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Ewan Birney et al. An Overview of Ensembl
Genome Res. 2004 14: 925-928.
http://www.genome.org/cgi/content/abstract/14/5/925

Arne Stabenau et al. The Ensembl Core Software Libraries
Genome Res. 2004 14: 929-933.
http://www.genome.org/cgi/content/abstract/14/5/929

Simon C. Potter et al. The Ensembl Analysis Pipeline
Genome Res. 2004 14: 934-941.
http://www.genome.org/cgi/content/abstract/14/5/934

Val Curwen et al. The Ensembl Automatic Gene Annotation System
Genome Res. 2004 14: 942-950.
http://www.genome.org/cgi/content/abstract/14/5/942

James Stalker et al. The Ensembl Web Site: Mechanics of a Genome Browser
Genome Res. 2004 14: 951-955.
http://www.genome.org/cgi/content/abstract/14/5/951

Stephen B. Montgomery et al Sockeye: A 3D Environment for Comparative Genomics
Genome Res. 2004 14: 956-962.
http://www.genome.org/cgi/content/abstract/14/5/956

Stephen M.J. Searle et al. The Otter Annotation System
Genome Res. 2004 14: 963-970.
http://www.genome.org/cgi/content/abstract/14/5/963

James A. Cuff et al. The Ensembl Computing Architecture
Genome Res. 2004 14: 971-975.
http://www.genome.org/cgi/content/abstract/14/5/971

Eduardo Eyras et al. ESTGenes: Alternative Splicing From ESTs in Ensembl
Genome Res. 2004 14: 976-987.
http://www.genome.org/cgi/content/abstract/14/5/976

Ewan Birney et al. GeneWise and Genomewise
Genome Res. 2004 14: 988-995.
http://www.genome.org/cgi/content/abstract/14/5/988

An overview of recent developments, focusing on the web site:

Hammond, M.P. & Birney, E. Genome information resources - developments at Ensembl
Trends in Genetics 20: 268-272 (2004)
(Issue 6, June 2004)
http://dx.doi.org/10.1016/j.tig.2004.04.002
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15145580

These short papers provide a good introduction to the development of the Ensembl project:

Hubbard, T. et al. The Ensembl genome database project.
Nucleic Acids Research 30: 38-41 (2002)
http://nar.oupjournals.org/cgi/content/full/30/1/38

Clamp, M. et al. Ensembl 2002: accommodating comparative genomics.
Nucleic Acids Research 31: 38-42 (2003)
http://nar.oupjournals.org/cgi/content/full/31/1/38

Birney, E. et al. Ensembl 2004
Nucleic Acids Research 32: D468-D470 (2004)
http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D468

EnsMart is described here:

Kasprzyk, A. et al. EnsMart: A Generic System for Fast and Flexible Access to Biological Data.
Genome Research 14:160-169 (2004)
http://www.genome.org/cgi/content/full/14/1/160

An update on the Anopheles gambiae genome and Ensembl:

Mongin, E. et al. The Anopheles gambiae genome: an update.
Trends in Parasitology 20: 49-52 (2004)
http://dx.doi.org/10.1016/j.pt.2003.11.003
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14747013&dopt=Abstract