-
1
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
-
(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
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..
-
2
-
-
58149187893
-
The GOA database in 2009 - an integrated Gene Ontology Annotation resource
-
Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 2009, 37:D396-D403.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
3
-
-
33847103869
-
Measuring semantic similarity between Gene Ontology terms
-
Couto F.M., Silva M.J., Coutinho P.M. Measuring semantic similarity between Gene Ontology terms. Data Knowl. Eng. 2007, 61:137-152.
-
(2007)
Data Knowl. Eng.
, vol.61
, pp. 137-152
-
-
Couto, F.M.1
Silva, M.J.2
Coutinho, P.M.3
-
4
-
-
0037480738
-
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
-
Lord P.W., Stevens R.D., Brass A., Goble C.A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19:1275-1283.
-
(2003)
Bioinformatics
, vol.19
, pp. 1275-1283
-
-
Lord, P.W.1
Stevens, R.D.2
Brass, A.3
Goble, C.A.4
-
6
-
-
58149312546
-
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data
-
Xu T., Du L., Zhou Y. Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics 2008, 9:472.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 472
-
-
Xu, T.1
Du, L.2
Zhou, Y.3
-
7
-
-
33646358998
-
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations
-
Wu X., Zhu L., Guo J., Zhang D.Y., Lin K. Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res. 2006, 34:2137-2150.
-
(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
-
8
-
-
20744441547
-
Modularized learning of genetic interaction networks from biological annotations and mRNA expression data
-
Lee P.H., Lee D. Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics 2005, 21:2739-2747.
-
(2005)
Bioinformatics
, vol.21
, pp. 2739-2747
-
-
Lee, P.H.1
Lee, D.2
-
9
-
-
33751393465
-
Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
-
Lei Z., Dai Y. Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics 2006, 7:491.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 491
-
-
Lei, Z.1
Dai, Y.2
-
10
-
-
34248361071
-
GOAnnotator: linking protein GO annotations to evidence text
-
Couto F.M., Silva M.J., Lee V., Dimmer E., Camon E., Apweiler R., Kirsch H., Rebholz-Schuhmann D. GOAnnotator: linking protein GO annotations to evidence text. J. Biomed. Discov. Collab. 2006, 1:19.
-
(2006)
J. Biomed. Discov. Collab.
, vol.1
, pp. 19
-
-
Couto, F.M.1
Silva, M.J.2
Lee, V.3
Dimmer, E.4
Camon, E.5
Apweiler, R.6
Kirsch, H.7
Rebholz-Schuhmann, D.8
-
11
-
-
4243130503
-
Semantic search among heterogeneous biological databases based on gene ontology
-
Cao S.-L., Qin L., He W.-Z., Zhong Y., Zhu Y.-Y., Li Y.-X. Semantic search among heterogeneous biological databases based on gene ontology. Acta Biochim. Biophys. Sin. 2004, 36:365-370.
-
(2004)
Acta Biochim. Biophys. Sin.
, vol.36
, pp. 365-370
-
-
Cao, S.-L.1
Qin, L.2
He, W.-Z.3
Zhong, Y.4
Zhu, Y.-Y.5
Li, Y.-X.6
-
12
-
-
33645821454
-
Assessing semantic similarity measures for the characterization of human regulatory pathways
-
Guo X., Liu R., Shriver C.D., Hu H., Liebman M.N. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22:967-973.
-
(2006)
Bioinformatics
, vol.22
, pp. 967-973
-
-
Guo, X.1
Liu, R.2
Shriver, C.D.3
Hu, H.4
Liebman, M.N.5
-
13
-
-
33644856110
-
Improving missing value estimation in microarray data with gene ontology
-
Tuikkala J., Elo L., Nevalainen O.S., Aittokallio T. Improving missing value estimation in microarray data with gene ontology. Bioinformatics 2006, 22:566-572.
-
(2006)
Bioinformatics
, vol.22
, pp. 566-572
-
-
Tuikkala, J.1
Elo, L.2
Nevalainen, O.S.3
Aittokallio, T.4
-
14
-
-
84891725921
-
A shortest-path graph kernel for estimating gene product semantic similarity
-
Alvarez M.A., Qi X., Yan C. A shortest-path graph kernel for estimating gene product semantic similarity. J. Biomed. Semant. 2011, 2:3.
