-
1
-
-
33748792021
-
Bio-ontologies: Current trends and future directions
-
1847325 16899495
-
Bodenreider O Stevens R Bio-ontologies: Current trends and future directions Brief Bioinform 2006, 7:256-74. 1847325 16899495
-
(2006)
Brief Bioinform
, vol.7
, pp. 256-274
-
-
Bodenreider, O.1
Stevens, R.2
-
2
-
-
33748776559
-
Automated protein function prediction - The genomic challenge
-
16772267
-
Friedberg I Automated protein function prediction - the genomic challenge Brief Bioinform 2006, 7:225-42. 16772267
-
(2006)
Brief Bioinform
, vol.7
, pp. 225-242
-
-
Friedberg, I.1
-
3
-
-
20444456581
-
Automatic annotation of protein function
-
15922590
-
Valencia A Automatic annotation of protein function Curr Opin Struct Biol 2005, 15:267-74. 15922590
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 267-274
-
-
Valencia, A.1
-
6
-
-
34547840224
-
Information theory applied to the sparse gene ontology annotation network to predict novel gene function
-
17646340
-
Tao Y Sam L Li J Friedman C Lussier YA Information theory applied to the sparse gene ontology annotation network to predict novel gene function Bioinformatics 2007, 23:i529-38. 17646340
-
(2007)
Bioinformatics
, vol.23
-
-
Tao, Y.1
Sam, L.2
Li, J.3
Friedman, C.4
Lussier, Y.A.5
-
7
-
-
24044446835
-
A semantic analysis of the annotations of the human genome
-
2435251 15955782
-
Khatri P Done B Rao A Done A Draghici S A semantic analysis of the annotations of the human genome Bioinformatics 2005, 21:3416-21. 2435251 15955782
-
(2005)
Bioinformatics
, vol.21
, pp. 3416-3421
-
-
Khatri, P.1
Done, B.2
Rao, A.3
Done, A.4
Draghici, S.5
-
8
-
-
0346728473
-
Systematic genome-wide screens of gene function
-
14708012
-
Carpenter AE Sabatini DM Systematic genome-wide screens of gene function Nat Rev Genet 2004, 5:11-22. 14708012
-
(2004)
Nat Rev Genet
, vol.5
, pp. 11-22
-
-
Carpenter, A.E.1
Sabatini, D.M.2
-
9
-
-
1342330530
-
A graph-theoretic modeling on GO space for biological interpretation of gene clusters
-
14960465
-
Lee SG Hur JU Kim YS A graph-theoretic modeling on GO space for biological interpretation of gene clusters Bioinformatics 2004, 20:381-8. 14960465
-
(2004)
Bioinformatics
, vol.20
, pp. 381-388
-
-
Lee, S.G.1
Hur, J.U.2
Kim, Y.S.3
-
14
-
-
25444482341
-
Theme discovery from gene lists for identification and viewing of multiple functional groups
-
1190153 15987504
-
Pehkonen P Wong G Toronen P Theme discovery from gene lists for identification and viewing of multiple functional groups BMC Bioinformatics 2005, 6:162. 1190153 15987504
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 162
-
-
Pehkonen, P.1
Wong, G.2
Toronen, P.3
-
15
-
-
41349115432
-
The DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene lists
-
2375021 17784955
-
Huang DW Sherman BT Tan Q Collins JR Alvord WG Roayaei J Stephens R Baseler MW Lane HC Lempicki RA The DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene lists Genome Biol 2007, 8:R183. 2375021 17784955
-
(2007)
Genome Biol
, vol.8
-
-
Huang, D.W.1
Sherman, B.T.2
Tan, Q.3
Collins, J.R.4
Alvord, W.G.5
Roayaei, J.6
Stephens, R.7
Baseler, M.W.8
Lane, H.C.9
Lempicki, R.A.10
-
16
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools, limitations, and open problems
-
2435250 15994189
-
Khatri P Draghici S Ontological analysis of gene expression data: current tools, limitations, and open problems Bioinformatics 2005, 21:3587-95. 2435250 15994189
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
18
-
-
33748335463
-
A new measure for functional similarity of gene products based on Gene Ontology
-
1559652 16776819
-
Schlicker A Domingues FS Rahnenfuhrer J Lengauer T A new measure for functional similarity of gene products based on Gene Ontology BMC Bioinformatics 2006, 7:302. 1559652 16776819
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 302
