The Athey Lab

Department of Computational Medicine and Bioinformatics

University of Michigan Medical School

Brian Athey, Ph.D.

Principal Investigator

Brian Athey, PhD. is the Michael A. Savageau Collegiate Professor and Founding Chair of the Department of Computational Medicine and Bioinformatics (DCMB) at the University of Michigan Medical School; DCMB currently has 16 primary faculty members and 14 secondary appointees. Brian also serves as a Professor of Psychiatry and Internal Medicine at the UM Medical School. In addition, he served as co-founder and co-director of the campus-wide Michigan Institute for Data Science (MIDAS), from 2015-2018. Brian earned his Ph.D. in Cellular and Molecular Biology (Biophysics concentration) at UM in 1990; and has been at UM for 37 years, joining the faculty of the Medical School in 1994.

Athey serves as PI of the UM NIGMS T32 UM Bioinformatics Training Program (in Year 15 of 16). The Bioinformatics Graduate Program in DCMB has graduated over 90 Ph.D. students and 65 MS students since 2005. DCMB faculty are deeply committed to translational bioinformatics, genomics, epigenomics, transcriptomics, proteomics, metabolomics, network systems, and multi-scale ‘omics integration research, a focus he launched in 2005 which started Bioinformatics at Michigan and launched the NIH National Center for Biomedical Informatics (NCIBI), which he led for 9 years. He was Co-founder and later CSO of the tranSMART Foundation (2012-2017), a data integration and analytics platform utilized by the pharmaceutical industry globally.

In 2007, Athey was founding Associate Director of the Michigan Institute for Clinical and Health Research (MICHR), home of the UM Clinical and Translational Science Award (CTSA), where he served as Director of its Biomedical Informatics Core (2006-2013). Athey has served as Acting CIO of the University of Michigan Health System (2010-2012), and he has also served as Director of Academic Informatics for the UM Medical School (2009-2011). He served as the Assistant CIO of the UM for 2 years in the late 1990s.

Athey has more than 25 years of experience in trans-disciplinary team science-based leadership experience as overall Principal Investigator of national biomedical informatics and computational sciences centers and consortia. These include the National Library of Medicine (NLM) Visible Human Project, the DARPA Telepathology and Virtual Solider Projects, and the NIH National Center for Integrative Biomedical Informatics (NCIBI).

Trained as a biophysicist, as a graduate student Athey proposed the double helical crossed-linker model for chromatin, now considered by most to be its correct structural motif. Earlier in his career, Athey was considered to be an expert in microscopic biological imaging and scattering, and is an expert in several of modalities of microscopy from electron to 2-photon. For nearly 10 years, shared a laboratory with Professor Emmett Leith, the internationally renowned inventor of off-axis Holography, with whom he trained 2 PhD. students. Athey has trained over 12 PhD students, 7 post doctoral fellows, and has over 100 peer- reviewed papers and conference proceedings.

He is currently an active researcher in ‘pharmacoepigenomics’, a field he helped establish, and he is a leader in the field of pharmacogenomics. With his collaborators Gerald A. Higgins, Ph.D., Ivo Dinov, Ph.D., John Wiley, M.D., and his doctoral students, the team has been engaged in intensive studies to help define a new class of genomic signatures to inform Pharmacogenomics testing by using a novel Pharmacogenomics Informatics Pipeline (PIP) that has allowed for the discovery of a new large class of intragenic and intronic Structural Variants (SVs) that govern the cis- and trans- genetic regulation and alternative splicing of pharmacokinetic (PK) and pharmacodynamic (PD) genes and pharmacometabolomic markers related to neuropsychiatric and stress-related diseases, cardiovascular (warfarin), and gastro-intestinal (GI) medications.

A more recent focus involves studies of pharmacological mechanisms and pharmacoepigenomics biomarkers of Lithium, Valproic Acid, and Ketamine response to bipolar disease and depression. These markers allow for modeling tissue-specific activities and the inclusion of epigenomically-related assignments of chromatin state and location of causal genes in specific topological associated domains (TADs) of the chromosome territory within each allele. This new class of pharmacoepigenomic markers holds promise to be clinically validated and translated to new and improved pharmacogenomics tests which will not only all for improved patient-specific assignment of cis-regulated PK and PD gene sets; and will also provide spatially-linked trans- markers which indicates patient-specific adverse event co-variation. Seven provisional patent applications have been filed to the USPTO. The first of these 7, a broad pharmacoepigenomics and pharmacophenomics platform patent has been allowed by the USPTO (Dec. 2018), and was issued April, 2019.

A complimentary area of research focus is “High Throughput Microscopic Analysis of Chromatin State within the Nucleus (4-D Nucleome)”. This research focus merges bioinformatics information within the spatial-temporal context of the placement of sequence data within context of the chromatin within the 4D nucleus of cells and tissues. These methods make use of Machine Learning methods that can classify visual biomarkers within the cell and its nucleus to allow for patient-specific classification of activated topological associated domains (TADs) which will inform patient specific assignment of pharmco-epigenomic traits. A new collaboration with a for-profit imaging company, Visiongate 3D (Phoenix, AR), is being established to license and continue co-development of our patent-protected methods (2 provisional patents has been filed with USPTO).