-
(2011)
J. Biomed. Semant.
, vol.2
, pp. 3
-
-
Alvarez, M.A.1
Qi, X.2
Yan, C.3
-
15
-
-
68249087607
-
Semantic similarity in biomedical ontologies
-
Pesquita C., Faria D., Falcao A.O., Lord P., Couto F.M. Semantic similarity in biomedical ontologies. PLoS Comput. Biol. 2009, 5:e1000443.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Pesquita, C.1
Faria, D.2
Falcao, A.O.3
Lord, P.4
Couto, F.M.5
-
16
-
-
0024480920
-
Development and application of a metric on semantic nets
-
Rada R., Mili H., Bicknell E., Blettner M. Development and application of a metric on semantic nets. IEEE Trans. Syst. Man Cybern. 1989, 19:17-30.
-
(1989)
IEEE Trans. Syst. Man Cybern.
, vol.19
, pp. 17-30
-
-
Rada, R.1
Mili, H.2
Bicknell, E.3
Blettner, M.4
-
20
-
-
3142749026
-
A knowledge-based clustering algorithm driven by gene ontology
-
Cheng J., Cline M., Martin J., Finkelstein D., Awad T., Kulp D., Siani-Rose M.A. A knowledge-based clustering algorithm driven by gene ontology. J. Biopharm. Stat. 2004, 14:687-700.
-
(2004)
J. Biopharm. Stat.
, vol.14
, pp. 687-700
-
-
Cheng, J.1
Cline, M.2
Martin, J.3
Finkelstein, D.4
Awad, T.5
Kulp, D.6
Siani-Rose, M.A.7
-
21
-
-
20444381674
-
Broadly predicting specific gene functions with expression similarity and taxonomy similarity
-
Yu H., Gao L., Tu K., Guo Z. Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene 2005, 352:75.
-
(2005)
Gene
, vol.352
, pp. 75
-
-
Yu, H.1
Gao, L.2
Tu, K.3
Guo, Z.4
-
26
-
-
34248833974
-
Introduction to wordnet: an on-line lexical database*
-
Miller G.A., Beckwith R., Fellbaum C., Gross D., Miller K.J. Introduction to wordnet: an on-line lexical database*. Int. J. Lexicogr. 1990, 3:235-244.
-
(1990)
Int. J. Lexicogr.
, vol.3
, pp. 235-244
-
-
Miller, G.A.1
Beckwith, R.2
Fellbaum, C.3
Gross, D.4
Miller, K.J.5
-
28
-
-
33748335463
-
A new measure for functional similarity of gene products based on Gene Ontology
-
Schlicker A., Domingues F.S., Rahnenführer J., Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 302
-
-
Schlicker, A.1
Domingues, F.S.2
Rahnenführer, J.3
Lengauer, T.4
-
30
-
-
46849085587
-
Xoa: web-enabled cross-ontological analytics
-
Riensche R.M., Baddeley B.L., Sanfilippo A.P., Posse C., Gopalan B. Xoa: web-enabled cross-ontological analytics. Services, 2007 IEEE Congress on, IEEE 2007, 99-105.
-
(2007)
Services, 2007 IEEE Congress on, IEEE
, pp. 99-105
-
-
Riensche, R.M.1
Baddeley, B.L.2
Sanfilippo, A.P.3
Posse, C.4
Gopalan, B.5
-
31
-
-
3042514191
-
Coexpression analysis of human genes across many microarray data sets
-
Lee H.K., Hsu A.K., Sajdak J., Qin J., Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004, 14:1085-1094.
-
(2004)
Genome Res.
, vol.14
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
32
-
-
33746898247
-
Gene function prediction from congruent synthetic lethal interactions in yeast
-
Ye P., Peyser B.D., Pan X., Boeke J.D., Spencer F.A., Bader J.S. Gene function prediction from congruent synthetic lethal interactions in yeast. Mol. Syst. Biol. 2005, 1.
-
(2005)
Mol. Syst. Biol.
, vol.1
-
-
Ye, P.1
Peyser, B.D.2
Pan, X.3
Boeke, J.D.4
Spencer, F.A.5
Bader, J.S.6
-
33
-
-
49949096013
-
Gene ontology term overlap as a measure of gene functional similarity
-
Mistry M., Pavlidis P. Gene ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics 2008, 9:327.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 327
-
-
Mistry, M.1
Pavlidis, P.2
-
34
-
-
47149083877
-
Metrics for GO based protein semantic similarity: a systematic evaluation
-
Pesquita C., Faria D., Bastos H., Ferreira A.E., Falcão A.O., Couto F.M. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 2008, 9:S4.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Pesquita, C.1
Faria, D.2
Bastos, H.3
Ferreira, A.E.4
Falcão, A.O.5
Couto, F.M.6
-
35
-
-
41349115432
-
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
-
Alvord G., Roayaei J., Stephens R., Baseler M.W., Lane H.C., Lempicki R.A. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007, 8:R183.
-
(2007)
Genome Biol.
