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Jeffrey R. O'Connell, DPhil

Academic Title:

Associate Professor

Primary Appointment:


Secondary Appointment(s):

Epidemiology & Public Health



Phone (Primary):

(410) 706-8959


(410) 706-1622

Education and Training

University of Delaware, Newark, DE

Drexel University, Philadelphia, PA

Drexel University, Philadelphia, PA

Oxford University, Oxford, UK




D. Phil







Computer Science

Mathematical Biology


Dr. O'Connell was trained in mathematics and computer science before transitioning to genetics and computational biology in 1993. His primary research area has been in human genetics, but expanded to animal genetic since 2007 with a part-time appointment at USDA Animal Improvement Laboratory (AIPL). Primary research focus is developing, implementing and applying methods to analyze genomic data in large pedigree and population data. He works extensively on the analysis of large pedigree data such as the Old Order Amish and Holstein using mixed model methods developed and implemented into MMAP (Mixed Models for Analysis of Pedigree/Populations). MMAP implements a broad selection of analysis options for genome-wide association (GWA) analysis, variance components estimation, linkage analysis, genotype imputation, genomic prediction, haplotyping and mega analysis.

He collaborates in a large number of consortia efforts: the Genetics of Liver Disease (GOLD) consortium, the Genetic Factors for Osteoporosis (GEFOS) consortium, the Cohorts of Heart and Aging Research in Genetic Epidemiology (CHARGE) musculoskeletal, adiposity, and lipid groups, and Gene-by-Lifestyle Interaction consortium.

He is a member of TOPMed whole genome sequencing effort and heavily involved in development of analytical tools for cloud-based computing to run genome-wide association and rare variant analysis, generalized linear mixed models for binary and threshold traits and multi- and correlated trait models for analysis of large omics data sets.  


Research/Clinical Keywords

Developing, implementing and applying methods to analyze genomic data in large pedigree and population data

Highlighted Publications

  1. O'Connell JR. Zero-recombinant haplotyping: applications to fine mapping using SNPs. Genetic epidemiology. 2000;19 Suppl 1:S64-70. doi: 10.1002/1098-2272(2000)19:1+<::AID-GEPI10>3.0.CO;2-G. PubMed PMID: 11055372.
  2. O'Connell JR, Weeks DE. An optimal algorithm for automatic genotype elimination. American journal of human genetics. 1999;65(6):1733-40. doi: 10.1086/302663. PubMed PMID: 10577928; PubMed Central PMCID: PMC1288385.
  3. O'Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. American journal of human genetics. 1998;63(1):259-66. doi: 10.1086/301904. PubMed PMID: 9634505; PubMed Central PMCID: PMC1377228.
  4. O'Connell JR, Weeks DE. The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nature genetics. 1995;11(4):402-8. doi: 10.1038/ng1295-402. PubMed PMID: 7493020.
  5. Sun C, VanRaden PM, Cole JB, O'Connell JR. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. PloS one. 2014;9(8):e103934. doi: 10.1371/journal.pone.0103934. PubMed PMID: 25084281; PubMed Central PMCID: PMC4118992.
  6. VanRaden PM, Cooper TA, Wiggans GR, O'Connell JR, Bacheller LR. Confirmation and discovery of maternal grandsires and great-grandsires in dairy cattle. Journal of dairy science. 2013;96(3):1874-9. doi: 10.3168/jds.2012-6176. PubMed PMID: 23332849.
  7. Sun C, VanRaden PM, O'Connell JR, Weigel KA, Gianola D. Mating programs including genomic relationships and dominance effects. Journal of dairy science. 2013;96(12):8014-23. doi: 10.3168/jds.2013-6969. PubMed PMID: 24119810.
  8. VanRaden PM, O'Connell JR, Wiggans GR, Weigel KA. Genomic evaluations with many more genotypes. Genetics, selection, evolution : GSE. 2011;43:10. doi: 10.1186/1297-9686-43-10. PubMed PMID: 21366914; PubMed Central PMCID: PMC3056758. 
  9. Ma L, O'Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, et al. Cattle sex-specific recombination and genetic control from a large pedigree. BMC Genetics (in press). 2015Albert JS, Yerges-Armstrong LM, Horenstein RB, Pollin TI, Sreenivasan UT, Chai S, Blaner WS, Snitker S, O'Connell JR, et al. Null mutation in hormone-sensitive lipase gene and risk of type 2 diabetes. The New England journal of medicine. 2014;370(24):2307-15. doi: 10.1056/NEJMoa1315496. PubMed PMID: 24848981; PubMed Central PMCID: PMC4096982..
  10. Lewis JP, Ryan K, O'Connell JR, Horenstein RB, Damcott CM, Gibson Q, Pollin TI, Mitchell BD, Beitelshees AL, et al. Genetic variation in PEAR1 is associated with platelet aggregation and cardiovascular outcomes. Circulation Cardiovascular genetics. 2013;6(2):184-92. doi: 10.1161/CIRCGENETICS.111.964627. PubMed PMID: 23392654; PubMed Central PMCID: PMC3715320.
  11. Shuldiner AR, O'Connell JR, Bliden KP, Gandhi A, Ryan K, Horenstein RB, Damcott CM, Pakyz R, Tantry US, et al. Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA : the journal of the American Medical Association. 2009;302(8):849-57. doi: 10.1001/jama.2009.1232. PubMed PMID: 19706858; PubMed Central PMCID: PMC3641569.
  12. Rampersaud E, Mitchell BD, Pollin TI, Fu M, Shen H, O'Connell JR, Ducharme JL, Hines S, Sack P, et al. Physical activity and the association of common FTO gene variants with body mass index and obesity. Archives of internal medicine. 2008;168(16):1791-7. doi: 10.1001/archinte.168.16.1791. PubMed PMID: 18779467; PubMed Central PMCID: PMC3635949.
  13. Pollin TI, Damcott CM, Shen H, Ott SH, Shelton J, Horenstein RB, Post W, McLenithan JC, Bielak LF,..,O’Connell, JR,et al. A mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection. Science. 2008;322(5908):1702-5. doi: 10.1126/science.1161524. PubMed PMID: 19074352; PubMed Central PMCID: PMC2673993. 
  14. McArdle PF, Parsa A, Chang YP, Weir MR, O'Connell JR, Mitchell BD, Shuldiner AR. Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish. Arthritis and rheumatism. 2008;58(9):2874-81. doi: 10.1002/art.23752. PubMed PMID: 18759275; PubMed Central PMCID: PMC2779583.

Additional Publication Citations

Awards and Affiliations

Positions and Honors

1985-1986       Mathematics Lecturer, University of Maryland, Pacific Division, Seoul, South Korea

1986-1993       Mathematics Instructor, Math Department, Drexel University, Philadelphia, PA

1993-1999       Programmer Analyst, Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA

2000-2002       Assistant Professor, Department of Human Genetics, University of Pittsburgh, PA

2004-2006       Adjunct Assistant Professor, College of Public Health, University of Iowa, IA

2007-2012       Adjunct Assistant Professor, Nationwide Children’s Hospital, Columbus, OH

2002-2008       Assistant Professor, Department of Medicine, University of Maryland, Baltimore, MD

2007-2012       Research Scientist, Animal Improvement Laboratory USDA, Beltsville, MD

2012-2014       Visiting Research Scientist, Animal Improvement Laboratory USDA, Beltsville, MD

2014-present   Research Scientist, Animal Genetics Improvement Laboratory USDA, Beltsville, MD

2009-present  Associate Professor, Department of Medicine, University of Maryland, Baltimore, MD