Athey’s earlier work as Chairman of the Scientific Advisory Board (SAB) of Assurex Health, Inc. (Mason, Ohio; now a subsidiary of Myriad Genetics, Salt Lake City, UT) in Psychiatric Pharmacogenomics helped to refine, clinically validate, and market the most successful pharmacogenomics test now on the market, with over 1,300,000 combinatoric genotypes provided to physicians to recommend medications to patients with Major Depressive Disorder (MDD). To translate his laboratory’s new Pharmacoepigenomics technology, Brian has co-founded a new company called Phenomics Health, Inc. (Ann Arbor, MI, and Shenzhen, China) with the former CEO and Executive Chairman of Assurex Health, Dr. James S. Burns.

Athey has also served as a consultant to the Defense Science Office (DSO), DARPA (6 years), and to the NIH Office of the Director (OD) and the NIH CIO (3.5 years). In the late 1990s, Brian was awarded the Peace Fellowship from the Federation of American Scientists (FAS) for his work with DARPA to prevent biological terrorism. From 2005-2011 Brian was the Co-Founder, Scientist and Engineers for America (SEA); Chairman of the Board, 2009-2011.

Brian is an elected fellow of the American College of Medical Informatics (FACMI). He currently serves as a life and medical sciences consultant to the VP (Academic), Chinese University Hong Kong, Shenzhen (CUHK-SZ), where he also serves as a member of the Shenzhen Research Institute for Big Data (SRIBD).

Work Titles

Michael Savageau Collegiate Professor & Chair

Department of Computational Medicine & Bioinformatics

Professor of Psychiatry and Internal Medicine

University of Michigan

Education

Degrees

Ph.D., Biophysics, University of Michigan (1990)

B.S., University of Michigan-Dearborn; Dearborn, MI (1982)

Classical Studies, St. Johns College, Annapolis, MD (1976-1977)

Fellowships

1991-1993 NIH Postdoctoral Fellowship

1990-1991 NIH Postdoctoral Fellowship

Contact Information

Work Email Address:

bleu@umich.edu

Website:

DCMB Website

MI Experts Profile


Fax Number:

734--615-6553

Office Number:

734-615-9292

Administrative Contact

Janet Peake

janetp@med.umich.edu


Lab Address:

NCRC Building 520, Room 3393

1600 Huron Parkway

Ann Arbor, MI 48105

Office Address:

2017F Palmer Commons

100 Washtenaw Ave.

Ann Arbor, MI 48109-2218

Athey Lab Members

Brian Athey, Ph.D.
Principal Investigator
Alex Ade
Applications Programmer/Analyst


Gerry Higgins, Ph.D.
Research Professor of Computational Medicine and Bioinformatics
Faculty Profile
Samuel Handelman
Research Assistant Professor of Internal Medicine
Faculty Profile
Alex Kalinin, Ph.D.
Postdoctoral FellowUM/Shenzhen Research Institute for Big Data (SRIBD)
Faculty Profile
Bokai Chen
Masters Student
Xinhai Hou (Renly)
CUHK-SZ/UM AMDP Student

