-
1
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
TCGA Research Network 10.1038/nature10166
-
TCGA Research Network: Integrated genomic analyses of ovarian carcinoma. Nature. 2011, 474 (7353): 609-615. 10.1038/nature10166.
-
(2011)
Nature
, vol.474
, Issue.7353
, pp. 609-615
-
-
-
2
-
-
79952284127
-
Hallmarks of cancer: The next generation
-
Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell. 2011, 144 (5): 646-674. 10.1016/j.cell.2011.02.013.
-
(2011)
Cell
, vol.144
, Issue.5
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.A.2
-
3
-
-
67650095110
-
Gene Ontology and the annotation of pathogen genes: The case of Candida albicans
-
Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G: Gene Ontology and the annotation of pathogen genes: the case of Candida albicans. Trends in Microbiology. 2009, 17 (7): 295-303. 10.1016/j.tim.2009.04.007.
-
(2009)
Trends in Microbiology
, vol.17
, Issue.7
, pp. 295-303
-
-
Arnaud, M.B.1
Costanzo, M.C.2
Shah, P.3
Skrzypek, M.S.4
Sherlock, G.5
-
4
-
-
33846796225
-
Ontology annotation: Mapping genomic regions to biological function
-
Thomas PD, Mi H, Lewis S: Ontology annotation: mapping genomic regions to biological function. Current Opinion in Chemical Biology. 2007, 11 (1): 4-11. 10.1016/j.cbpa.2006.11.039.
-
(2007)
Current Opinion in Chemical Biology
, vol.11
, Issue.1
, pp. 4-11
-
-
Thomas, P.D.1
Mi, H.2
Lewis, S.3
-
5
-
-
67650095108
-
Understanding animal viruses using the Gene Ontology
-
McCarthy FM, Mahony TJ, Parcells MS, Burgess SC: Understanding animal viruses using the Gene Ontology. Trends in Microbiology. 2009, 17 (7): 328-335. 10.1016/j.tim.2009.04.006.
-
(2009)
Trends in Microbiology
, vol.17
, Issue.7
, pp. 328-335
-
-
McCarthy, F.M.1
Mahony, T.J.2
Parcells, M.S.3
Burgess, S.C.4
-
6
-
-
67650236491
-
Applying the Gene Ontology in microbial annotation
-
Giglio MG, Collmer CW, Lomax J, Ireland A: Applying the Gene Ontology in microbial annotation. Trends in Microbiology. 2009, 17 (7): 262-268. 10.1016/j.tim.2009.04.003.
-
(2009)
Trends in Microbiology
, vol.17
, Issue.7
, pp. 262-268
-
-
Giglio, M.G.1
Collmer, C.W.2
Lomax, J.3
Ireland, A.4
-
7
-
-
67650065206
-
Describing commonalities in microbial effector delivery using the Gene Ontology
-
Chibucos MC, Tseng TT, Setubal JC: Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 2009, 17 (7): 312-319. 10.1016/j.tim.2009.05.001.
-
(2009)
Trends in Microbiology
, vol.17
, Issue.7
, pp. 312-319
-
-
Chibucos, M.C.1
Tseng, T.T.2
Setubal, J.C.3
-
8
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry M, Davis A, Dolinski K, Dwight S, Eppig J, et al: Gene Ontology: tool for the unification of biology. Nature Genetics. 2000, 25 (1): 25-29. 10.1038/75556.
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.2
Blake, J.3
Botstein, D.4
Butler, H.5
Cherry, M.6
Davis, A.7
Dolinski, K.8
Dwight, S.9
Eppig, J.10
-
9
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research. 2009, 37 (1): 1-13. 10.1093/nar/gkn923.
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.1
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
10
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources
-
1:CAS:528:DC%2BD1cXhsFCkurnI
-
Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protocols. 2009, 4 (1): 44-57.
