-
1
-
-
74549221383
-
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
-
10.1371/journal.pcbi.1000605, 2781113, 20011109
-
Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies. PLoS Comput Biol 2009, 5(12):e1000605. 10.1371/journal.pcbi.1000605, 2781113, 20011109.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.12
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
2
-
-
34250790725
-
Estimating the annotation error rate of curated GO database sequence annotations
-
10.1186/1471-2105-8-170, 1892569, 17519041
-
Jones CE, Brown AL, Baumann U. Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 2007, 8:170. 10.1186/1471-2105-8-170, 1892569, 17519041.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 170
-
-
Jones, C.E.1
Brown, A.L.2
Baumann, U.3
-
3
-
-
34547844156
-
Manual curation is not sufficient for annotation of genomic databases
-
10.1093/bioinformatics/btm229, 2516305, 17646325
-
Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 2007, 23(13):i41-48. 10.1093/bioinformatics/btm229, 2516305, 17646325.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Baumgartner, W.A.1
Cohen, K.B.2
Fox, L.M.3
Acquaah-Mensah, G.4
Hunter, L.5
-
4
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
3013648, 21051339
-
Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, 39(Database):D214-219. 3013648, 21051339.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE
-
-
-
5
-
-
79958759599
-
Analysis of protein function and its prediction from amino acid sequence
-
10.1002/prot.23029, 21671271
-
Clark WT, Radivojac P. Analysis of protein function and its prediction from amino acid sequence. Proteins 2011, 79(7):2086-2096. 10.1002/prot.23029, 21671271.
-
(2011)
Proteins
, vol.79
, Issue.7
, pp. 2086-2096
-
-
Clark, W.T.1
Radivojac, P.2
-
6
-
-
84858602406
-
InterPro in 2011: new developments in the family and domain prediction database
-
3245097, 22096229
-
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 2012, 40(Database):D306-312. 3245097, 22096229.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE
-
-
Hunter, S.1
Jones, P.2
Mitchell, A.3
Apweiler, R.4
Attwood, T.K.5
Bateman, A.6
Bernard, T.7
Binns, D.8
Bork, P.9
Burge, S.10
-
7
-
-
84862231127
-
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis
-
3245158, 22139938
-
Lees J, Yeats C, Perkins J, Sillitoe I, Rentzsch R, Dessailly BH, Orengo C. Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res 2012, 40(Database):D465-471. 3245158, 22139938.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE
-
-
Lees, J.1
Yeats, C.2
Perkins, J.3
Sillitoe, I.4
Rentzsch, R.5
Dessailly, B.H.6
Orengo, C.7
-
8
-
-
80555156606
-
Genome-scale phylogenetic function annotation of large and diverse protein families
-
10.1101/gr.104687.109, 3205580, 21784873
-
Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res 2011, 21(11):1969-1980. 10.1101/gr.104687.109, 3205580, 21784873.
-
(2011)
Genome Res
, vol.21
, Issue.11
, pp. 1969-1980
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Srouji, J.R.3
Brenner, S.E.4
-
9
-
-
13244268370
-
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
-
10.1186/1471-2105-5-178, 535938, 15550167
-
Martin DM, Berriman M, Barton GJ. GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004, 5:178. 10.1186/1471-2105-5-178, 535938, 15550167.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 178
-
-
Martin, D.M.1
Berriman, M.2
Barton, G.J.3
-
10
-
-
59849089151
-
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
-
10.1002/prot.22172, 18655063
-
Hawkins T, Chitale M, Luban S, Kihara D. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins 2009, 74(3):566-582. 10.1002/prot.22172, 18655063.
-
(2009)
Proteins
, vol.74
, Issue.3
, pp. 566-582
-
-
Hawkins, T.1
Chitale, M.2
Luban, S.3
Kihara, D.4
-
11
-
-
0037460964
-
Prediction of human protein function according to Gene Ontology categories
-
10.1093/bioinformatics/btg036, 12651722
-
Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics 2003, 19(5):635-642. 10.1093/bioinformatics/btg036, 12651722.