Publications

  1. Williams SP*, Athey BD*, Muglia LJ, Schappe RS, Gough AH, Langmore JP (1986) Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophysical Journal 49(1):233-248. PMID: 3955173. PMCID: PMC1329627 *Indicates Co-First Author. First Publication of the Double Helical Crossed-Linker Model for Chromatin.
  2. Smith MF, Athey BD, Williams SP, Langmore JP (1990) Radial density distribution of chromatin: evidence that chromatin fibers have solid cores. Journal of Cell Biology 110:245-254. PMID: 2298806. PMCID: PMC2116005
  3. Athey BD, Smith MF, Rankert DA, Williams SP, Langmore JP (1990) The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin. Journal of Cell Biology 111(3):795-806. PMID: 2391364. PMCID: PMC2116296. First Publication of Cryo-Electron Microscopy of Chromatin.
  4. Raphael Y, Athey BD, Wang Y, Hawkins JE Jr (1993) Structure of the reticular lamina and repair after noise injury. Rev Laryngol Otol Rhinol 1993;114(3):171-175. PMID: 8191059.
  5. Grober JS, Bowen BL, Ebling H, Athey B, Thompson CB, Fox DA, Stoolman LM (1993) Monocyte-endothelial adhesion in chronic rheumatoid arthritis. In situ detection of selectin and integrin-dependent interactions. Journal of Clinical Investigations 91:2609-2619. PMID: 7685772. PMCID: PMC443325
  6. Raphael Y, Athey BD, Wang Y, Lee MK, Altschuler RA (1994) F-actin, tubulin and spectrin in the organ of Corti: comparative distribution in different cell types and mammalian species. Hearing Research 76(1-2):173-187. PMID: 7928710.
  7. Nurko S, Sogabe K, Davis JA, Roeser NF, Defrain M, Chien A, Hinshaw D, Athey B, Meixner W, Venkatachalam MA, Weinberg JM (1996) Contribution of actin cytoskeleton alterations to ATP depletion and calcium-induced proximal tubule cell injury. American Journal of Physiology:Renal Physiology 270:F39-F52. PMID: 8769821.
  8. Brakenhoff GJ, Squier J, Norris T, Bliton AC, Wade MH, Athey B (1996). Real-time two-photon confocal microscopy using a femtosecond, amplified Ti:sapphire system. Journal of Microscopy 181:253-259. PMID: 8642584. First 2-Photon Microscopy Experiment on Living Cells.
  9. Clark HA, Barker SLR, Brasuel M, Miller MT, Monson E, Parus S, Shi Z.-Y, Song A, Thorsrud B, Kopelman R, Ade AS, Meixner WM, Athey BD, Hoyer M, Hill D, Lightle R, Philbert MA (1998) Subcellular Optochemical Nanobiosensors: Probes encapsulated by biologically localized embedding (PEBBLES). Sensors and Actuators B - Chemical, 1998, 51(1):12-16.
  10. Higgins G, Athey B, Bassingthwaighte J, Burgess J, Champion H, Cleary K, Dev P, Duncan J, Hopmeier M, Jenkins D, Johnson C, Kelly H, Leitch R, Lorensen W, Metaxas D, Spitzer V, Vaidehi N, Vosburgh K, Winslow R (2001) Final report of the meeting “modeling & simulation in medicine: towards an integrated framework.” Computer Aided Surgery 6(1):32-39. PMID: 11335957.
  11. Mills KD, Deslaurier L, Dilworth DS, Grannell SM, Hoover BG, Athey BD, Leith EN (2001) Investigation of ultrafast time gating by spatial filtering. Applied Optics 40:2282- 2289. PMID: 18357236
  12. Lee I, Athey BD, Wetzel AW, and Baker Jr JR (2001) Molecular Dynamics Studies on Folic Acid and Fluorescein-Derivatized PAMAM Dendrimers. Technical Proceedings of the 2001 International Conference on Modeling and Simulation of Microsystems 13-16.
  13. Hacker TJ, Athey BD (2001) A methodology for account management in grid computing environments. Lecture Notes in Computer Science, Vol. 2242:133-144. Springer Verlag Press.
  14. Mangrulkar R, Athey B, Brebner E, Moidu K, Pulido P, Woolliscroft J (2002) Telemedicine/telehealth: an international perspective. Telemedicine and medical/health education. Telemedicine Journal and e-Health, 2002 Spring 8(1):49-60. PMID: 20120405.
  15. Hoover BG, Deslauriers L, Grannell SM, Ahmed RE, Dilworth DS, Athey BD, Leith EN (2002) Correlations among angular wave component amplitudes in elastic multiple- scattering random media. Physical Review E, Statistical, Nonlinear, and Soft Matter Physics 65(2):026614(1-8). PMID: 11863685.
  16. Leith EN, Mills KD, Grannell S, Dilworth DS, Athey BD, Lopez J (2002) Analysis of time-gated imaging through scattering media by a Fourier optics approach. Journal of the Optical Society of America, 19(3):532-536. PMID: 11876318.
  17. Lee I, Athey BD, Baker JR, Wetzel A, Meixner WM, Baker, Jr JR (2002) Structural molecular dynamic studies on therapeutically-applied polyamidoamine dendrimers for a Therapeutic Application: Effects of pH and Generation. Macromolecules 35(11):4510- 4520.
  18. Walker D, Lee WY, Skov N, Berger C, Athey BD (2002) Investigating user requirements: computer-based anatomy learning modules for multiple user testbeds. Journal of the America Medical Informatics Association 9(4):311-319.
  19. Leith EN, Chien WC, Mills KD, Athey BD, Dilworth DS (2003) Optical sectioning by holographic coherence imaging: a generalized analysis. Optical Society of America 20(2): 380-387. PMID: 12570305.
  20. Lee I, Dombkowski AA, Athey BD (2004) Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray. Nucleic Acids Research 32(2):681-690. PMID: 14757833. PMCID: PMC373323
  21. Leith EN, Chien WC, Mills KD, Athey BD, Dilworth DS, Beals JL (2004) Noise suppression and optical sectioning by non-phase-recording interferometry. Applied Optics 43(23):4512-4519. PMID: 15376427
