-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 17 (1997), 3389-3402.
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
-
2
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner, M., Ball, C.A., Blake, J.A., et al. Gene Ontology: tool for the unification of biology. Nat Genet 25, 1 (2000), 25-29.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
3
-
-
33748940447
-
Analysis and comparison of benchmarks for multiple sequence alignment
-
Blackshields, G., Wallace, I.M., Larkin, M., and Higgins, D.G. Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biology 6, 4 (2006), 321-339.
-
(2006)
Silico Biology
, vol.6
, Issue.4
, pp. 321-339
-
-
Blackshields, G.1
Wallace, I.M.2
Larkin, M.3
Higgins, D.G.4
-
4
-
-
0034060929
-
Powers and pitfalls in sequence analysis: The 70% hurdle
-
Bork, P. Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Research 10, 4 (2000), 398-400.
-
(2000)
Genome Research
, vol.10
, Issue.4
, pp. 398-400
-
-
Bork, P.1
-
5
-
-
0033119399
-
Errors in genome annotation
-
Brenner, S.E. Errors in genome annotation. Trends in Genetics 15, 4 (1999), 132-133.
-
(1999)
Trends in Genetics
, vol.15
, Issue.4
, pp. 132-133
-
-
Brenner, S.E.1
-
6
-
-
0034308142
-
Practical limits of function prediction
-
Devos, D. and Valencia, A. Practical limits of function prediction. Proteins: Structure, Function, and Genetics 41, 1 (2000), 98-107.
-
(2000)
Proteins: Structure, Function, and Genetics
, vol.41
, Issue.1
, pp. 98-107
-
-
Devos, D.1
Valencia, A.2
-
7
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S.R. Profile hidden Markov models. Bioinformatics 14, 9 (1998), 755-763.
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
8
-
-
0035798406
-
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
-
Gough, J., Karplus, K., Hughey, R., and Chothia, C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Journal of Molecular Biology 313, 4 (2001), 903-919.
-
(2001)
Journal of Molecular Biology
, vol.313
, Issue.4
, pp. 903-919
-
-
Gough, J.1
Karplus, K.2
Hughey, R.3
Chothia, C.4
-
9
-
-
34250790725
-
Estimating the annotation error rate of curated GO database sequence annotations
-
Jones, C., Brown, A., and Baumann, U. Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8, 1 (2007), 170.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.1
, pp. 170
-
-
Jones, C.1
Brown, A.2
Baumann, U.3
-
10
-
-
2342526611
-
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
-
Kolker, E., Makarova, K.S., Shabalina, S., et al. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucl. Acids Res. 32, 8 (2004), 2353-2361.
-
(2004)
Nucl. Acids Res.
, vol.32
, Issue.8
, pp. 2353-2361
-
-
Kolker, E.1
Makarova, K.S.2
Shabalina, S.3
-
11
-
-
13844316454
-
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations
-
Kolker, E., Picone, A.F., Galperin, M.Y., et al. Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. PNAS 102, 6 (2005), 2099-2104.
-
(2005)
PNAS
, vol.102
, Issue.6
, pp. 2099-2104
-
-
Kolker, E.1
Picone, A.F.2
Galperin, M.Y.3
-
12
-
-
0038444287
-
Initial proteome analysis of model microorganism haemophilus influenzae strain Rd KW20
-
Kolker, E., Purvine, S., Galperin, M.Y., et al. Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20. J. Bacteriol. 185, 15 (2003), 4593-4602.
-
(2003)
J. Bacteriol.
, vol.185
, Issue.15
, pp. 4593-4602
-
-
Kolker, E.1
Purvine, S.2
Galperin, M.Y.3
-
14
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
-
Lord, P.W., Stevens, R.D., Brass, A., and Goble, C.A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19, 10 (2003), 1275-1283.
-
(2003)
Bioinformatics
, vol.19
, Issue.10
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
15
-
-
80053457313
-
Quantifying protein function specificity in the gene ontology
-
in press
-
Louie, B., Bergen, S., Higdon, R., and Kolker, E. Quantifying Protein Function Specificity in the Gene Ontology. Standards in Genomic Sciences (in press), .
-
Standards in Genomic Sciences
-
-
Louie, B.1
Bergen, S.2
Higdon, R.3
Kolker, E.4
-
16
-
-
70449552832
-
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions
-
Louie, B., Higdon, R., and Kolker, E. A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions. PLoS ONE 4, 10 (2009), e7546.
-
(2009)
PLoS ONE
, vol.4
, Issue.10
-
-
Louie, B.1
Higdon, R.2
Kolker, E.3
-
17
-
-
51349145617
-
Validating annotations for uncharacterized proteins in Shewanella oneidensis
-
Louie, B., Tarczy-Hornoch, P., Higdon, R., and Kolker, E. Validating annotations for uncharacterized proteins in Shewanella oneidensis. Omics: A Journal of Integrative Biology 12, 3 (2008), 211-215.
-
(2008)
Omics: A Journal of Integrative Biology
, vol.12
, Issue.3
, pp. 211-215
-
-
Louie, B.1
Tarczy-Hornoch, P.2
Higdon, R.3
Kolker, E.4
-
18
-
-
13444272087
-
Entrez gene: Gene-centered information at NCBI
-
Maglott, D., Ostell, J., Pruitt, K.D., and Tatusova, T. Entrez Gene: gene-centered information at NCBI. Nucl. Acids Res. 33, suppl. 1 (2005), D54-58.
-
(2005)
Nucl. Acids Res.
, vol.33
, Issue.SUPPL. 1
-
-
Maglott, D.1
Ostell, J.2
Pruitt, K.D.3
Tatusova, T.4
-
19
-
-
0028341506
-
Comparative analysis of multiple protein-sequence alignment methods
-
McClure, M.A., Vasi, T.K., and Fitch, W.M. Comparative analysis of multiple protein-sequence alignment methods. Molecular Biology and Evolution 11, 4 (1994), 571-592.
-
(1994)
Molecular Biology and Evolution
, vol.11
, Issue.4
, pp. 571-592
-
-
McClure, M.A.1
Vasi, T.K.2
Fitch, W.M.3
-
20
-
-
47149083877
-
Metrics for GO based protein semantic similarity: A systematic evaluation
-
Pesquita, C., Faria, D., Bastos, H., Ferreira, A., Falcao, A., and Couto, F. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 9, Suppl 5 (2008), S4.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 5
-
-
Pesquita, C.1
Faria, D.2
Bastos, H.3
Ferreira, A.4
Falcao, A.5
Couto, F.6
-
21
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. Twilight zone of protein sequence alignments. Protein Eng. 12, 2 (1999), 85-94.
-
(1999)
Protein Eng.
, vol.12
, Issue.2
, pp. 85-94
-
-
Rost, B.1
-
22
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson, J., Plewniak, F., and Poch, O. A comprehensive comparison of multiple sequence alignment programs. Nucl. Acids Res. 27, 13 (1999), 2682-2690.
-
(1999)
Nucl. Acids Res.
, vol.27
, Issue.13
, pp. 2682-2690
-
-
Thompson, J.1
Plewniak, F.2
Poch, O.3
-
23
-
-
20444456581
-
Automatic annotation of protein function
-
Valencia, A. Automatic annotation of protein function. Current Opinion in Structural Biology 15, 3 (2005), 267-274.
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.3
, pp. 267-274
-
-
Valencia, A.1
|