohorts project. - Matthias Geihs; Ying Yan; Klaudia Walter; Jie Huang; Yasin Memari; Josine L. Min; Daniel Mead; Tim J. P. Hubbard; Nicholas J. Timpson; Thomas A. Down; Nicole Soranzo (Bioinform., 2015)

WormBase 2016: expanding to enable helminth genomic research. - Kevin L. Howe; Bruce J. Bolt; Scott Cain; Juancarlos Chan; Wen J. Chen; Paul Davis 001; James Done; Thomas A. Down; Sibyl Gao; Christian A. Grove; Todd W. Harris; Ranjana Kishore; et al. (Nucleic Acids Res., 2016)