  22. Boyd AD, Wright ZC, Ade AS, Bookstein F, Ogden JC, Meixner W, Athey BD, Morris T (2005) Challenges in presenting high dimensional data to aid in triage in the DARPA virtual soldier project. Studies in Health Technology and Informatics Vol. 111:68-74. 2005. MMVR 13. Eds: J.D. Westwood, et. al. PMID: 15718701. PMCID: PMC1283542
  23. Dai, M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Research 33(20):e175, pp. 1-9. PMID: 16284200. PMCID: PMC1283542
  24. Kim YJ, Boyd A, Athey BD, Patel JM (2005) miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST. Nucleic Acids Research 33(13):4335-44. PMID: 16061938. PMCID: PMC1182166
  25. Boyd AD, Hunscher DA, Kramer AJ, Hosner C, Saxman P, Athey BD, Greden JF, Clauw DC (2005) The “Honest Broker” method of integrating interdisciplinary research data. AMIA Annual Symposium Proceedings/AMIA Symposium. 2005:902. PMID:16779189.
  26. Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, Athey B, Watson SJ, Meng F (2006) SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics Jul 15; 22(14):e523-529. PMID: 16873516.
  27. Boyd AD, Hosner C, Hunscher DA, Athey BD, Clauw DJ, Green LA (2007) An ‘Honest Broker’ mechanism to maintain privacy for patient care and academic medical research. International Journal of Medical Informatics 76(5-6):407-411, May-June 2007. PMID: 17081800.
  28. Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey BD, States D, Jagadish HV (2007) Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Research 2007, 35:D566-D571. PMID: 17130145. PMCID: PMC1716720
  29. Xuan W, Dai M, Mirel B, Wilson J, Athey B, Watson SJ, Meng F (2007) An active visual search interface for Medline. Computational Systems Bioinformatics Conference 2007; 6:359-369. PMID: 17951838. http://www.lifesciencessociety.org/CSB2007/toc/PDF/359.2007.pdf
  30. Sarntivijai S, Ade AS, Athey BD, States DJ (2007) The Cell Line Ontology and its use in tagging cell line names in biomedical text. AMIA Annual Symposium Proc. 2007 October 11:1103. PMID: 18694200.
  31. Yu C, Hanauer DA, Athey BD, Jagadish HV, States DJ (2007) Simplifying access to a Clinical Data Repository using schema summarization. AMIA Annual Symposium Proc. 2007 October 11:1163. PMID: 18694259.
  32. Xuan W, Dai M, Mirel B, Wilson J, Athey B, Watson SJ, Meng F (2007) Interactive Medline Search Engine Utilizing Biomedical Concepts and Data Integration. BioLink SIG 2007: Linking Literature, Information and Knowledge for Biology. In 15th Annual International Conference on Intelligent Systems for Molecular Biology: Special Interest Group Meeting (SIGs) Program Materials: 55-58.
  33. Yu B, Jakupovic E, Wilson J, Dai M, Xuan W, Mirel B, Athey B, Watson SJ, Meng F (2008) A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration. Summit on Translat Bioinforma 2008 Mar 1;2008:130-4. PMID: 21347131. PMCID:PMC3041526
  34. Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, Athey BD, (2008) Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Nucleic Acids Research 36:e27, pp. 1-10, January 2008. PMID: 18208839. PMCID: PMC2275156
  35. States D, Ade AS, Wright ZC, Bookvich AV, Athey B, (2008) MiSearch Adaptive PubMed Search Tool. Bioinformatics (March 11, 2008) PMID: 18326507. PMCID: PMC2660869
  36. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohan I, Delp S, Parker DS, Toga AW. (2008) iTools: a framework for classification, categorization and integration of computational biology resources. Plos ONE May 28;3(5):e2265. PMID: 18509477. PMCID:PMC2386255
  37. Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, Wright Z, Chapman A, Jayapandian M, Ozgur A, Tian Y, Cavalcoli J, Mirel B, Patel J, Radev D, Athey B, States D, Jagadish HV (2008) Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Research (October 31, 2008). PMID: 18978014. PMCID: PMC2686565
  38. Lee I, Majoros IJ, Williams CR, Athey, B.D., Baker Jr JR (2008) Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis. Computational and Theoretical Nanoscience 2008; 6:1-7. PMID: 20700476. PMCID: PMC2917823
  39. Smith KA, Athey BD, Chahal AP, Sahai P (2008) Delivering Informatics Capabilities to an AHC Research Community through Public/Private Partnerships (PPP). AMIA Annual Symposium Proc. November 6:1216-7. PMID: 18999086.
  40. Sarntivijai S, Ade AS, Athey BD, States DJ (2008) A bioinformatics analysis of the cell line nomenclature. Bioinformatics December 1;24(23):2760-6. PMID: 18849319. PMCID: PMC2639272
  41. Xuan W, Dai M, Mirel B, Song J, Athey B, Watson SJ and Meng F (2009) Open Biomedical Ontology-based Medline exploration. BMC Bioinformatics. May 6;10 Suppl 5:S6. PMID: 19426463. PMCID: PMC2679406
  42. Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, and Athey BD (2009) New class of microRNA targets containing simultaneous 5’-UTR and 3’-UTR interaction sites. Genome Research July;19(7):1175-83. PMID:19336450. PMCID: PMC2704433
  43. Bernstam EV, Hersh WR, Johnson SB, Chute CG, Nguyen H, Sim I, Nahm M, Weiner M, Miller P, DiLaura RP, Overcash M, Lehmann HP, Eichmann D, Athey BD, Scheuermann RH, Anderson N, Starren JB, Harris PA, Smith JW, Barbour E, Silverstein JS, Krusch DA, Nagarajan R and Becich MJ (2009) Synergies and Distinctions between Computational Disciplines in Biomedical Research: Perspective from the Clinical and Translational Science Award Programs. Academic Medicine, July 84(7): 964-970. PMID: 19550198. PMCID: PMC2884382