-
-
Schlicker, A.1
Domingues, F.S.2
Rahnenfuhrer, J.3
Lengauer, T.4
-
20
-
-
34548558977
-
Total ancestry measure: Quantifying the similarity in tree-like classification, with genomic applications
-
17540677
-
Yu H Jansen R Stolovitzky G Gerstein M Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications Bioinformatics 2007, 23:2163-73. 17540677
-
(2007)
Bioinformatics
, vol.23
, pp. 2163-2173
-
-
Yu, H.1
Jansen, R.2
Stolovitzky, G.3
Gerstein, M.4
-
21
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
-
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, 19:1275-83. 12835272
-
(2003)
Bioinformatics
, vol.19
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
23
-
-
34547421112
-
Defining functional distance using manifold embeddings of gene ontology annotations
-
2040899 17595300
-
Lerman G Shakhnovich BE Defining functional distance using manifold embeddings of gene ontology annotations Proc Natl Acad Sci USA 2007, 104:11334-11339. 2040899 17595300
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 11334-11339
-
-
Lerman, G.1
Shakhnovich, B.E.2
-
24
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
10802651
-
Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski T Dwight SS Eppig JT et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-9. 10802651
-
(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
Eppig, J.T.10
-
25
-
-
9144257282
-
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
-
524302 15486203
-
Ruepp A Zollner A Maier D Albermann K Hani J Mokrejs M Tetko I Guldener U Mannhaupt G Munsterkotter M et al.: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Nucleic Acids Res 2004, 32:5539-45. 524302 15486203
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5539-5545
-
-
Ruepp, A.1
Zollner, A.2
Maier, D.3
Albermann, K.4
Hani, J.5
Mokrejs, M.6
Tetko, I.7
Guldener, U.8
Mannhaupt, G.9
Munsterkotter, M.10
-
26
-
-
0036796319
-
Using text analysis to identify functionally coherent gene groups
-
187532 12368251
-
Raychaudhuri S Schutze H Altman RB Using text analysis to identify functionally coherent gene groups Genome Res 2002, 12:1582-90. 187532 12368251
-
(2002)
Genome Res
, vol.12
, pp. 1582-1590
-
-
Raychaudhuri, S.1
Schutze, H.2
Altman, R.B.3
-
27
-
-
39749095475
-
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
-
2323239 17672896
-
Zheng B Lu X Novel metrics for evaluating the functional coherence of protein groups via protein semantic network Genome Biol 2007, 8:R153. 2323239 17672896
-
(2007)
Genome Biol
, vol.8
-
-
Zheng, B.1
Lu, X.2
-
29
-
-
34547763236
-
A transversal approach to predict gene product networks from ontology-based similarity
-
1940024 17605807
-
Chabalier J Mosser J Burgun A A transversal approach to predict gene product networks from ontology-based similarity BMC Bioinformatics 2007, 8:235. 1940024 17605807
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 235
-
-
Chabalier, J.1
Mosser, J.2
Burgun, A.3
-
30
-
-
13444306676
-
CYGD: The Comprehensive Yeast Genome Database
-
540007 15608217
-
Guldener U Munsterkotter M Kastenmuller G Strack N van Helden J Lemer C Tichelles J Wodak SJ Garcia-Martinez J Perez-Ortin JE et al.: CYGD: the Comprehensive Yeast Genome Database Nucleic Acids Res 2005, 33:D364-8. 540007 15608217
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Guldener, U.1
Munsterkotter, M.2
Kastenmuller, G.3
Strack, N.4
van Helden, J.5
Lemer, C.6
Richelles, J.7
Wodak, S.J.8
Garcia-Martinez, J.9
Perez-Ortin, J.E.10
-
32
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
11805826
-
Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM et al.: Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415:141-7. 11805826
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
-
33
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
11805837
-
Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL Millar A Taylor P Bennett K Boutilier K et al.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415:180-3. 11805837
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
-
34
-
-
10744227471
-
High-definition macromolecular composition of yeast RNA-processing complexes
-
14759368
-
Krogan NJ Peng WT Cagney G Robinson MD Haw R Zhong G Guo X Zhang X Canadien V Richards DP et al.: High-definition macromolecular composition of yeast RNA-processing complexes Mol Cell 2004, 13:225-39. 14759368
-
(2004)
Mol Cell
, vol.13
, pp. 225-239
-
-
Krogan, N.J.1
Peng, W.T.2
Cagney, G.3
Robinson, M.D.4
Haw, R.5
Zhong, G.6
Guo, X.7
Zhang, X.8
Canadien, V.9
Richards, D.P.10
-
36
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
14735121
-
Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5:101-13. 14735121
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
37
-
-
33947730844
-
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
-
17370254
-
Pu S Vlasblom J Emili A Greenblatt J Wodak SJ Identifying functional modules in the physical interactome of Saccharomyces cerevisiae Proteomics 2007, 7:944-60. 17370254
-
(2007)
Proteomics
, vol.7
, pp. 944-960
-
-
Pu, S.1
Vlasblom, J.2
Emili, A.3
Greenblatt, J.4
Wodak, S.J.5
-
38
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
16554755
-
Krogan NJ Cagney G Yu H Zhong G Guo X Ignatchenko A Li J Pu S Datta N Tikuisis AP et al.: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006, 440:637-43. 16554755
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
-
39
-
-
33748701649
-
Detecting functional modules in the yeast protein-protein interaction network
-
16837529
-
Chen J Yuan B Detecting functional modules in the yeast protein-protein interaction network Bioinformatics 2006, 22:2283-90. 16837529
-
(2006)
Bioinformatics
, vol.22
, pp. 2283-2290
-
-
Chen, J.1
Yuan, B.2
-
40
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
17200106
-
Collins SR Kemmeren P Zhao XC Greenblatt JF Spencer F Holstege FC Weissman JS Krogan NJ Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae Mol Cell Proteomics 2007, 6:439-50. 17200106
-
(2007)
Mol Cell Proteomics
, vol.6
, pp. 439-450
-
-
Collins, S.R.1
Kemmeren, P.2
Zhao, X.C.3
Greenblatt, J.F.4
Spencer, F.5
Holstege, F.C.6
Weissman, J.S.7
Krogan, N.J.8
-
41
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
16429126
-
Gavin AC Aloy P Grandi P Krause R Boesche M Marzioch M Rau C Jensen LJ Bastuck S Dumpelfeld B et al.: Proteome survey reveals modularity of the yeast cell machinery Nature 2006, 440:631-6. 16429126
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
-
42
-
-
34547840254
-
Identification of functional modules from conserved ancestral protein-protein interactions
-
17646291
-
Dutkowski J Tiuryn J Identification of functional modules from conserved ancestral protein-protein interactions Bioinformatics 2007, 23:i149-58. 17646291
-
(2007)
Bioinformatics
, vol.23
-
-
Dutkowski, J.1
Tiuryn, J.2
-
43
-
-
33646358998
-
Prediction of yeast protein-protein interaction network: Insights from the Gene Ontology and annotations
-
1449908 16641319
-
Wu X Zhu L Guo J Zhang DY Lin K Prediction of yeast protein-protein interaction network: Insights from the Gene Ontology and annotations Nucleic Acids Res 2006, 34:2137-50. 1449908 16641319
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2137-2150
-
-
Wu, X.1
Zhu, L.2
Guo, J.3
Zhang, D.Y.4
Lin, K.5
-
45
-
-
33644856110
-
Improving missing value estimation in microarray data with gene ontology
-
16377613
-
Tuikkala J Elo L Nevalainen OS Aittokallio T Improving missing value estimation in microarray data with gene ontology Bioinformatics 2006, 22:566-72. 16377613
-
(2006)
Bioinformatics
, vol.22
, pp. 566-572
-
-
Tuikkala, J.1
Elo, L.2
Nevalainen, O.S.3
Aittokallio, T.4
|