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Linking MedDRA®-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.

Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.

Drug Saf. 2016 Mar 22. [Epub ahead of print]


Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis.

Wiley JW, Higgins GA, Athey BD.

Neurogastroenterol Motil. 2016 Jan;28(1):12-25. doi: 10.1111/nmo.12706. Review.


A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.

Higgins GA, Allyn-Feuer A, Barbour E, Athey BD.

Pharmacogenomics. 2015;16(14):1547-63. doi: 10.2217/pgs.15.106. Epub 2015 Sep 7.


Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response.

Higgins GA, Allyn-Feuer A, Athey BD.

Pharmacogenomics. 2015;16(14):1565-83. doi: 10.2217/pgs.15.105. Epub 2015 Sep 4.


The epigenome, 4D nucleome and next-generation neuropsychiatric pharmacogenomics.

Higgins GA, Allyn-Feuer A, Handelman S, Sadee W, Athey BD.

Pharmacogenomics. 2015;16(14):1649-69. doi: 10.2217/pgs.15.111. Epub 2015 Sep 4.


MetDisease--connecting metabolites to diseases via literature.

Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A.

Bioinformatics. 2014 Aug 1;30(15):2239-41. doi: 10.1093/bioinformatics/btu179. Epub 2014 Apr 8.


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.


tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.

Athey BD, Braxenthaler M, Haas M, Guo Y.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:6-8. eCollection 2013.


Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines.

Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y.

PLoS One. 2012;7(11):e49941. doi: 10.1371/journal.pone.0049941. Epub 2012 Nov 28.


Researchers' needs for resource discovery and collaboration tools: a qualitative investigation of translational scientists.

Bhavnani SK, Warden M, Zheng K, Hill M, Athey BD.

J Med Internet Res. 2012 Jun 5;14(3):e75. doi: 10.2196/jmir.1905.


Needs for an expanded ontology-based classification of adverse drug reactions and related mechanisms.

Zhichkin PE, Athey BD, Avigan MI, Abernethy DR.

Clin Pharmacol Ther. 2012 Jun;91(6):963-5. doi: 10.1038/clpt.2012.41.


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.


Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.

Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS.

Bioinformatics. 2012 Feb 1;28(3):373-80. doi: 10.1093/bioinformatics/btr661. Epub 2011 Nov 30.


The NIH National Center for Integrative Biomedical Informatics (NCIBI).

Athey BD, Cavalcoli JD, Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isokpehi RD, DeLisi C; NCIBI faculty, trainees, and staff.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):166-70. doi: 10.1136/amiajnl-2011-000552. Epub 2011 Nov 19.


Integrated metabolome and transcriptome analysis of the NCI60 dataset.

Su G, Burant CF, Beecher CW, Athey BD, Meng F.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S36. doi: 10.1186/1471-2105-12-S1-S36.


Cross-domain neurobiology data integration and exploration.

Xuan W, Dai M, Buckner J, Mirel B, Song J, Athey B, Watson SJ, Meng F.

BMC Genomics. 2010 Dec 1;11 Suppl 3:S6. doi: 10.1186/1471-2164-11-S3-S6.


2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research.

Yang JY, Niemierko A, Bajcsy R, Xu D, Athey BD, Zhang A, Ersoy OK, Li GZ, Borodovsky M, Zhang JC, Arabnia HR, Deng Y, Dunker AK, Liu Y, Ghafoor A.

BMC Genomics. 2010 Dec 1;11 Suppl 3:I1. doi: 10.1186/1471-2164-11-S3-I1.


GSearcher: agile attribute querying for biological networks.

Su G, Athey BD, Meng F.

Bioinformatics. 2010 Dec 15;26(24):3138-9. doi: 10.1093/bioinformatics/btq597. Epub 2010 Nov 18.


The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P.

J Biomed Inform. 2011 Feb;44(1):137-45. doi: 10.1016/j.jbi.2010.10.003. Epub 2010 Oct 16.


Unified translation repression mechanism for microRNAs and upstream AUGs.

Ajay SS, Athey BD, Lee I.

BMC Genomics. 2010 Mar 5;11:155. doi: 10.1186/1471-2164-11-155.

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