  44. Yang MQ, Athey BD, Arabnia HR, Sung AH, Liu Q, Yang JY, Mao J, Deng Y (2009) High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics. BMC Genomics July 7:10 suppl 1:I1. PMID: 19594867. PMCID: PMC2709251
  45. 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 (2009) The University of Michigan Honest Broker: A Web-based Service for Clinical and Translational Research and Practice. JAMIA 10.1197 M2985. Aug. 28, 2009. PMID: 19717803. PMCID: PMC3002130
  46. Xuan W, Dai M, Buckner J, Mirel B, Song J, Athey B, Watson SJ, and Meng F (2009) Cross-Domain Neurobiology Data Integration and Exploration. Bioinformatics, Systems Biology and Intelligent Computing, International Joint Conference (IJCBS’09) 10.1109/IJCBS.2009.92. PMID: 21143788. PMCID: PMC2999351
  47. Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F (2009) The gputools package enables GPU computing in R. Bioinformatics. Oct 22. PMID: 19850754. PMCID: PMC2796814
  48. Sartor M, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS (2010) ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics. Feb 15;26(4):456-63. PMID: 20007254. PMCID: PMC2852214
  49. Ajay SS, Athey BD, and Lee I (2010) Unified translation repression mechanism for microRNAs and upstream AUGs. BMC Genomics. March, 11:155. PMID: 20205738. PMCID: PMC2842251
  50. Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey, B.D., Omenn GS, Burant CF, Jagadish HV (2010) Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics. April1:26(7):971-3, PMID: 20139469. PMCID: PMC2844990
  51. 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 (2010) The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. Biomed. Inform. October 16. PMID: 20955817. PMCID: PMC3050430
  52. Su G, Athey BD, Meng F (2010) GSearcher: agile attribute querying for biological networks. Bioinformatics. December 15;26(24):3138-9. PMID: 21088028. PMCID: PMC2995125
  53. 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 (2010) 2K09 and thereafter: the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics. December 1;11 Suppl 3:I1. PMID: 21143775. PMCID: PMC2999338
  54. Xuan W, Dai M, Buckner J, Mirel B, Song J, Athey B, Watson SJ, Meng F (2010) Cross-domain neurobiology data integration and exploration. BMC Genomics. December 1;11 Suppl 3:S6. PMID: 21143788. PMCID: PMC2999351
  55. Su G, Burant CF, Beecher, CW, Athey BD, Meng F (2011) Integrated metabolome and transcriptome analysis of the NCI60 dataset. BMC Bioinformatics. February 12 Suppl 1:S36. PMID: 21342567. PMCID: PMC3044292
  56. Athey BD., Cavalcoli, J., Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isopheki R, DeLisi C, the NCIBI faculty, trainees, and staff. 2011. The NIH National Center for Integrative Biomedical Informatics (NCIBI). J. Am. Med. Inform. Assoc. 2012 March 1;19(2):166-170. PMID:22101971. PMCID: PMC3277628
  57. Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A. Metab2MeSH: Annotating Compounds with Medical Subject Headings (MeSH). Bioinformatics. 2012 Apr 6. PMID: 22492643. PMCID: PMC3348562
  58. Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS. Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics. 2012 Feb 1;28(3):373-80. Epub 2011 Nov 30. PMID: 22135418. PMCID: PMC3268237
  59. Zhichkin PE, Athey BD, Avigan MI, Abernethy DR. Needs for an Expanded Ontology- Based Classification of Adverse Drug Reactions (ADRs) and Related Mechanisms. Clinical Pharmacology & Therapeutics.2012 June;91(6);963-5. PMID: 22609907
  60. Bhavnani SK, Warden M, Zheng K, Hill M, Athey BD. Researchers’ Needs for Resource Discovery and Collaboration Tools: A Qualitative Investigation of Translational Scientists. Journal of Medical Internet Research. 2012 June 5;14(3):e75. PMID:22668750. PMCID: PMC3415064
  61. Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y. Ontology-based Combinatorial Comparative Analysis of Adverse Events Associated with Killed and Live Influenza Vaccines. PLOS One. 2012:7(11):e49941. PMID:23209624. PMCID: PMC3509157
  62. Athey BD, Braxenthaler M, Haas M, Guo Y. tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research. AMIA Jt. Summits Transl. Sci. Proc. 2013 March 18;2013:6-8. eCollection 2013. PMID:24303286. PMCID: PMC3814495
  63. Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A. MetDisease—connecting metabolites to diseases via literature. Bioinformatics. 2014 April 23. PMID:24713438.
  64. Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schurer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush M, Haendel MA, Zheng, J, Stoechert CJ, Peters B, Mungall CJ, Carey TE, States D, Athey BD and He Y. CLO:“The Cell Line Ontology.” Journal of Biomedical Semantics. 2014 DOI: 10.1186/2041-1480-5-37, ISSN: 2041-1480. PMID:25852852 PMCID: PMC4387853.
  65. Higgins GA, Allyn-Feuer A, Handelman S, Sadee W, Athey BD (2015). The epigenome, 4D Nucleome and next-generation neuropsychiatric pharmacogenomics. Pharmacogenomics. (14),1649-69. PMID: 26338265
  66. Higgins GA, Allyn-Feuer A, Athey BD. "Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response." Journal of Pharmacogenomics. September 4, 2015. DOI: 10.2217. PMID:26340055.
