-
1
-
-
33846107312
-
GO PaD: The gene ontology partition database
-
Alterovitz, G. et al. (2007) GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res., 35, D322-D327.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Alterovitz, G.1
-
2
-
-
34748833491
-
Exploring inconsistencies in genome-wide protein function annotations: A machine learning approach
-
Andorf, C. et al. (2007) Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. BMC Bioinformatics, 8, 284-284.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 284-284
-
-
Andorf, C.1
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner, M. 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
-
4
-
-
77953916879
-
Controlling the False Discovery Rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 12.
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 12
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
0037396730
-
The Gene Ontology Annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro
-
Camon, E. et al. (2003) The Gene Ontology Annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res., 13, 662-672.
-
(2003)
Genome Res
, vol.13
, pp. 662-672
-
-
Camon, E.1
-
6
-
-
84866716243
-
Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles
-
Cheung, W.A., Francis Ouellette, B. and Wasserman, W.W. (2012) Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med., 4, 75.
-
(2012)
Genome Med
, vol.4
, pp. 75
-
-
Cheung, W.A.1
Francis Ouellette, B.2
Wasserman, W.W.3
-
7
-
-
33646823604
-
Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome
-
Collins, M.O. et al. (2006) Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome. J. Neurochem., 97 (Suppl. 1), 16-23.
-
(2006)
J. Neurochem
, vol.97
, Issue.SUPPL. 1
, pp. 16-23
-
-
Collins, M.O.1
-
8
-
-
0035424599
-
Intrinsic errors in genome annotation
-
Devos, D. and Valencia, A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
-
(2001)
Trends Genet
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
9
-
-
79951979882
-
The impact of multifunctional genes on "Guilt by Association" analysis
-
Gillis, J. and Pavlidis, P. (2011a) The impact of multifunctional genes on "Guilt by Association" analysis. PloS One, 6, e17258-e17258.
-
(2011)
PloS One
, vol.6
-
-
Gillis, J.1
Pavlidis, P.2
-
10
-
-
79959404103
-
The role of indirect connections in gene networks in predicting function
-
Gillis, J. and Pavlidis, P. (2011b) The role of indirect connections in gene networks in predicting function. Bioinformatics, 27, 1860-1866.
-
(2011)
Bioinformatics
, vol.27
, pp. 1860-1866
-
-
Gillis, J.1
Pavlidis, P.2
-
11
-
-
84861179768
-
"Guilt by Association" is the exception rather than the rule in gene networks
-
Gillis, J. and Pavlidis, P. (2012) "Guilt by Association" is the exception rather than the rule in gene networks. PLoS Comput. Biol., 8, e1002444-e1002444.
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Gillis, J.1
Pavlidis, P.2
-
12
-
-
84864057493
-
Accurate evaluation and analysis of functional genomics data and methods
-
Greene, C.S. and Troyanskaya, O.G. (2012) Accurate evaluation and analysis of functional genomics data and methods. Ann. N Y Acad. Sci., 1260, 95-100.
-
(2012)
Ann. N y Acad. Sci
, vol.1260
, pp. 95-100
-
-
Greene, C.S.1
Troyanskaya, O.G.2
-
13
-
-
84870448958
-
Impact of ontology evolution on functional analyses
-
Gross, A. et al. (2012) Impact of ontology evolution on functional analyses. Bioinformatics, 28, 2671-2677.
-
(2012)
Bioinformatics
, vol.28
, pp. 2671-2677
-
-
Gross, A.1
-
14
-
-
36448946146
-
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
-
Grossmann, S. et al. (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics, 23, 3024-3031.
-
(2007)
Bioinformatics
, vol.23
, pp. 3024-3031
-
-
Grossmann, S.1
-
15
-
-
79960655055
-
GO trimming: Systematically reducing redundancy in large Gene Ontology datasets
-
Jantzen, S.G. et al. (2011) GO trimming: systematically reducing redundancy in large Gene Ontology datasets. BMC Res Notes, 4, 267.
