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Items: 1 to 20 of 149

1.

Identifying cross-category relations in gene ontology and constructing genome-specific term association networks.

Peng J, Chen J, Wang Y.

BMC Bioinformatics. 2013;14 Suppl 2:S15. doi: 10.1186/1471-2105-14-S2-S15. Epub 2013 Jan 21.

2.

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

Peng J, Uygun S, Kim T, Wang Y, Rhee SY, Chen J.

BMC Bioinformatics. 2015 Feb 14;16:44. doi: 10.1186/s12859-015-0474-7.

3.

Integration of molecular network data reconstructs Gene Ontology.

Gligorijević V, Janjić V, Pržulj N.

Bioinformatics. 2014 Sep 1;30(17):i594-600. doi: 10.1093/bioinformatics/btu470.

4.

IntelliGO: a new vector-based semantic similarity measure including annotation origin.

Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD.

BMC Bioinformatics. 2010 Dec 1;11:588. doi: 10.1186/1471-2105-11-588.

5.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.

Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2012 Mar 20;2012:bas001. doi: 10.1093/database/bas001. Print 2012.

6.

Additional gene ontology structure for improved biological reasoning.

Myhre S, Tveit H, Mollestad T, Laegreid A.

Bioinformatics. 2006 Aug 15;22(16):2020-7. Epub 2006 Jun 20.

PMID:
16787968
7.
8.

Towards integrative gene functional similarity measurement.

Peng J, Wang Y, Chen J.

BMC Bioinformatics. 2014;15 Suppl 2:S5. doi: 10.1186/1471-2105-15-S2-S5. Epub 2014 Jan 24.

9.

A new method to measure the semantic similarity of GO terms.

Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF.

Bioinformatics. 2007 May 15;23(10):1274-81. Epub 2007 Mar 7.

PMID:
17344234
10.

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.

Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA.

BMC Microbiol. 2009 Feb 19;9 Suppl 1:S8. doi: 10.1186/1471-2180-9-S1-S8. Review.

11.

Modular biological function is most effectively captured by combining molecular interaction data types.

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.

12.

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2011 Mar 15;2011:bar004. doi: 10.1093/database/bar004. Print 2011.

13.

A sensitive method for computing GO-based functional similarities among genes with 'shallow annotation'.

Chen X, Yang R, Xu J, Ma H, Chen S, Bian X, Liu L.

Gene. 2012 Nov 1;509(1):131-5. doi: 10.1016/j.gene.2012.07.078. Epub 2012 Aug 10.

PMID:
22903005
14.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

Mazandu GK, Mulder NJ.

BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

15.

Topology-function conservation in protein-protein interaction networks.

Davis D, Yaveroğlu ÖN, Malod-Dognin N, Stojmirovic A, Pržulj N.

Bioinformatics. 2015 May 15;31(10):1632-9. doi: 10.1093/bioinformatics/btv026. Epub 2015 Jan 20.

16.

Cross-organism learning method to discover new gene functionalities.

Domeniconi G, Masseroli M, Moro G, Pinoli P.

Comput Methods Programs Biomed. 2016 Apr;126:20-34. doi: 10.1016/j.cmpb.2015.12.002. Epub 2015 Dec 17.

PMID:
26724853
17.

GO-Elite: a flexible solution for pathway and ontology over-representation.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N.

Bioinformatics. 2012 Aug 15;28(16):2209-10. doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.

18.

Information theory applied to the sparse gene ontology annotation network to predict novel gene function.

Tao Y, Sam L, Li J, Friedman C, Lussier YA.

Bioinformatics. 2007 Jul 1;23(13):i529-38.

19.

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914.

PMID:
26631125
20.

Gene ontology based transfer learning for protein subcellular localization.

Mei S, Fei W, Zhou S.

BMC Bioinformatics. 2011 Feb 2;12:44. doi: 10.1186/1471-2105-12-44.

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