  67. Higgins GA, Allyn-Feuer A, Barbour E and Athey BD. “A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.” Journal of Pharmacogenomics. September 7, 2015. DOI: 10.2217. PMID:26343379.
  68. Higgins GA, Allyn-Feuer A, Handelman S, Sadee W, Athey BD. “The epigenome, 4D nucleome and next-generation neuropsychiatric pharmacogenomics.” Journal of Pharmacogenomics. September 4, 2015. DOI: 10.2217. PMID:26338265.
  69. Wiley JW, Higgins GA and Athey BD. “Stress and Glucocorticoid Receptor Transcriptional Programming in Time and Space: Implications for the Brain-Gut Axis.” Neurogastroenterology and Motility.January 28, 2016. PMID:26690871.
  70. Sarntivijai S, Zhang S, Jagannathan DG, Xiang, Zuoshuang, Burkhart K, Omenn GS, He Y, Athey BD and Abernethy DR. “Linking MedDRA-Coded Clinical Phenotypes to Biological Mechanisms by The Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.” Journal of Drug Safety. March 22, 2016. DOI: 10.1007/s40264-016- 0414-0. PMID:27003817.
  71. Higgins GA, Georgoff P, Nikolian V, Allyn-Feuer A, Pauls B, Higgins, R, Athey BD, Alam HE. “Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury.” Pharm. Research, March 7, 2017. DOI: 10.1007/s11095-017-2130-6. PMID:28271248.
  72. Higgins G.A., Allyn-Feuer A, Georgoff P, Nikolian V, Alam HB, Athey BD. “Mining the Topography and Dynamics of the 4D Nucleome to Identify Novel CNS Drug Pathways.” Methods. 2017 Jul 1;123:102-118. PMID: 28385536.
  73. Georgoff PE, Nikolian VC, Higgins G, Chtraklin, K, Eidy H, Ghandour MH, Williams A, Athey B, Alam HB. “Valproic Acid Induces Pro-Survival Transcriptomic Changes in Swine Subjected to Traumatic Injury and Hemorrhagic Shock” J Trauma and Acute Care Surg. 2018 Apr;84(4):642-649. PMID: 29251706.
  74. Allyn-Feuer A, Ade A, Luzum J, Higgins GA, Athey BD. (2018). “The Pharmacoepigenomics Informatics Pipeline Defines a Pathway of Novel and Known Warfarin Pharmacogenomics Variants,” Pharmacogenomics. 2018 Apr;19(5):413-434. PMID: 29400612.
  75. Kalinin AA, Allyn-Feuer A, Ade A, Fon G-V, Meixner W, Dilworth D, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley JW, Verdone JE, Veltri RW, Pienta KJ, Coffey DS, Athey, B.D., Dinov ID. “3D Cell Nuclear Morphology: Microscopy Imaging Dataset and Voxel-Based Morphometry Classification Results.” ISBI. January 29, 2018. Preprint doi: https://doi.org/10.1101/208207.
  76. Kalinin AL, Higgins GA, Reamaroon N, Soroushmehr SM, Allyn-Feuer A, Dinov ID, Najarian K, Athey, BD. January 23, 2018. “Deep Learning in Pharmacogenomics: From Gene Regulation to Patient Stratification” Pharmacogenomics. 2018 May;19(7):629-650. PMID: 29697304.
  77. Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Chen PY, Higgins, GA, Baldi P, Smale S, Hero A (2018) Genome architecture mediates transcriptional control of human myogenic reprogramming. iScience. 6:232-246.PMID: 30240614.
  78. Nikolian VC, Dekker SE, Bambakidis T, Higgins GA, Dennahy IS, Georgoff PE, Williams AM, Andjelkovic AV, Alam HB (2018). Improvement of blood-brain barrier integrity in traumatic brain injury and hemorrhagic shock following treatment with valproic acid and fresh frozen plasma. Critical Care Medicine. 46(1):e59-66. PMID: 29095204.
  79. Zhang, H., Zhu, F., Dodge, H. H., Higgins, G. A., Omenn, G. S., Guan, Y., & Alzheimer's Disease Neuroimaging Initiative. (2018). A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease. GigaScience, 7(7), giy085.
  80. Weykamp M, Nikolian VC, Dennahy IS, Higgins, GA, Georgoff PE, Remmer H, Ghandour MH, Alam HB (2018) Rapid valproic acid-induced modulation of the traumatic proteome in a porcine model of traumatic brain injury and hemorrhagic shock. Journal of Surgical Research. 228:84-92. PMID:29907235.
  81. Nikolian, VC, Dennahy, IS, Higgins, GA, Williams, AM, Weykamp, M, Georgoff, PE, ... & Alam, HB (2018) Transcriptomic changes following valproic acid treatment promote neurogenesis and minimize secondary brain injury. Journal of Trauma and Acute Care Surgery, 84(3), 459-465. PMID:29251707.
  82. Kalinin A, Allyn-Feuer A, Ade A, Fon G, Meixner W, Dilworth D, Husain SS, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley J, Verdone JE, Veltri R, Pienta KJ, Coffey DS, Athey B, Dinov I. “3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification” Nature Journals. 2018 DOI: 10.1038/s41598-018-31924-2.
  83. Allyn-Feuer, A., Higgins, G. A., & Athey, B. D. (2018). Pharmacogenomics in the Age of GWAS, Omics Atlases, and PheWAS. arXiv preprint arXiv:1808.09481.
  84. Aaron M. Williams, Gerald A. Higgins, Simone Dekker, Umar F. Bhatti, Ben E. Biesterveld, Yuzi Tian, Zenhu Wu, Michael T. Kemp, Glenn A. Wakam, Baoling Liu, Benjamin Buller, Hasan B. Alam, (2019) Early mesenchymal stem cell-derived exosome treatment promotes transcriptomic changes involving neuroprotection in swine model of traumatic brain injury and hemorrhagic shock, Journal of Neurotrauma, in press
  85. Higgins GA, Williams AW, Ade AS, Hasan AB, Athey BD (2019) Druggable Transcriptional Networks in the Human Neurogenic Epigenome: Transcription factors and chromatin remodeling complexes reveal novel drug-disease pathways. Pharmacological Reviews, 1521-0081/71;1-19, Ocotber 2019.
  86. Chen H, Liu S, Seaman L, Najarian C, Wu W, Ljungman M, Higgins GA, Hero A, Wicha M, Rajapakse I (2019) Parental allele-specific genome architecture and transcription during the cell cycle, Cell, in press

