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Items: 50

1.

Druggable Transcriptional Networks in the Human Neurogenic Epigenome.

Higgins GA, Williams AM, Ade AS, Alam HB, Athey BD.

Pharmacol Rev. 2019 Oct;71(4):520-538. doi: 10.1124/pr.119.017681. Review.

PMID:
31530573
2.

Publisher Correction: 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.

Kalinin AA, Allyn-Feuer A, Ade A, Fon GV, Meixner W, Dilworth D, Husain SS, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley JW, Verdone JE, Veltri RW, Pienta KJ, Coffey DS, Athey BD, Dinov ID.

Sci Rep. 2018 Oct 26;8(1):16142. doi: 10.1038/s41598-018-33574-w.

3.

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.

Kalinin AA, Allyn-Feuer A, Ade A, Fon GV, Meixner W, Dilworth D, Husain SS, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley JW, Verdone JE, Veltri RW, Pienta KJ, Coffey DS, Athey BD, Dinov ID.

Sci Rep. 2018 Sep 12;8(1):13658. doi: 10.1038/s41598-018-31924-2. Erratum in: Sci Rep. 2018 Oct 26;8(1):16142.

4.

Deep learning in pharmacogenomics: from gene regulation to patient stratification.

Kalinin AA, Higgins GA, Reamaroon N, Soroushmehr S, Allyn-Feuer A, Dinov ID, Najarian K, Athey BD.

Pharmacogenomics. 2018 May;19(7):629-650. doi: 10.2217/pgs-2018-0008. Epub 2018 Apr 26. Review.

5.

The pharmacoepigenomics informatics pipeline defines a pathway of novel and known warfarin pharmacogenomics variants.

Allyn-Feuer A, Ade A, Luzum JA, Higgins GA, Athey BD.

Pharmacogenomics. 2018 Apr;19(5):413-434. doi: 10.2217/pgs-2017-0186. Epub 2018 Feb 5.

6.

Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathways.

Higgins GA, Allyn-Feuer A, Georgoff P, Nikolian V, Alam HB, Athey BD.

Methods. 2017 Jul 1;123:102-118. doi: 10.1016/j.ymeth.2017.03.012. Epub 2017 Apr 4. Review.

PMID:
28385536
7.

Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury.

Higgins GA, Georgoff P, Nikolian V, Allyn-Feuer A, Pauls B, Higgins R, Athey BD, Alam HE.

Pharm Res. 2017 Aug;34(8):1658-1672. doi: 10.1007/s11095-017-2130-6. Epub 2017 Mar 7.

8.

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 Jul;39(7):697-707. doi: 10.1007/s40264-016-0414-0.

9.

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.

10.

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.

11.

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.

12.

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. Review.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.

Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey BD, Omenn GS, Burant CF, Jagadish HV.

Bioinformatics. 2010 Apr 1;26(7):971-3. doi: 10.1093/bioinformatics/btq048. Epub 2010 Feb 7.

25.

The University of Michigan Honest Broker: a Web-based service for clinical and translational research and practice.

Boyd AD, Saxman PR, Hunscher DA, Smith KA, Morris TD, Kaston M, Bayoff F, Rogers B, Hayes P, Rajeev N, Kline-Rogers E, Eagle K, Clauw D, Greden JF, Green LA, Athey BD.

J Am Med Inform Assoc. 2009 Nov-Dec;16(6):784-91. doi: 10.1197/jamia.M2985. Epub 2009 Aug 28.

26.

High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics.

Yang MQ, Athey BD, Arabnia HR, Sung AH, Liu Q, Yang JY, Mao J, Deng Y.

BMC Genomics. 2009 Jul 7;10 Suppl 1:I1. doi: 10.1186/1471-2164-10-S1-I1.

27.

Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs.

Bernstam EV, Hersh WR, Johnson SB, Chute CG, Nguyen H, Sim I, Nahm M, Weiner MG, Miller P, DiLaura RP, Overcash M, Lehmann HP, Eichmann D, Athey BD, Scheuermann RH, Anderson N, Starren J, Harris PA, Smith JW, Barbour E, Silverstein JC, Krusch DA, Nagarajan R, Becich MJ; CTSA Biomedical Informatics Key Function Committee.