-
(2011)
BMC Res Notes
, vol.4
, pp. 267
-
-
Jantzen, S.G.1
-
16
-
-
13444274741
-
Gene Ontology: Looking backwards and forwards
-
Lewis, S.E. (2005) Gene Ontology: looking backwards and forwards. Genome Biol., 6, 103.
-
(2005)
Genome Biol
, vol.6
, pp. 103
-
-
Lewis, S.E.1
-
17
-
-
0038478096
-
Semantic similarity measures as tools for exploring the gene ontology
-
Lord, P.W. et al. (2003) Semantic similarity measures as tools for exploring the gene ontology. Pac. Symp. Biocomput., 8, 601-612.
-
(2003)
Pac. Symp. Biocomput
, vol.8
, pp. 601-612
-
-
Lord, P.W.1
-
18
-
-
49949096013
-
Gene Ontology term overlap as a measure of gene functional similarity
-
Mistry, M. and Pavlidis, P. (2008) Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics, 9, 327.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 327
-
-
Mistry, M.1
Pavlidis, P.2
-
19
-
-
9144265895
-
Retrieving sequences of enzymes experimentally characterized but erroneously annotated: The case of the putrescine carbamoyltransferase
-
Naumoff, D.G. et al. (2004) Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase. BMC Genomics, 5, 52.
-
(2004)
BMC Genomics
, vol.5
, pp. 52
-
-
Naumoff, D.G.1
-
20
-
-
84860741138
-
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
-
O'Roak, B.J. et al. (2012) Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature, 485, 246-250.
-
(2012)
Nature
, vol.485
, pp. 246-250
-
-
O'Roak, B.J.1
-
21
-
-
51849099551
-
Generating GO slim using relational database management systems to support proteomics analysis
-
Onsongo, G. et al. (2008) Generating GO slim using relational database management systems to support proteomics analysis. In: 21st IEEE International Symposium on Computer-Based Medical Systems, Vol. 27, pp. 215-217.
-
(2008)
21st IEEE International Symposium on Computer-Based Medical Systems
, vol.27
, pp. 215-217
-
-
Onsongo, G.1
-
22
-
-
15944411333
-
GOChase: Correcting Errors from gene ontology-based annotations for gene products
-
Park, Y.R. et al. (2005) GOChase: correcting Errors from gene ontology-based annotations for gene products. Bioinformatics, 21, 829-831.
-
(2005)
Bioinformatics
, vol.21
, pp. 829-831
-
-
Park, Y.R.1
-
23
-
-
47549116997
-
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
-
Pena-Castillo, L. et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol., 9 (Suppl. 1), S2.
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Pena-Castillo, L.1
-
24
-
-
79851502150
-
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
-
Rossin, E.J. et al. (2011) Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet., 7, e1001273.
-
(2011)
PLoS Genet
, vol.7
-
-
Rossin, E.J.1
-
26
-
-
84856918212
-
HIPPIE: Integrating protein interaction networks with experiment based quality scores
-
Schaefer, M.H. et al. (2012) HIPPIE: integrating protein interaction networks with experiment based quality scores. PloS One, 7, e31826-e31826.
-
(2012)
PloS One
, vol.7
-
-
Schaefer, M.H.1
-
27
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
Schnoes, A.M. et al. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605-e1000605.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Schnoes, A.M.1
-
28
-
-
84863693531
-
Quality of computationally inferred gene ontology annotations
-
Skunca, N. et al. (2012) Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol., 8, e1002533-e1002533.
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Skunca, N.1
-
29
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
30
-
-
84861123821
-
On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: A short report
-
Thomas, P.D. et al. (2012) On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: a short report. PLoS Comput. Biol., 8, e1002386-e1002386.
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Thomas, P.D.1
-
31
-
-
77954269901
-
The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function
-
Warde-Farley, D. et al. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res., 38, W214-W220.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Warde-Farley, D.1
-
33
-
-
79955771442
-
GO-Module: Functional synthesis and improved interpretation of Gene Ontology patterns
-
Yang, X. et al. (2011) GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics, 27, 1444-1446.
-
(2011)
Bioinformatics
, vol.27
, pp. 1444-1446
-
-
Yang, X.1
|