-
(2009)
Nature Protocols
, vol.4
, Issue.1
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
11
-
-
23144464901
-
WebGestalt: An integrated system for exploring gene sets in various biological contexts
-
Zhang B, Kirov S, Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Research. 2005, 33 (Web Server): W741-W748. 10.1093/nar/gki475.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. W741-W748
-
-
Zhang, B.1
Kirov, S.2
Snoddy, J.3
-
12
-
-
0035704901
-
Profiling gene expression using Onto-express
-
Khatri P, Draghici S, Ostermeier GC, Krawetz SA: Profiling gene expression using Onto-express. Genomics. 2002, 79 (2): 266-270. 10.1006/geno.2002.6698.
-
(2002)
Genomics
, vol.79
, Issue.2
, pp. 266-270
-
-
Khatri, P.1
Draghici, S.2
Ostermeier, G.C.3
Krawetz, S.A.4
-
13
-
-
67650721347
-
CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories
-
Hu ZL, Bao J, Reecy JM: CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories. Online Journal of Bioinformatics. 2008, 9 (2): 108-112.
-
(2008)
Online Journal of Bioinformatics
, vol.9
, Issue.2
, pp. 108-112
-
-
Hu, Z.L.1
Bao, J.2
Reecy, J.M.3
-
14
-
-
33750483615
-
AgBase: A functional genomics resource for agriculture
-
McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, et al: AgBase: a functional genomics resource for agriculture. BMC Genomics. 2006, 7 (229)
-
(2006)
BMC Genomics
, vol.7
, Issue.229
-
-
McCarthy, F.M.1
Wang, N.2
Magee, G.B.3
Nanduri, B.4
Lawrence, M.L.5
Camon, E.B.6
Barrell, D.G.7
Hill, D.P.8
Dolan, M.E.9
Williams, W.P.10
-
15
-
-
58349111875
-
AmiGO: Online access to ontology and annotation data
-
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, Hub A, Group WPW: AmiGO: online access to ontology and annotation data. Bioinformatics. 2009, 25 (2): 288-289. 10.1093/bioinformatics/btn615.
-
(2009)
Bioinformatics
, vol.25
, Issue.2
, pp. 288-289
-
-
Carbon, S.1
Ireland, A.2
Mungall, C.J.3
Shu, S.4
Marshall, B.5
Lewis, S.6
Hub, A.7
-
16
-
-
21044451527
-
KEGG API: A web service using SOAP/WSDL to access the KEGG system
-
Kawashima S, Katayama T, Sato Y, Kaneshia M: KEGG API: a web service using SOAP/WSDL to access the KEGG system. Genome Informatics. 2003, 14: 673-674.
-
(2003)
Genome Informatics
, vol.14
, pp. 673-674
-
-
Kawashima, S.1
Katayama, T.2
Sato, Y.3
Kaneshia, M.4
-
17
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (43): 15545-15550. 10.1073/pnas.0506580102.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
-
18
-
-
77049094012
-
GOGrapher: A Python library for GO graph representation and analysis
-
Muller B, Richards AJ, Jin B, Lu X: GOGrapher: A Python library for GO graph representation and analysis. BMC research notes. 2009, 2: 122-10.1186/1756-0500-2-122.
-
(2009)
BMC Research Notes
, vol.2
, pp. 122
-
-
Muller, B.1
Richards, A.J.2
Jin, B.3
Lu, X.4
-
19
-
-
77957225888
-
Identifying informative subsets of the Gene Ontology with information bottleneck methods
-
2944202 1:CAS:528:DC%2BC3cXht1WhtLbP 20702400
-
Jin B, Lu X: Identifying informative subsets of the Gene Ontology with information bottleneck methods. Bioinformatics. 2010, 26 (18): 2445-2451.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
, pp. 2445-2451
-
-
Jin, B.1
Lu, X.2
-
22
-
-
0037480738
-
Investigating semantic similarity measures across the gene ontology: The relationship between sequence and annotation
-
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.
