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Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study.

Pett SL, Kunisaki KM, Wentworth D, Griffin TJ, Kalomenidis I, Nahra R, Montejano Sanchez R, Hodgson SW, Ruxrungtham K, Dwyer D, Davey RT, Wendt CH; INSIGHT FLU003 Plus Study Group .

Open Forum Infect Dis. 2017 Oct 25;5(1):ofx228. doi: 10.1093/ofid/ofx228. eCollection 2018 Jan.


CLO: The cell line ontology.

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.

J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014.


Metab2MeSH: annotating compounds with medical subject headings.

Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A.

Bioinformatics. 2012 May 15;28(10):1408-10. doi: 10.1093/bioinformatics/bts156. Epub 2012 Apr 6.


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.


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.


Predictors of bacterial pneumonia in Evaluation of Subcutaneous Interleukin-2 in a Randomized International Trial (ESPRIT).

Pett SL, Carey C, Lin E, Wentworth D, Lazovski J, Miró JM, Gordin F, Angus B, Rodriguez-Barradas M, Rubio R, Tambussi G, Cooper DA, Emery S; INSIGHT-ESPRIT Study Group.

HIV Med. 2011 Apr;12(4):219-27. doi: 10.1111/j.1468-1293.2010.00875.x. Epub 2010 Aug 31.


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.


Systematic comparison of the human saliva and plasma proteomes.

Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT.

Proteomics Clin Appl. 2009 Jan 1;3(1):116-134.


Interleukin-2 therapy in patients with HIV infection.

INSIGHT-ESPRIT Study Group; SILCAAT Scientific Committee, Abrams D, Lévy Y, Losso MH, Babiker A, Collins G, Cooper DA, Darbyshire J, Emery S, Fox L, Gordin F, Lane HC, Lundgren JD, Mitsuyasu R, Neaton JD, Phillips A, Routy JP, Tambussi G, Wentworth D.

N Engl J Med. 2009 Oct 15;361(16):1548-59. doi: 10.1056/NEJMoa0903175.


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.


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.


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.


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. doi: 10.1093/nar/gkn722. Epub 2008 Oct 31.


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.


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.


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.


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.


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.


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.


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.

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