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Results: 1 to 20 of 63

1.

GLay: community structure analysis of biological networks.

Su G, Kuchinsky A, Morris JH, States DJ, Meng F.

Bioinformatics. 2010 Dec 15;26(24):3135-7. doi: 10.1093/bioinformatics/btq596.

PMID:
21123224
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Literature-based discovery of diabetes- and ROS-related targets.

Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ, Jagadish HV, Feldman EL.

BMC Med Genomics. 2010 Oct 27;3:49. doi: 10.1186/1755-8794-3-49.

PMID:
20979611
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Understanding distal transcriptional regulation from sequence, expression and interactome perspectives.

Rao A, States DJ, Hero AO 3rd, Engel JD.

J Bioinform Comput Biol. 2010 Apr;8(2):219-46.

PMID:
20401945
[PubMed - indexed for MEDLINE]
4.

Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription.

Chen Y, Lin G, Huo JS, Barney D, Wang Z, Livshiz T, States DJ, Qin ZS, Schwartz J.

Endocrinology. 2009 Aug;150(8):3645-54. doi: 10.1210/en.2009-0212. Epub 2009 Apr 30.

PMID:
19406940
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.

Hur J, Schuyler AD, States DJ, Feldman EL.

Bioinformatics. 2009 Mar 15;25(6):838-40. doi: 10.1093/bioinformatics/btp049. Epub 2009 Feb 2.

PMID:
19188191
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.

Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ.

Cancer Res. 2009 Jan 1;69(1):300-9. doi: 10.1158/0008-5472.CAN-08-2145.

PMID:
19118015
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A bioinformatics analysis of the cell line nomenclature.

Sarntivijai S, Ade AS, Athey BD, States DJ.

Bioinformatics. 2008 Dec 1;24(23):2760-6. doi: 10.1093/bioinformatics/btn502. Epub 2008 Oct 10.

PMID:
18849319
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Integrating and annotating the interactome using the MiMI plugin for cytoscape.

Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ.

Bioinformatics. 2009 Jan 1;25(1):137-8. doi: 10.1093/bioinformatics/btn501. Epub 2008 Sep 23.

PMID:
18812364
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Simplifying access to a Clinical Data Repository using schema summarization.

Yu C, Hanauer DA, Athey BD, Jagadish HV, States DJ.

AMIA Annu Symp Proc. 2007 Oct 11:1163.

PMID:
18694259
[PubMed - indexed for MEDLINE]
10.

The Cell Line Ontology and its use in tagging cell line names in biomedical text.

Sarntivijai S, Ade AS, Athey BD, States DJ.

AMIA Annu Symp Proc. 2007 Oct 11:1103.

PMID:
18694200
[PubMed - indexed for MEDLINE]
11.

Using directed information to build biologically relevant influence networks.

Rao A, Hero AO 3rd, States DJ, Engel JD.

J Bioinform Comput Biol. 2008 Jun;6(3):493-519.

PMID:
18574860
[PubMed - indexed for MEDLINE]
12.

A mouse plasma peptide atlas as a resource for disease proteomics.

Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, Omenn GS, States DJ, Hanash SM.

Genome Biol. 2008;9(6):R93. doi: 10.1186/gb-2008-9-6-r93. Epub 2008 Jun 3.

PMID:
18522751
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Cytoscape ESP: simple search of complex biological networks.

Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ.

Bioinformatics. 2008 Jun 15;24(12):1465-6. doi: 10.1093/bioinformatics/btn208. Epub 2008 Apr 28.

PMID:
18445605
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications.

Du X, Yang F, Manes NP, Stenoien DL, Monroe ME, Adkins JN, States DJ, Purvine SO, Camp DG 2nd, Smith RD.

J Proteome Res. 2008 Jun;7(6):2195-203. doi: 10.1021/pr070510t. Epub 2008 Apr 19.

PMID:
18422353
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Motif discovery in tissue-specific regulatory sequences using directed information.

Rao A, Hero AO 3rd, States DJ, Engel JD.

EURASIP J Bioinform Syst Biol. 2007:13853. doi: 10.1155/2007/13853.

PMID:
18340376
[PubMed]
Free PMC Article
16.

MiSearch adaptive pubMed search tool.

States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD.

Bioinformatics. 2009 Apr 1;25(7):974-6. doi: 10.1093/bioinformatics/btn033. Epub 2008 Mar 6.

PMID:
18326507
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Inferring time-varying network topologies from gene expression data.

Rao A, Hero AO 3rd, States DJ, Engel JD.

EURASIP J Bioinform Syst Biol. 2007:51947. doi: 10.1155/2007/51947.

PMID:
18309363
[PubMed]
Free PMC Article
18.

Human Proteinpedia enables sharing of human protein data.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A.

Nat Biotechnol. 2008 Feb;26(2):164-7. doi: 10.1038/nbt0208-164. No abstract available.

PMID:
18259167
[PubMed - indexed for MEDLINE]
19.

Using directed information to build biologically relevant influence networks.

Rao A, Hero AO 3rd, States DJ, Engel JD.

Comput Syst Bioinformatics Conf. 2007;6:145-56.

PMID:
17951820
[PubMed - indexed for MEDLINE]
Free Article
20.

Evolutionary-conserved gene expression response profiles across mammalian tissues.

Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ.

OMICS. 2007 Spring;11(1):96-115.

PMID:
17411398
[PubMed - indexed for MEDLINE]

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