-
(2003)
Bioinformatics
, vol.19
, Issue.10
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
26
-
-
77954186057
-
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
-
Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X: Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics. 2010, 26 (12): i79-i87. 10.1093/bioinformatics/btq203.
-
(2010)
Bioinformatics
, vol.26
, Issue.12
, pp. i79-i87
-
-
Richards, A.J.1
Muller, B.2
Shotwell, M.3
Cowart, L.A.4
Rohrer, B.5
Lu, X.6
-
27
-
-
34250246836
-
A fast algorithm for Steiner trees
-
Kou LT, Markowsky G, Berman L: A fast algorithm for Steiner trees. Acta Informatica. 1981, 15 (2): 141-145. 10.1007/BF00288961.
-
(1981)
Acta Informatica
, vol.15
, Issue.2
, pp. 141-145
-
-
Kou, L.T.1
Markowsky, G.2
Berman, L.3
-
29
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
1347471 1:CAS:528:DC%2BD28XisFyhsA%3D%3D 16381927
-
Stark C, Breikruetz B-J, Reguly T, Boucher L, Brietkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Research. 2006, 34 (Database Issue): D535-539.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breikruetz, B.-J.2
Reguly, T.3
Boucher, L.4
Brietkreutz, A.5
Tyers, M.6
-
30
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
Segal E, Friedman N, Koller D, Regev A: A module map showing conditional activity of expression modules in cancer. Nature Genetics. 2004, 36 (10): 1090-1098. 10.1038/ng1434.
-
(2004)
Nature Genetics
, vol.36
, Issue.10
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
31
-
-
85018498522
-
Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers
-
(Electronic)
-
Lu S, Lu X: Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. AMIA Summits Translational Science Proceedings. 2012, 72-78. 2153-4063 (Electronic)
-
(2012)
AMIA Summits Translational Science Proceedings
, vol.72-78
, pp. 2153-4063
-
-
Lu, S.1
Lu, X.2
-
32
-
-
84872198906
-
A gene ontology inferred from molecular networks
-
Dutkowski J, Kramer M, Surma M, Balakrishnan R, Cherry M, Krogan N, Ideker T: A gene ontology inferred from molecular networks. Nature Biotechnology. 2012, 31 (1): 38-45. 10.1038/nbt.2463.
-
(2012)
Nature Biotechnology
, vol.31
, Issue.1
, pp. 38-45
-
-
Dutkowski, J.1
Kramer, M.2
Surma, M.3
Balakrishnan, R.4
Cherry, M.5
Krogan, N.6
Ideker, T.7
-
33
-
-
84876573596
-
From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data
-
Lu S, Jin B, Cowart LA, Lu X: From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS ONE. 2013
-
(2013)
PLoS ONE
-
-
Lu, S.1
Jin, B.2
Cowart, L.A.3
Lu, X.4
-
34
-
-
30344446931
-
Correlation between Gene Expression and GO Semantic Similarity
-
Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Angel R: Correlation between Gene Expression and GO Semantic Similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2005, 2 (4): 330-338. 10.1109/TCBB.2005.50.
-
(2005)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.2
, Issue.4
, pp. 330-338
-
-
Sevilla, J.L.1
Segura, V.2
Podhorski, A.3
Guruceaga, E.4
Mato, J.M.5
Martinez-Cruz, L.A.6
Corrales, F.J.7
Angel, R.8
-
35
-
-
68249087607
-
Semantic Similarity in Biomedical Ontologies
-
Pesquita C, Faria D, Falcão AO, Lord P, Couto FM: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology. 2009, 5 (7): 1-12.
-
(2009)
PLoS Computational Biology
, vol.5
, Issue.7
, pp. 1-12
-
-
Pesquita, C.1
Faria, D.2
Falcão, A.O.3
Lord, P.4
Couto, F.M.5
|