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 635-642
-
-
Jensen, L.J.1
Gupta, R.2
Staerfeldt, H.H.3
Brunak, S.4
-
12
-
-
48449088976
-
FFPred: an integrated feature-based function prediction server for vertebrate proteomes
-
10.1093/nar/gkn193, 2447771, 18463141
-
Lobley AE, Nugent T, Orengo CA, Jones DT. FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 2008, 36(Web Server):W297-302. 10.1093/nar/gkn193, 2447771, 18463141.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.WEB SERVER
-
-
Lobley, A.E.1
Nugent, T.2
Orengo, C.A.3
Jones, D.T.4
-
13
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
10.1073/pnas.95.25.14863, 24541, 9843981
-
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
14
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
10.1073/pnas.97.1.262, 26651, 10618406
-
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000, 97(1):262-267. 10.1073/pnas.97.1.262, 26651, 10618406.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.1
, pp. 262-267
-
-
Brown, M.P.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
Furey, T.S.6
Ares, M.7
Haussler, D.8
-
15
-
-
78649679994
-
Recent advances in clustering methods for protein interaction networks
-
10.1186/1471-2164-11-S3-S10, 2999340, 21143777
-
Wang J, Li M, Deng Y, Pan Y. Recent advances in clustering methods for protein interaction networks. BMC Genomics 2010, 11(Suppl 3):S10. 10.1186/1471-2164-11-S3-S10, 2999340, 21143777.
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 3
-
-
Wang, J.1
Li, M.2
Deng, Y.3
Pan, Y.4
-
16
-
-
33746903958
-
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium
-
0002, 1681453, 16729037
-
Tanay A, Steinfeld I, Kupiec M, Shamir R. Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol 2005, 1:2005. 0002, 1681453, 16729037.
-
(2005)
Mol Syst Biol
, vol.1
, pp. 2005
-
-
Tanay, A.1
Steinfeld, I.2
Kupiec, M.3
Shamir, R.4
-
17
-
-
47549098812
-
A race through the maze of genomic evidence
-
10.1186/gb-2008-9-s1-s1, 2447543, 18613945
-
Hughes TR, Roth FP. A race through the maze of genomic evidence. Genome Biol 2008, 9(Suppl 1):S1. 10.1186/gb-2008-9-s1-s1, 2447543, 18613945.
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Hughes, T.R.1
Roth, F.P.2
-
18
-
-
47549116997
-
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
-
10.1186/gb-2008-9-s1-s2, 2447536, 18613946
-
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 2008, 9(Suppl 1):S2. 10.1186/gb-2008-9-s1-s2, 2447536, 18613946.
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Pena-Castillo, L.1
Tasan, M.2
Myers, C.L.3
Lee, H.4
Joshi, T.5
Zhang, C.6
Guan, Y.7
Leone, M.8
Pagnani, A.9
Kim, W.K.10
-
19
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, 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
Eppig, J.T.10
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, 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
-
21
-
-
34347388470
-
UniRef: comprehensive and non-redundant UniProt reference clusters
-
10.1093/bioinformatics/btm098, 17379688
-
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 2007, 23(10):1282-1288. 10.1093/bioinformatics/btm098, 17379688.
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
23
-
-
75549085495
-
EggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
-
10.1093/nar/gkp951, 2808932, 19900971
-
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, 38(Database):D190-195. 10.1093/nar/gkp951, 2808932, 19900971.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.DATABASE
-
-
Muller, J.1
Szklarczyk, D.2
Julien, P.3
Letunic, I.4
Roth, A.5
Kuhn, M.6
Powell, S.7
von Mering, C.8
Doerks, T.9
Jensen, L.J.10
-
24
-
-
58149187893
-
The GOA database in 2009--an integrated Gene Ontology Annotation resource
-
10.1093/nar/gkn803, 2686469, 18957448
-
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2009, 37(Database):D396-403. 10.1093/nar/gkn803, 2686469, 18957448.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
25
-
-
84879307762
-
Human protein function prediction: application of machine learning for integration of heterogeneous data sources
-
London: University College London
-
Lobley AE. Human protein function prediction: application of machine learning for integration of heterogeneous data sources. Doctoral Thesis 2010, London: University College London.
-
(2010)
Doctoral Thesis
-
-
Lobley, A.E.1
-
26
-
-
47149083877
-
Metrics for GO based protein semantic similarity: a systematic evaluation
-
10.1186/1471-2105-9-S5-S4, 2367622, 18460186
-
Pesquita C, Faria D, Bastos H, Ferreira AE, Falcao AO, Couto FM. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 2008, 9(Suppl 5):S4. 10.1186/1471-2105-9-S5-S4, 2367622, 18460186.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 5
-
-
Pesquita, C.1
Faria, D.2
Bastos, H.3
Ferreira, A.E.4
Falcao, A.O.5
Couto, F.M.6
-
27
-
-
65449147869
-
The use of gene ontology evidence codes in preventing classifier assessment bias
-
10.1093/bioinformatics/btp122, 19254922
-
Rogers MF, Ben-Hur A. The use of gene ontology evidence codes in preventing classifier assessment bias. Bioinformatics 2009, 25(9):1173-1177. 10.1093/bioinformatics/btp122, 19254922.
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1173-1177
-
-
Rogers, M.F.1
Ben-Hur, A.2
-
28
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
|