Biomedical Engineering Reference
In-Depth Information
38. Powell, J.R. (1996)
Progress and Prospects in Evolutionary Biology: The Drosophila Model
,
Oxford University Press, New York.
39. Cherry, J.M., Adler, C., Ball, C.
et al
. (1998) SGD:
Saccharomyces
Genome Database.
Nucleic
Acids Research
,
26
, 73-79. The SGD database provides comprehensive resources for the model
organism
S. cerevisiae
.
40. Bult, C.J., Blake, J.A., Richardson, J.E.
et al
. (2004) The Mouse Genome Database (MGD):
integrating biology with the genome.
Nucleic Acids Research
,
32
, D476-D481.
41. Stein, L., Sternberg, P., Durbin, R.
et al
. (2001) WormBase: network access to the genome and
biology of
Caenorhabditis elegans
.
Nucleic Acids Research
,
29
, 82-86.
42. Sprague, J., Clements, D., Conlin, T.
et al
. (2003) The Zebrafish Information Network (ZFIN):
the zebrafish model organism database.
Nucleic Acids Research
,
31
, 241-243.
43. Bader, G.D. and Hogue, C.W. (2000) BIND - a data specification for storing and describing
biomolecular interactions, molecular complexes and pathways.
Bioinformatics
,
16
, 465-477.
44. Breitkreutz, B.J., Stark, C., Reguly, T.
et al
. (2008) The BioGRID Interaction Database: 2008
update.
Nucleic Acids Research
,
36
, D637-D640. BioGRID is an up-to-date repository of
protein-protein interactions for a variety of species.
45. Kersey, P.J., Duarte, J., Williams, A.
et al
. (2004) The International Protein Index: an integrated
database for proteomics experiments.
Proteomics
,
4
, 1985-1988.
46. Bairoch, A., Apweiler, R., Wu, C.H.
et al
. (2005) The Universal Protein Resource (UniProt).
Nucleic Acids Research
,
33
, D154-D159.
47. Bussey, K.J., Kane, D., Sunshine, M.
et al
. (2003) MatchMiner: a tool for batch navigation among
gene and gene product identifiers.
Genome Biology
,
4
, R27.
48. Iragne, F., Barre, A., Goffard, N. and De Daruvar, A. (2004) AliasServer: a web server to handle
multiple aliases used to refer to proteins.
Bioinformatics
,
20
, 2331-2332.
49. Cote, R.G., Jones, P., Martens, L.
et al
. (2007) The Protein Identifier Cross-Referencing (PICR)
service: reconciling protein identifiers across multiple source databases.
BMC Bioinformatics
,
8
, 401.
50. Berriz, G.F. and Roth, F.P. (2008) The Synergizer service for translating gene, protein and other
biological identifiers.
Bioinformatics
,
24
, 2272-2273.
51. Altschul, S.F., Gish, W., Miller, W.
et al
. (1990) Basic local alignment search tool.
Journal
of Molecular Biology
,
215
, 403-410. BLAST is an important sequence analysis tool for both
experimental and computational biologists.
52. Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks.
Pro-
ceedings of the National Academy of Sciences of the United States of America
,
89
, 10915-10919.
53. Caspi, R., Foerster, H., Fulcher, C.A.
et al
. (2008) The MetaCyc database of metabolic pathways
and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Research
,
36
, D623-D631.
54. Martin, D.M., Berriman, M. and Barton, G.J. (2004) GOtcha: a new method for prediction of
protein function assessed by the annotation of seven genomes.
BMC Bioinformatics
,
5
, 178.
55. Chalmel, F., Lardenois, A., Thompson, J.D.
et al
. (2005) GOAnno: GO annotation based on
multiple alignment.
Bioinformatics
,
21
, 2095-2096.
56. Plewniak, F., Bianchetti, L., Brelivet, Y.
et al
. (2003) PipeAlign: a new toolkit for protein family
analysis.
Nucleic Acids Research
,
31
, 3829-3832.