-
1
-
-
77955042462
-
From complete genome sequence to 'complete' understanding?
-
10.1016/j.tibtech.2010.05.006, 3065831, 20647113
-
Galperin MY, Koonin EV. From complete genome sequence to 'complete' understanding?. Trends in Biotechnology 2010, 28(8):398-406. 10.1016/j.tibtech.2010.05.006, 3065831, 20647113.
-
(2010)
Trends in Biotechnology
, vol.28
, Issue.8
, pp. 398-406
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
2
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
10.1006/jmbi.2001.4513, 11286560
-
Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology 2001, 307(4):1113-1143. 10.1006/jmbi.2001.4513, 11286560.
-
(2001)
Journal of Molecular Biology
, vol.307
, Issue.4
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
3
-
-
0034308142
-
Practical limits of function prediction
-
10.1002/1097-0134(20001001)41:1<98::AID-PROT120>3.0.CO;2-S, 10944397
-
Devos D, Valencia A. Practical limits of function prediction. Proteins 2000, 41(1):98-107. 10.1002/1097-0134(20001001)41:1<98::AID-PROT120>3.0.CO;2-S, 10944397.
-
(2000)
Proteins
, vol.41
, Issue.1
, pp. 98-107
-
-
Devos, D.1
Valencia, A.2
-
4
-
-
0142106373
-
How well is enzyme function conserved as a function of pairwise sequence identity?
-
10.1016/j.jmb.2003.08.057, 14568541
-
Tian WD, Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. Journal of Molecular Biology 2003, 333(4):863-882. 10.1016/j.jmb.2003.08.057, 14568541.
-
(2003)
Journal of Molecular Biology
, vol.333
, Issue.4
, pp. 863-882
-
-
Tian, W.D.1
Skolnick, J.2
-
5
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
10.1016/S0022-2836(02)00016-5, 12051862
-
Rost B. Enzyme function less conserved than anticipated. Journal of Molecular Biology 2002, 318(2):595-608. 10.1016/S0022-2836(02)00016-5, 12051862.
-
(2002)
Journal of Molecular Biology
, vol.318
, Issue.2
, pp. 595-608
-
-
Rost, B.1
-
6
-
-
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 Research 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Research
, 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
-
7
-
-
84874637479
-
HMMER
-
HMMER. , http://hmmer.janelia.org/
-
-
-
-
8
-
-
75549090603
-
The Pfam protein families database
-
10.1093/nar/gkp985, 2808889, 19920124
-
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Research 2010, 38:D211-D222. 10.1093/nar/gkp985, 2808889, 19920124.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
Holm, L.11
Sonnhammer, E.L.12
Eddy, S.R.13
Bateman, A.14
-
9
-
-
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, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nature Genetics
, 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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
10
-
-
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 Research 2009, 37:D396-403. 10.1093/nar/gkn803, 2686469, 18957448.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
11
-
-
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
-
12
-
-
24644503098
-
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
-
10.1093/bioinformatics/bti610, 16081474
-
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3674-3676
-
-
Conesa, A.1
Gotz, S.2
Garcia-Gomez, J.M.3
Terol, J.4
Talon, M.5
Robles, M.6
-
13
-
-
45549089420
-
High-throughput functional annotation and data mining with the Blast2GO suite
-
10.1093/nar/gkn176, 2425479, 18445632
-
Götz S, Garcia-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research 2008, 36:3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 3420-3435
-
-
Götz, S.1
Garcia-Gómez, J.M.2
Terol, J.3
Williams, T.D.4
Nagaraj, S.H.5
Nueda, M.J.6
Robles, M.7
Talón, M.8
Dopazo, J.9
Conesa, A.10
-
14
-
-
43949138227
-
Blast2GO:A comprehensive suite for functional analysis in plant genomics
-
Conesa A, Gotz S. Blast2GO:A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 2008, 2008:Article ID 619832.
-
(2008)
International Journal of Plant Genomics
, vol.2008
-
-
Conesa, A.1
Gotz, S.2
-
15
-
-
41249098849
-
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
-
10.1371/journal.pone.0001326, 2147077, 18094749
-
Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2007, 2(12):e1326. 10.1371/journal.pone.0001326, 2147077, 18094749.
-
(2007)
PLoS One
, vol.2
, Issue.12
-
-
Velasco, R.1
Zharkikh, A.2
Troggio, M.3
Cartwright, D.A.4
Cestaro, A.5
Pruss, D.6
Pindo, M.7
Fitzgerald, L.M.8
Vezzulli, S.9
Reid, J.10
Malacarne, G.11
Iliev, D.12
Coppola, G.13
Wardell, B.14
Micheletti, D.15
Macalma, T.16
Facci, M.17
Mitchell, J.T.18
Perazzolli, M.19
Eldredge, G.20
Gatto, P.21
Oyzerski, R.22
Moretto, M.23
Gutin, N.24
Stefanini, M.25
Chen, Y.26
Segala, C.27
Davenport, C.28
Demattè, L.29
Mraz, A.30
more..
