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Items: 1 to 20 of 73

1.

Robust and accurate data enrichment statistics via distribution function of sum of weights.

Stojmirović A, Yu YK.

Bioinformatics. 2010 Nov 1;26(21):2752-9. doi: 10.1093/bioinformatics/btq511. Epub 2010 Sep 8.

2.

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.

Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z.

BMC Bioinformatics. 2009 Feb 3;10:48. doi: 10.1186/1471-2105-10-48.

3.

Mass spectrometry-based protein identification with accurate statistical significance assignment.

Alves G, Yu YK.

Bioinformatics. 2015 Mar 1;31(5):699-706. doi: 10.1093/bioinformatics/btu717. Epub 2014 Oct 31.

4.

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution.

Alves G, Yu YK.

Bioinformatics. 2016 Sep 1;32(17):2642-9. doi: 10.1093/bioinformatics/btw225. Epub 2016 Apr 29.

PMID:
27153659
5.

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.

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.

PMID:
17344234
7.

Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy.

Alves G, Yu YK.

PLoS One. 2011;6(8):e22647. doi: 10.1371/journal.pone.0022647. Epub 2011 Aug 31.

8.
9.

ITM Probe: analyzing information flow in protein networks.

Stojmirović A, Yu YK.

Bioinformatics. 2009 Sep 15;25(18):2447-9. doi: 10.1093/bioinformatics/btp398. Epub 2009 Jun 27.

10.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management.

Maruschke M, Reuter D, Koczan D, Hakenberg OW, Thiesen HJ.

BJU Int. 2011 Jul;108(2 Pt 2):E29-35. doi: 10.1111/j.1464-410X.2010.09794.x. Epub 2011 Mar 16.

11.

caCORE: a common infrastructure for cancer informatics.

Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH.

Bioinformatics. 2003 Dec 12;19(18):2404-12.

PMID:
14668224
12.

SR4GN: a species recognition software tool for gene normalization.

Wei CH, Kao HY, Lu Z.

PLoS One. 2012;7(6):e38460. doi: 10.1371/journal.pone.0038460. Epub 2012 Jun 5.

13.

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).

Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I.

PLoS One. 2013 Oct 4;8(10):e75185. doi: 10.1371/journal.pone.0075185. eCollection 2013.

14.

"Good annotation practice" for chemical data in biology.

Degtyarenko K, Ennis M, Garavelli JS.

In Silico Biol. 2007;7(2 Suppl):S45-56.

PMID:
17822390
15.

Retro: concept-based clustering of biomedical topical sets.

Yeganova L, Kim W, Kim S, Wilbur WJ.

Bioinformatics. 2014 Nov 15;30(22):3240-8. doi: 10.1093/bioinformatics/btu514. Epub 2014 Jul 29.

16.

DNorm: disease name normalization with pairwise learning to rank.

Leaman R, Islamaj Dogan R, Lu Z.

Bioinformatics. 2013 Nov 15;29(22):2909-17. doi: 10.1093/bioinformatics/btt474. Epub 2013 Aug 21.

17.
18.

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores.

Stojmirovic A, Bliskovsky A, Yu YK.

Bioinformatics. 2012 Mar 15;28(6):893-4. doi: 10.1093/bioinformatics/bts041. Epub 2012 Feb 15.

19.

DeCoaD: determining correlations among diseases using protein interaction networks.

Hamaneh MB, Yu YK.

BMC Res Notes. 2015 Jun 6;8:226. doi: 10.1186/s13104-015-1211-z.

20.

SEMEDA: ontology based semantic integration of biological databases.

Köhler J, Philippi S, Lange M.

Bioinformatics. 2003 Dec 12;19(18):2420-7.

PMID:
14668226

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