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Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature.

Raychaudhuri S, Chang JT, Sutphin PD, Altman RB.

Genome Res. 2002 Jan;12(1):203-14.


Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM.

Nucleic Acids Res. 2002 Jan 1;30(1):69-72.


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.


Using text analysis to identify functionally coherent gene groups.

Raychaudhuri S, Schütze H, Altman RB.

Genome Res. 2002 Oct;12(10):1582-90.


Adaptive classifiers, topic drifts and GO annotations.

Srinivasan P.

AMIA Annu Symp Proc. 2007 Oct 11:681-5.


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.


Applying Support Vector Machines for Gene Ontology based gene function prediction.

Vinayagam A, König R, Moormann J, Schubert F, Eils R, Glatting KH, Suhai S.

BMC Bioinformatics. 2004 Aug 26;5:116.


Evaluation of BioCreAtIvE assessment of task 2.

Blaschke C, Leon EA, Krallinger M, Valencia A.

BMC Bioinformatics. 2005;6 Suppl 1:S16. Epub 2005 May 24.


Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets.

Aubry M, Monnier A, Chicault C, de Tayrac M, Galibert MD, Burgun A, Mosser J.

BMC Bioinformatics. 2006 May 4;7:241.


Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.

Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I.

BMC Bioinformatics. 2007 Jul 10;8:243.


The use of gene ontology evidence codes in preventing classifier assessment bias.

Rogers MF, Ben-Hur A.

Bioinformatics. 2009 May 1;25(9):1173-7. doi: 10.1093/bioinformatics/btp122. Epub 2009 Mar 2.


An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.

BMC Bioinformatics. 2005;6 Suppl 1:S17. Epub 2005 May 24.


Combining multisource information through functional-annotation-based weighting: gene function prediction in yeast.

Ray SS, Bandyopadhyay S, Pal SK.

IEEE Trans Biomed Eng. 2009 Feb;56(2):229-36. doi: 10.1109/TBME.2008.2005955. Epub 2008 Sep 30.


Incorporating functional inter-relationships into protein function prediction algorithms.

Pandey G, Myers CL, Kumar V.

BMC Bioinformatics. 2009 May 12;10:142. doi: 10.1186/1471-2105-10-142.


Correlating information contents of gene ontology terms to infer semantic similarity of gene products.

Gan M.

Comput Math Methods Med. 2014;2014:891842. doi: 10.1155/2014/891842. Epub 2014 May 22.


Dynamically weighted clustering with noise set.

Shen Y, Sun W, Li KC.

Bioinformatics. 2010 Feb 1;26(3):341-7. doi: 10.1093/bioinformatics/btp671. Epub 2009 Dec 9.


Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology.

Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G.

BMC Genomics. 2008 Jul 24;9:347. doi: 10.1186/1471-2164-9-347.

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