Conference Proceedings

  1. 6th Joint Conference on Information Science (JCIS). Mar. 2002. Pp.1147-1150.
  2. Leith EN, Mills K, Chien WC, Athey BD, Dilworth D (2002) A Generalization of the Theory of Holographic Coherence Confocal Imaging. The Art and Science of Holography: A Tribute to Emmett Leith and Yuri Denisyuk. July 9, 2002. Proceedings of SPIE Vol. 4737:1-9.
  3. Hacker TJ, Noble B, and Athey BD (2002) The Effects of Systemic Packet Loss on Aggregate TCP Flows. Proceedings of Supercomputing 2002 IEEE/ACM SIGARCH, Nov. 2002.
  4. Hacker T, Athey BD, Noble B (2002) The End-to-end Performance Effects of Parallel TCP Sockets on a Lossy Wide-area Network. Parallel and Distributed Processing Symposium. 16th IEEE-CS/ACM International Proceedings. Apr. 2002, pp. 434-443. ISBN:0-795-1573-8.
  5. Singh G, Song H, Liu D, Wildman D, Goodman M, Bliton C, Kostov G, Athey BD (2003) A Non-Homology Shieu DY, Athey BD, Anderson DJ (1993) An Efficient Surface Rendering Technique Utilizing Fourier Descriptors to Visualize three Dimensional Biomedical Image Data Sets. Circuits and Systems. 1993 Proceedings of the 36th Midwest Symposium. Aug 16-18 1993, Vol. 2: 1247-1250. ISBN: 0-7803-1760-2
  6. Bookstein FL, Athey BD, Green WD, Wetzel AW (2000) Navigating Solid Medical Images by Pencils of Sectioning Planes. Proceedings of SPIE 4121:117-127.
  7. Lee I, Athey BD, Wetzel AW, Baker Jr. JR (2001) Molecular Dynamics Studies on Folic Acid and Fluorescein-Derivatized PAMAM Dendrimers. Technical Proceedings of the 2001 International Conference on Computational Nanoscience and Nanotechnology. Nanotech 2001 Vol. 2:13-16.
  8. Leith EN, Mills KD, Deslaurier L, Grannell SM, Hoover BG, Dilworth DS, Chen HS, Shih MP, Lopez J, Athey BD (2001) Information Optics Concepts Applied to Image Formation in Highly Scattering Media. Optical Processing and Computing. Eds: Casasent, David P.; Caulfield, H. John; Dallas, William J.; and Harold H Szu. Proceedings of SPIE Vol. 4392(4):1-8.
  9. Leith EN, Mills KD, Dilworth, DS, Athey BD, Grannell SM (2001) Holographic Methods for Imaging into Volume Media. Wave Optics and VLSI Photonic Devices for Information Processing Eds: Pierre Ambs and Fred R. Beyette. Dec. 2001. Proceedings of SPIE 4435:1-6.
  10. Thigpen B, Hacker TJ, McGinnis L, Athey BD (2002) Distributed Accounting on the Grid. Proceedings of the Method for Sensitive Information Retrieval from Biological Databases. Proceedings of 7th Joint Conference on Information Sciences (JCIS), Mar. 2003. Pp. 915-918.
  11. Kirschner B, Hacker TJ, Adamson W, Athey BD (2004) Walden: A Scalable Solution for Grid Account Management. Fifth IEEE/ACM International Workshop on Grid Computing GRID ’04. Pp.102-109.
  12. Hacker TJ, Noble DB, Athey BD (2004) Improving Throughput and Maintaining Fairness Using Parallel TCP. INFOCOM 2004, Hong Kong. Twenty-third Annual Joint Conference of the IEEE Computer and Communications Societies 4:2480-2489.
  13. Hacker TJ, Noble B.D., Athey BD (2005) Adaptive Data Block Scheduling for Parallel TCP Streams. Proceedings of the14th IEEE International Symposium on High Performance Distributed Computing (HPDC-14) ISBN 0780390377:265-275. Research Triangle Park, NC, July 24-27 2005.
  14. Xuan W, Dai M, Mirel B, Wilson J, Athey BD, Watson SJ, Meng F (2007) Pubviz: An Active Visual Search Interface for Medline. Proceedings of the Computational Systems Bioinformatics Conference (CSB2007). Pp. 359-369.
  15. Xuan W, Dai M, Mirel B, Wilson J, Athey BD, Watson SJ, Meng F (2007) Interactive Medline Search Engine Utilizing Biomedical Concepts and Data Integration. BioLink SIG 2007: Linking Literature, Information and Knowledge for Biology. ISMB 2007: Special Interest Group Meeting (SIGs) Program Materials. pp. 55-58.
  16. Xuan W, Dai M, Buckner J, Mirel B, Song J, Dong H, Athey BD, Watson SJ, and Meng F (2009) Cross-Domain Neurobiology Data Integration and Exploration. Proceedings of the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS’09).
  17. Athey BD, Braxenthaler M, Haas M, Guo Y (2013) tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research. AMIA Summits Tranl Sci Proc. pp.6-8.
  18. Kalinin AA, Athey BD, Dinov ID. Evaluation of methods for cell nuclear structure analysis from microscopy data. In: Supplementary Proceedings of the Seventh International Conference on Analysis of Images, Social Networks and Texts (AIST 2018). July 5 - 7, 2018.

