-
1
-
-
0031897589
-
Predicting functions from protein sequences-where are the bottlenecks?
-
Bork, P. and Koonin, E.V. (1998) Predicting functions from protein sequences-where are the bottlenecks? Nat. Genet., 18, 313-318.
-
(1998)
Nat. Genet.
, vol.18
, pp. 313-318
-
-
Bork, P.1
Koonin, E.V.2
-
2
-
-
0032229196
-
Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
-
Galperin, M.Y. and Koonin, E.V. (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1, 55-67.
-
(1998)
Silico Biol.
, vol.1
, pp. 55-67
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
3
-
-
33746664765
-
Can sequence determine function?
-
Gerlt, J.A. and Babbitt, P.C. (2000) Can sequence determine function? Genome Biol., 1, REVIEWS0005.
-
(2000)
Genome Biol.
, vol.1
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
4
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
-
(1970)
Syst. Zool.
, vol.19
, pp. 99-113
-
-
Fitch, W.M.1
-
5
-
-
0036851263
-
Signatures of domain shuffling in the human genome
-
Kaessmann, H., Zollner, S., Nekrutenko, A. and Li, W.H. (2002) Signatures of domain shuffling in the human genome. Genome Res., 12, 1642-1650.
-
(2002)
Genome Res.
, vol.12
, pp. 1642-1650
-
-
Kaessmann, H.1
Zollner, S.2
Nekrutenko, A.3
Li, W.H.4
-
6
-
-
0346734184
-
Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors
-
Rajalingam, R., Parham, P. and Abi-Rached, L. (2004) Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors. J. Immunol., 172, 356-369.
-
(2004)
J. Immunol.
, vol.172
, pp. 356-369
-
-
Rajalingam, R.1
Parham, P.2
Abi-Rached, L.3
-
7
-
-
0033119399
-
Errors in genome annotation
-
Brenner, S.E. (1999) Errors in genome annotation. Trends Genet., 15, 132-133.
-
(1999)
Trends Genet.
, vol.15
, pp. 132-133
-
-
Brenner, S.E.1
-
8
-
-
33745630672
-
Functional classification using phylogenomic inference
-
Brown, D. and Sjolander, K. (2006) Functional classification using phylogenomic inference. PLoS Comput. Biol., 2, e77.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Brown, D.1
Sjolander, K.2
-
9
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
Eisen, J.A. (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res., 8, 163-167.
-
(1998)
Genome Res.
, vol.8
, pp. 163-167
-
-
Eisen, J.A.1
-
10
-
-
1042280957
-
Phylogenomic inference of protein molecular function: Advances and challenges
-
Sjolander, K. (2004) Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20, 170-179.
-
(2004)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjolander, K.1
-
11
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
Storm, C.E. and Sonnhammer, E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18, 92-99.
-
(2002)
Bioinformatics
, vol.18
, pp. 92-99
-
-
Storm, C.E.1
Sonnhammer, E.L.2
-
12
-
-
0013017592
-
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
Zmasek, C.M. and Eddy, S.R. (2002) RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3, 14.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 14
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
13
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
-
14
-
-
33750474439
-
PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification
-
Krishnamurthy, N., Brown, D.P., Kirshner, D. and Sjolander, K. (2006) PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol., 7, R83.
-
(2006)
Genome Biol.
, vol.7
-
-
Krishnamurthy, N.1
Brown, D.P.2
Kirshner, D.3
Sjolander, K.4
-
15
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
16
-
-
34248145506
-
FlowerPower: Clustering proteins into domain architecture classes for phylogenomic inference of protein function
-
Krishnamurthy, N., Brown, D. and Sjolander, K. (2007) FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function. BMC Evol. Biol., 7(Suppl. 1), S12.
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Krishnamurthy, N.1
Brown, D.2
Sjolander, K.3
-
17
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
-
18
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
19
-
-
0029906607
-
Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology
-
Sjolander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I.S. and Haussler, D. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
-
(1996)
Comput. Appl. Biosci.
, vol.12
, pp. 327-345
-
-
Sjolander, K.1
Karplus, K.2
Brown, M.3
Hughey, R.4
Krogh, A.5
Mian, I.S.6
Haussler, D.7
-
20
-
-
0042594474
-
SATCHMO: Sequence align ment and tree construction using hidden Markov models
-
Edgar, R.C. and Sjolander, K. (2003) SATCHMO: sequence align ment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
-
(2003)
Bioinformatics
, vol.19
, pp. 1404-1411
-
-
Edgar, R.C.1
Sjolander, K.2
-
21
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
Edgar, R.C. and Sjolander, K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, 20, 1301-1308.
-
(2004)
Bioinformatics
, vol.20
, pp. 1301-1308
-
-
Edgar, R.C.1
Sjolander, K.2
-
22
-
-
2942544229
-
COACH: Profile-profile alignment of protein families using hidden Markov models
-
Edgar, R.C. and Sjolander, K. (2004) COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics, 20, 1309-1318.
-
(2004)
Bioinformatics
, vol.20
, pp. 1309-1318
-
-
Edgar, R.C.1
Sjolander, K.2
-
23
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev, R. and Grishin, N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
24
-
-
0031604140
-
Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
-
Sjolander, K. (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 165-174.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.6
, pp. 165-174
-
-
Sjolander, K.1
-
25
-
-
15944408886
-
Subfamily hmms in functional genomics
-
Brown, D., Krishnamurthy, N., Dale, J.M., Christopher, W. and Sjolander, K. (2005) Subfamily hmms in functional genomics. Pac. Symp. Biocomput., 10, 322-333.
-
(2005)
Pac. Symp. Biocomput.
, vol.10
, pp. 322-333
-
-
Brown, D.1
Krishnamurthy, N.2
Dale, J.M.3
Christopher, W.4
Sjolander, K.5
-
26
-
-
0035025126
-
ATV: Display and manipulation of annotated phylogenetic trees
-
Zmasek, C.M. and Eddy, S.R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17, 383-384.
-
(2001)
Bioinformatics
, vol.17
, pp. 383-384
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
27
-
-
84862541260
-
3.6a2.1 ed. Distributed by the author
-
University of Washingtion, Seattle
-
Felsenstein, J. (2005). 3.6a2.1 ed. Distributed by the author. Department of Genome Science, University of Washingtion, Seattle.
-
(2005)
Department of Genome Science
-
-
Felsenstein, J.1
-
28
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
-
29
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Kall, L., Krogh, A. and Sonnhammer, E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338, 1027-1036.
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 1027-1036
-
-
Kall, L.1
Krogh, A.2
Sonnhammer, E.L.3
-
30
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
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