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SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association.

Cheng L, Li J, Ju P, Peng J, Wang Y.

PLoS One. 2014 Jun 16;9(6):e99415. doi: 10.1371/journal.pone.0099415. eCollection 2014.


A new measure for functional similarity of gene products based on Gene Ontology.

Schlicker A, Domingues FS, Rahnenf├╝hrer J, Lengauer T.

BMC Bioinformatics. 2006 Jun 15;7:302.


Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases.

Oellrich A, Hoehndorf R, Gkoutos GV, Rebholz-Schuhmann D.

PLoS One. 2012;7(6):e38937. doi: 10.1371/journal.pone.0038937. Epub 2012 Jun 14.


Novel semantic similarity measure improves an integrative approach to predicting gene functional associations.

Vafaee F, Rosu D, Broackes-Carter F, Jurisica I.

BMC Syst Biol. 2013 Mar 14;7:22. doi: 10.1186/1752-0509-7-22.


Drug repositioning by applying 'expression profiles' generated by integrating chemical structure similarity and gene semantic similarity.

Tan F, Yang R, Xu X, Chen X, Wang Y, Ma H, Liu X, Wu X, Chen Y, Liu L, Jia X.

Mol Biosyst. 2014 May;10(5):1126-38. doi: 10.1039/c3mb70554d.


Measuring gene functional similarity based on group-wise comparison of GO terms.

Teng Z, Guo M, Liu X, Dai Q, Wang C, Xuan P.

Bioinformatics. 2013 Jun 1;29(11):1424-32. doi: 10.1093/bioinformatics/btt160. Epub 2013 Apr 9.


The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study.

Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ.

BMC Med Genomics. 2008 Oct 9;1:48. doi: 10.1186/1755-8794-1-48.


Constructing a gene semantic similarity network for the inference of disease genes.

Jiang R, Gan M, He P.

BMC Syst Biol. 2011 Dec 14;5 Suppl 2:S2. doi: 10.1186/1752-0509-5-S2-S2. Epub 2011 Dec 14.


Semantic particularity measure for functional characterization of gene sets using gene ontology.

Bettembourg C, Diot C, Dameron O.

PLoS One. 2014 Jan 28;9(1):e86525. doi: 10.1371/journal.pone.0086525. eCollection 2014.


Evaluation of gene ontology semantic similarities on protein interaction datasets.

Chen G, Li J, Wang J.

Int J Bioinform Res Appl. 2013;9(2):173-83. doi: 10.1504/IJBRA.2013.052448.


Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method.

Wu X, Pang E, Lin K, Pei ZM.

PLoS One. 2013 May 31;8(5):e66745. doi: 10.1371/journal.pone.0066745. Print 2013.


Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses.

Bien SJ, Park CH, Shim HJ, Yang W, Kim J, Kim JH.

J Am Med Inform Assoc. 2012 Sep-Oct;19(5):765-74. doi: 10.1136/amiajnl-2011-000659. Epub 2012 Feb 28.


Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization.

Yang J, Li Z, Fan X, Cheng Y.

J Chem Inf Model. 2014 Sep 22;54(9):2562-9. doi: 10.1021/ci500340n. Epub 2014 Aug 22.


Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks.

Wang J, Xie D, Lin H, Yang Z, Zhang Y.

Proteome Sci. 2012 Jun 21;10 Suppl 1:S18. doi: 10.1186/1477-5956-10-S1-S18.


A relation based measure of semantic similarity for Gene Ontology annotations.

Sheehan B, Quigley A, Gaudin B, Dobson S.

BMC Bioinformatics. 2008 Nov 4;9:468. doi: 10.1186/1471-2105-9-468.


An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology.

Jain S, Bader GD.

BMC Bioinformatics. 2010 Nov 15;11:562. doi: 10.1186/1471-2105-11-562.


Measure the Semantic Similarity of GO terms Using Aggregate Information Content.

Song X, Li L, Srimani PK, Yu PS, Wang JZ.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Dec 11. [Epub ahead of print]


A new gene ontology-based measure for the functional similarity of gene products.

Qi GL, Qian SY, Fang JQ.

Chin Med J (Engl). 2013;126(18):3561-6.


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.


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.

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