-
16
-
-
77957560949
-
The genome of the domesticated apple (Malus x domestica Borkh.)
-
10.1038/ng.654, 20802477
-
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, et al. The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics 2010, 42(10):833-839. 10.1038/ng.654, 20802477.
-
(2010)
Nature Genetics
, vol.42
, Issue.10
, pp. 833-839
-
-
Velasco, R.1
Zharkikh, A.2
Affourtit, J.3
Dhingra, A.4
Cestaro, A.5
Kalyanaraman, A.6
Fontana, P.7
Bhatnagar, S.K.8
Troggio, M.9
Pruss, D.10
Salvi, S.11
Pindo, M.12
Baldi, P.13
Castelletti, S.14
Cavaiuolo, M.15
Coppola, G.16
Costa, F.17
Cova, V.18
Dal Ri, A.19
Goremykin, V.20
Komjanc, M.21
Longhi, S.22
Magnago, P.23
Malacarne, G.24
Malnoy, M.25
Micheletti, D.26
Moretto, M.27
Perazzolli, M.28
Si-Ammour, A.29
Vezzulli, S.30
more..
-
17
-
-
84874396916
-
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology
-
10.1371/journal.pone.0004619, 2645684, 19247487
-
Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S. Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS One 2009, 4(2):e4619. 10.1371/journal.pone.0004619, 2645684, 19247487.
-
(2009)
PLoS One
, vol.4
, Issue.2
-
-
Fontana, P.1
Cestaro, A.2
Velasco, R.3
Formentin, E.4
Toppo, S.5
-
18
-
-
84874623783
-
Pfam2go
-
Pfam2go. , http://www.geneontology.org/external2go/pfam2go
-
-
-
-
19
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
-
10.1093/bioinformatics/btg153, 12835272
-
Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19(10):1275-1283. 10.1093/bioinformatics/btg153, 12835272.
-
(2003)
Bioinformatics
, vol.19
, Issue.10
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
20
-
-
0005180705
-
An Information-Theoretic Definition of Similarity
-
Morgan Kaufmann Publishers Inc
-
Lin D. An Information-Theoretic Definition of Similarity. Proceedings of the Fifteenth International Conference on Machine Learning (ICML'98): 24-27, July, 1998; Madison, Wisconsin, USA 1998, 296-304. Morgan Kaufmann Publishers Inc.
-
(1998)
Proceedings of the Fifteenth International Conference on Machine Learning (ICML'98): 24-27, July, 1998; Madison, Wisconsin, USA
, pp. 296-304
-
-
Lin, D.1
-
21
-
-
0002016474
-
Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language
-
Resnik P. Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 1999, 11:95-130.
-
(1999)
Journal of Artificial Intelligence Research
, vol.11
, pp. 95-130
-
-
Resnik, P.1
-
22
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Database
-
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The Universal Protein Resource (UniProt). Nucleic Acids Research 2005, (33 Database):D154-159.
-
(2005)
Nucleic Acids Research
, Issue.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
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.S.15
-
23
-
-
84874605648
-
Argot2 web site
-
Argot2 web site. , http://www.medcomp.medicina.unipd.it/Argot2
-
-
-
-
24
-
-
84874607207
-
Critical Assessment of Function Annotations (CAFA)
-
Critical Assessment of Function Annotations (CAFA). , http://biofunctionprediction.org/
-
-
-
-
25
-
-
79651474619
-
Supplementary material web site
-
Supplementary material web site. , http://www.medcomp.medicina.unipd.it/Argot2/suppl_mat_BMC/
-
-
-
-
26
-
-
70449552832
-
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions
-
10.1371/journal.pone.0007546, 2760442, 19844580
-
Louie B, Higdon R, Kolker E. A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PLoS One 2009, 4(10):e7546. 10.1371/journal.pone.0007546, 2760442, 19844580.
-
(2009)
PLoS One
, vol.4
, Issue.10
-
-
Louie, B.1
Higdon, R.2
Kolker, E.3
-
27
-
-
84860703077
-
Disjunctive shared information between ontology concepts: application to Gene Ontology
-
Couto FM, Silva MJ. Disjunctive shared information between ontology concepts: application to Gene Ontology. J Biomed Semantics 2011, 2(5).
-
(2011)
J Biomed Semantics
, vol.2
, Issue.5
-
-
Couto, F.M.1
Silva, M.J.2
|