, vol.8
-
-
Alvord, G.1
Roayaei, J.2
Stephens, R.3
Baseler, M.W.4
Lane, H.C.5
Lempicki, R.A.6
-
36
-
-
34547763236
-
A transversal approach to predict gene product networks from ontology-based similarity
-
Chabalier J., Mosser J., Burgun A. A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics 2007, 8:235.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 235
-
-
Chabalier, J.1
Mosser, J.2
Burgun, A.3
-
37
-
-
60849139073
-
A relation based measure of semantic similarity for Gene Ontology annotations
-
Sheehan B., Quigley A., Gaudin B., Dobson S. A relation based measure of semantic similarity for Gene Ontology annotations. BMC Bioinformatics 2008, 9:468.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 468
-
-
Sheehan, B.1
Quigley, A.2
Gaudin, B.3
Dobson, S.4
-
38
-
-
84899779262
-
A measure of semantic similarity between gene ontology terms based on semantic pathway covering
-
Rong L., Shunliang C., Yuanyuan L., Hao T., Yangyong Z., Yang Z., Yixue L. A measure of semantic similarity between gene ontology terms based on semantic pathway covering. Prog. Nat. Sci. 2006, 16:721-726.
-
(2006)
Prog. Nat. Sci.
, vol.16
, pp. 721-726
-
-
Rong, L.1
Shunliang, C.2
Yuanyuan, L.3
Hao, T.4
Yangyong, Z.5
Yang, Z.6
Yixue, L.7
-
39
-
-
33745771638
-
Protein function prediction via graph kernels
-
Borgwardt K.M., Ong C.S., Schönauer S., Vishwanathan S., Smola A.J., Kriegel H.-P. Protein function prediction via graph kernels. Bioinformatics 2005, 21:i47-i56.
-
(2005)
Bioinformatics
, vol.21
-
-
Borgwardt, K.M.1
Ong, C.S.2
Schönauer, S.3
Vishwanathan, S.4
Smola, A.J.5
Kriegel, H.-P.6
-
40
-
-
37849039292
-
A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences
-
Othman R.M., Deris S., Illias R.M. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. J. Biomed. Inform. 2008, 41:65-81.
-
(2008)
J. Biomed. Inform.
, vol.41
, pp. 65-81
-
-
Othman, R.M.1
Deris, S.2
Illias, R.M.3
-
42
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
Wang J.Z., Du Z., Payattakool R., Philip S.Y., Chen C.-F. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23:1274-1281.
-
(2007)
Bioinformatics
, vol.23
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Philip, S.Y.4
Chen, C.-F.5
-
43
-
-
30344446931
-
Correlation between gene expression and GO semantic similarity, Computational Biology and Bioinformatics
-
Sevilla J.L., Segura V., Podhorski A., Guruceaga E., Mato J.M., Martinez-Cruz L.A., Corrales F.J., Rubio A. Correlation between gene expression and GO semantic similarity, Computational Biology and Bioinformatics. IEEE/ACM Trans. 2005, 2:330-338.
-
(2005)
IEEE/ACM Trans.
, vol.2
, 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
Rubio, A.8
-
45
-
-
17044421977
-
Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships
-
IEEE
-
Wang H., Azuaje F., Bodenreider O., Dopazo J. Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. Computational Intelligence in Bioinformatics and Computational Biology, 2004. CIBCB'04. Proceedings of the 2004 IEEE Symposium on 2004, 25-31. IEEE.
-
(2004)
Computational Intelligence in Bioinformatics and Computational Biology, 2004. CIBCB'04. Proceedings of the 2004 IEEE Symposium on
, pp. 25-31
-
-
Wang, H.1
Azuaje, F.2
Bodenreider, O.3
Dopazo, J.4
-
46
-
-
78649946112
-
CESSM: collaborative evaluation of semantic similarity measures, JB2009: challenges in
-
Pesquita C., Pessoa D., Faria D., Couto F. CESSM: collaborative evaluation of semantic similarity measures, JB2009: challenges in. Bioinformatics 2009, 1-5.
-
(2009)
Bioinformatics
, pp. 1-5
-
-
Pesquita, C.1
Pessoa, D.2
Faria, D.3
Couto, F.4
-
47
-
-
79956272259
-
Evaluating go-based semantic similarity measures
-
Pesquita C., Faria D., Bastos H., Falcão A., Couto F. Evaluating go-based semantic similarity measures. Proc. 10th Annual Bio-Ontologies Meeting 2007, 37-40.
-
(2007)
Proc. 10th Annual Bio-Ontologies Meeting
, pp. 37-40
-
-
Pesquita, C.1
Faria, D.2
Bastos, H.3
Falcão, A.4
Couto, F.5
|