Acad Med. 2009 Jul;84(7):964-70. doi: 10.1097/ACM.0b013e3181a8144d. Review.

28.

New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites.

Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD.

Genome Res. 2009 Jul;19(7):1175-83. doi: 10.1101/gr.089367.108. Epub 2009 Mar 31.

29.
30.

Delivering informatics capabilities to an AHC research community through public/private partnerships (PPP).

Smith KA, Athey BD, Chahal AP, Sahai P.

AMIA Annu Symp Proc. 2008 Nov 6:1216-7.

PMID:
18999086
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.

32.

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
33.

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
34.

Investigation of ultrafast time gating by spatial filtering.

Mills KD, Deslaurier L, Dilworth DS, Grannell SM, Hoover BG, Athey BD, Leith EN.

Appl Opt. 2001 May 10;40(14):2282-9.

PMID:
18357236
35.

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.

36.

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).

Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, Athey BD.

Nucleic Acids Res. 2008 Mar;36(5):e27. doi: 10.1093/nar/gkm1165. Epub 2008 Jan 21.

37.

An 'Honest Broker' mechanism to maintain privacy for patient care and academic medical research.

Boyd AD, Hosner C, Hunscher DA, Athey BD, Clauw DJ, Green LA.

Int J Med Inform. 2007 May-Jun;76(5-6):407-11. Epub 2006 Nov 1. Review.

PMID:
17081800
38.

The "Honest Broker" method of integrating interdisciplinary research data.

Boyd AD, Hunscher DA, Kramer AJ, Hosner C, Saxman P, Athey BD, Greden JF, Clauw DC.

AMIA Annu Symp Proc. 2005:902.

39.

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST.

Kim YJ, Boyd A, Athey BD, Patel JM.

Nucleic Acids Res. 2005 Aug 1;33(13):4335-44. Print 2005.

40.

Challenges in presenting high dimensional data to aid in triage in the DARPA virtual soldier project.

Boyd AD, Wright ZC, Ade AS, Bookstein F, Ogden JC, Meixner W, Athey BD, Morris T.

Stud Health Technol Inform. 2005;111:68-74.

PMID:
15718701
41.

Noise suppression and optical sectioning by non-phase-recording interferometry.

Leith EN, Chien WC, Mills KD, Athey BD, Dilworth DS, Beals JL.

Appl Opt. 2004 Aug 10;43(23):4512-9.

PMID:
15376427
42.
43.

Optical sectioning by holographic coherence imaging: a generalized analysis.

Leith EN, Chien WC, Mills KD, Athey BD, Dilworth DS.

J Opt Soc Am A Opt Image Sci Vis. 2003 Feb;20(2):380-7.

PMID:
12570305
44.

Analysis of time-gated imaging through scattering media by a Fourier optics approach.

Leith EN, Mills KD, Grannell S, Dilworth DS, Athey BD, Lopez J.

J Opt Soc Am A Opt Image Sci Vis. 2002 Mar;19(3):532-6.

PMID:
11876318
45.

Correlations among angular wave component amplitudes in elastic multiple-scattering random media.

Hoover BG, Deslauriers L, Grannell SM, Ahmed RE, Dilworth DS, Athey BD, Leith EN.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Feb;65(2 Pt 2):026614. Epub 2002 Jan 25.

PMID:
11863685
46.

F-actin, tubulin and spectrin in the organ of Corti: comparative distribution in different cell types and mammalian species.

Raphael Y, Athey BD, Wang Y, Lee MK, Altschuler RA.

Hear Res. 1994 Jun 1;76(1-2):173-87.

47.

Structure of the reticular lamina and repair after noise injury.

Raphael Y, Athey BD, Wang Y, Hawkins JE Jr.

Rev Laryngol Otol Rhinol (Bord). 1993;114(3):171-5.

PMID:
8191059
48.
49.

Radial density distribution of chromatin: evidence that chromatin fibers have solid centers.

Smith MF, Athey BD, Williams SP, Langmore JP.

J Cell Biol. 1990 Feb;110(2):245-54.

50.

Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length.

Williams SP, Athey BD, Muglia LJ, Schappe RS, Gough AH, Langmore JP.

Biophys J. 1986 Jan;49(1):233-48.

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