PubMed

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. Epub 2009 Apr 30.PMID: 19406940 [PubMed - indexed for MEDLINE]Related articles

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. Epub 2009 Feb 2.PMID: 19188191 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 19118015 [PubMed - indexed for MEDLINE]Related articles

Michigan molecular interactions r2: from interacting proteins to pathways.

Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, Wright Z, Chapman A, Jayapandian M, Ozgür A, Tian Y, Cavalcoli J, Mirel B, Patel J, Radev D, Athey B, States D, Jagadish HV.

Nucleic Acids Res. 2009 Jan;37(Database issue):D642-6. Epub 2008 Oct 31.PMID: 18978014 [PubMed - indexed for MEDLINE]Related articlesFree article

Introducing meta-services for biomedical information extraction.

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A.

Genome Biol. 2008;9 Suppl 2:S6. Epub 2008 Sep 1.PMID: 18834497 [PubMed - indexed for MEDLINE]Related articlesFree article

A bioinformatics analysis of the cell line nomenclature.

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

Bioinformatics. 2008 Dec 1;24(23):2760-6. Epub 2008 Oct 10.PMID: 18849319 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Sep 23.PMID: 18812364 [PubMed - indexed for MEDLINE]Related articles

Identifying gene-disease associations using centrality on a literature mined gene-interaction network.

Ozgür A, Vu T, Erkan G, Radev DR.

Bioinformatics. 2008 Jul 1;24(13):i277-85.PMID: 18586725 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Apr 28.PMID: 18445605 [PubMed - indexed for MEDLINE]Related articlesFree article

MiSearch adaptive pubMed search tool.

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

Bioinformatics. 2009 Apr 1;25(7):974-6. Epub 2008 Mar 6.PMID: 18326507 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articles

Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function.

Chen Y, Blackwell TW, Chen J, Gao J, Lee AW, States DJ.

PLoS Comput Biol. 2007 Apr 6;3(4):e63.PMID: 17411336 [PubMed - indexed for MEDLINE]Related articlesFree article

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.

Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV.

Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27.PMID: 17130145 [PubMed - indexed for MEDLINE]Related articlesFree article

SAGA: a subgraph matching tool for biological graphs.

Tian Y, McEachin RC, Santos C, States DJ, Patel JM.

Bioinformatics. 2007 Jan 15;23(2):232-9. Epub 2006 Nov 16.PMID: 17110368 [PubMed - indexed for MEDLINE]Related articlesFree article

A dominant function of IKK/NF-kappaB signaling in global lipopolysaccharide-induced gene expression.

Carayol N, Chen J, Yang F, Jin T, Jin L, States D, Wang CY.

J Biol Chem. 2006 Oct 13;281(41):31142-51. Epub 2006 Aug 16.PMID: 16914552 [PubMed - indexed for MEDLINE]Related articlesFree article

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ.

Genome Biol. 2006;7(4):R35. Epub 2006 Apr 28.PMID: 16646984 [PubMed - indexed for MEDLINE]Related articlesFree article

Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH.

Huo JS, McEachin RC, Cui TX, Duggal NK, Hai T, States DJ, Schwartz J.

J Biol Chem. 2006 Feb 17;281(7):4132-41. Epub 2005 Dec 1.PMID: 16326703 [PubMed - indexed for MEDLINE]Related articlesFree article

Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction.

Santos C, Eggle D, States DJ.

Bioinformatics. 2005 Apr 15;21(8):1653-8. Epub 2004 Nov 25.PMID: 15564295 [PubMed - indexed for MEDLINE]Related articlesFree article