Peer-reviewed Electronic Publications

  1. Athey BD, Warner AJ, Laby JC, Meixner WM, Chung J Williams (1996) Using the Visible Human as an Image Database Locator. The 1st National Library of Medicine (NLM) Visible Human Project Conference Proceedings. Eds: Banvard RA, and Ackerman, MJ. October 7-8, 1996. http://www.nlm.nih.gov/research/visible/vhp_conf/vhpconf.htm http://www.nlm.nih.gov/research/visible/vhp_conf/athey/index.htm
  2. Ade AS, Meixner WM, Athey BD (1998) The Visible Human Female WWW Browser and the Next Generation Internet (NGI). The 2nd National Library of Medicine (NLM) Visible Human Conference proceedings. Eds: R.A. Banvard and M.J. Ackerman. Bethesda, MD. Oct 1-2, 1998. http://www.nlm.nih.gov/research/visible/vhpconf98/AUTHORS/ATHEY/ATHEY.HTM
  3. Ade AS, Bookstein FL, Athey BD (2000) “The University of Michigan Next Generation Internet Implementation to Serve Visible Human Datasets.” The 3rd National Library of Medicine (NLM) Conference on the Visible Human. Eds: R.A. Banvard and M.J. Ackerman. Bethesda, MD. Oct. 5-6, 2000.
  4. Wetzel AW, Ade AS, Bookstein FL, Green W, Athey BD (2000) Representation and Performance Issues in Navigating Visible Human Datasets. The 3rd National Library of Medicine (NLM) Conference on the Visible Human. Eds: R.A. Banvard and M.J. Ackerman. Bethesda, MD. Oct 5-6, 2000 http://www.nlm.nih.gov/research/visible/vhpconf2000/AUTHORS/WETZEL/WETZEL.PDF
  5. Hacker TJ, Athey BD, Sommerfield J (2002) Experiences Using Web100 for End-To- End Network Performance Tuning. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/015.pdf
  6. Durka-Pelok G, Pomerantz S, Gadd C, Weymouth T, Gest T, Huang J, Nave D, Wetzel A, Lee WY, Athey BD (2002) Evaluation of a Volume Browser: PSC- VB. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/018.pdf
  7. Wetzel AW, Pomerantz SM, Nave D, Kar A, Sommerfield J, Mathis M, Deerfield DW, Bookstein FL, Green WD, Ade A, Athey BD (2002) A Networked Environment for Interactively Viewing and Manipulating Visible Human Datasets. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/021.pdf
  8. Nave D, Pomerantz SM, Wetzel AW, Durka-Pelok G, Gest T, Meixner W, Athey BD (2002) Semi-Automated reconstruction of Biological Surfaces from Few Contours in the Visible Female Dataset. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/023.pdf
  9. Weymouth T, Durka-Pelok G, Gest T, Huang J, Pomerantz S, Wetzel A, Berger C, Athey BD (2002) Using a Knowledge Base: The University of Michigan Visible Human Project. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/025.pdf
  10. Ade A, Athey BD (2002) Web-based Interactive Volume Rendering of the Visible Human Female. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/031.pdf
  11. Durka-Pelok G, Gest T, Nieder G, Weymouth T, Huang J, Wetzel A, Pomerantz S, Nave D, Athey BD (2002) Creation of an educational visual module: integration of QTVR and the Visible Human Data Set. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/036.pdf
  12. Walker D, Lee WY, Skov N, Berger C, Athey BD (2002) Investigating User Requirements: Design of Computer-based Anatomy Learning Modules for Multiple User Groups. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/041.pdf
  13. Durka-Pelok G, Weymouth T, Gest T, Pomerantz S, Nave D, Wetzel A, Lee WY, Athey BD (2002) Bookmarking the Visible Human Dataset. Eds. R.A. Banvard and M.J. Ackerman. 4th Visible Human Conference, Oct. 17-19, 2002. Keystone, CO. http://www.uchsc.edu/sm/chs/events/vh_conf/pdfs/042.pdf
  14. Xuan W, Dai M, Athey B, Watson SJ, Meng F (2008) PubOnto: Open Biomedical Ontology-Based Medline Exploration. ISMB 2008 Bio-Ontologies SIG: Knowledge in Biology 37-40. http://www.bio-ontologies.org.uk/download/Bio-Ontologies2008.pdf
  15. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW (2008) iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. PLoS ONE 3(5): e2265. doi:10.1371/journal.pone.0002265. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002265
  16. Sarntivijai S, Xiang Z, Meehan TF, Diehl AD, Vempati U, Schurer S, Pang C, Malone J, Parkinson H, Athey BD, He Y. “Cell Line Ontology: Redesigning Cell Line Knowledgebase to Aid Integrative Translational Informatics.” International Conference on Biomedical Ontology (ICBO Conference), July 2011. Buffalo, NY. http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/index.html

Book Chapters

  1. Leith EN, Mills K, Chien WC, Athey BD, Dilworth D (2004) A Generalization of the Theory of Holographic Coherence Confocal Imaging. The Art and Science of Holography: A Tribute to Emmett Leith and Yuri Denisyuk. Ch. 3, 31-44. SPIE Press. ISBN 9780819450197 Jan. 22, 2004.
  2. Higgins GA and Athey BD. “Emerging DNA Sequencing Technologies and Applications.” Next Generation DNA Sequencing Informatics, Second Edition. (Cold Spring Harbor Laboratory Press; Oxford University Press). March 2015. ISBN 978-1-621821-23-6.