Mark A. Abney

Research Associate Professor
Research Summary
My research focus is on developing both new statistical methods and computational techniques to overcome the difficult problems in the analysis of genetic and genomic data. A primary interest is on developing models and approximations that are highly computationally efficient while leveraging as much of the information in the data as possible. As novel technologies are developed to collect ever larger and more specific genetic and genomic data, there arises a concurrent need for innovative methods to extract scientific insight from the data. My research focuses on developing such methods.
Statistical Genetics, Computational Biology
  • University of California San Diego, San Diego, B.S. Physics 06/1989
  • University of Chicago, Chicago, Ph.D. Physics 08/1996
Biosciences Graduate Program Association
  1. Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2. Am J Hum Genet. 2020 Jan 02; 106(1):138. View in: PubMed

  2. Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2. Am J Hum Genet. 2019 12 05; 105(6):1222-1236. View in: PubMed

  3. Kinpute: using identity by descent to improve genotype imputation. Bioinformatics. 2019 11 01; 35(21):4321-4326. View in: PubMed

  4. Genome wide association analysis in a mouse advanced intercross line. Nat Commun. 2018 12 04; 9(1):5162. View in: PubMed

  5. Investigating multiple sclerosis genetic susceptibility on the founder population of east-central Sardinia via association and linkage analysis of immune-related loci. Mult Scler. 2018 12; 24(14):1815-1824. View in: PubMed

  6. A LASSO penalized regression approach for genome-wide association analyses using related individuals: application to the Genetic Analysis Workshop 19 simulated data. BMC Proc. 2016; 10(Suppl 7):221-226. View in: PubMed

  7. Occurrence of Brown Marmorated Stink Bug (Hemiptera: Pentatomidae) on Wild Hosts in Nonmanaged Woodlands and Soybean Fields in North Carolina and Virginia. Environ Entomol. 2015 Aug; 44(4):1011-21. View in: PubMed

  8. Directional dominance on stature and cognition in?diverse human populations. Nature. 2015 Jul 23; 523(7561):459-462. View in: PubMed

  9. Permutation testing in the presence of polygenic variation. Genet Epidemiol. 2015 May; 39(4):249-58. View in: PubMed

  10. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population. PLoS Comput Biol. 2015 Mar; 11(3):e1004139. View in: PubMed

  11. High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice. Genetics. 2014 Sep; 198(1):103-16. View in: PubMed

  12. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One. 2014; 9(8):e104396. View in: PubMed

  13. Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies. G3 (Bethesda). 2013 Oct 03; 3(10):1861-7. View in: PubMed

  14. Genome-wide association study of lung function phenotypes in a founder population. J Allergy Clin Immunol. 2014 Jan; 133(1):248-55.e1-10. View in: PubMed

  15. Estimating the human mutation rate using autozygosity in a founder population. Nat Genet. 2012 Nov; 44(11):1277-81. View in: PubMed

  16. Using identity by descent estimation with dense genotype data to detect positive selection. Eur J Hum Genet. 2013 Feb; 21(2):205-11. View in: PubMed

  17. GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations. Bioinformatics. 2012 Jun 01; 28(11):1553-4. View in: PubMed

  18. Rising prevalence of asthma is sex-specific in a US farming population. J Allergy Clin Immunol. 2011 Oct; 128(4):774-9. View in: PubMed

  19. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet. 2011 Jul 27; 12:66. View in: PubMed

  20. Identity by descent estimation with dense genome-wide genotype data. Genet Epidemiol. 2011 Sep; 35(6):557-67. View in: PubMed

  21. Fine-mapping alleles for body weight in LG/J ? SM/J F2 and F(34) advanced intercross lines. Mamm Genome. 2011 Oct; 22(9-10):563-71. View in: PubMed

  22. Genetic variance components estimation for binary traits using multiple related individuals. Genet Epidemiol. 2011 Jul; 35(5):291-302. View in: PubMed

  23. The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS Genet. 2010 Jun 03; 6(6):e1000974. View in: PubMed

  24. Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations. Genetics. 2010 Jul; 185(3):1033-44. View in: PubMed

  25. Colloquium papers: Heritability of reproductive fitness traits in a human population. Proc Natl Acad Sci U S A. 2010 Jan 26; 107 Suppl 1:1772-8. View in: PubMed

  26. A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics. 2009 Jun 15; 25(12):1561-3. View in: PubMed

  27. Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q. J Lipid Res. 2009 May; 50(5):798-806. View in: PubMed

  28. Identity-by-descent estimation and mapping of qualitative traits in large, complex pedigrees. Genetics. 2008 Jul; 179(3):1577-90. View in: PubMed

  29. Confidence intervals for putative quantitative trait loci - development and applications of new linkage methods. BMC Proc. 2007; 1 Suppl 1:S91. View in: PubMed

  30. Homozygosity by descent mapping of blood pressure in the Old Order Amish: evidence for sex specific genetic architecture. BMC Genet. 2007 Oct 01; 8:66. View in: PubMed

  31. Heritability estimation of sex-specific effects on human quantitative traits. Genet Epidemiol. 2007 May; 31(4):338-47. View in: PubMed

  32. The sex-specific genetic architecture of quantitative traits in humans. Nat Genet. 2006 Feb; 38(2):218-22. View in: PubMed

  33. Sex differences in the genetic basis of morning serum cortisol levels: genome-wide screen identifies two novel loci specific to women. J Clin Endocrinol Metab. 2005 Aug; 90(8):4747-52. View in: PubMed

  34. Variation in ITGB3 has sex-specific associations with plasma lipoprotein(a) and whole blood serotonin levels in a population-based sample. Hum Genet. 2005 Jun; 117(1):81-7. View in: PubMed

  35. Sex-specific genetic architecture of whole blood serotonin levels. Am J Hum Genet. 2005 Jan; 76(1):33-41. View in: PubMed

  36. Testing for Hardy-Weinberg equilibrium in samples with related individuals. Genetics. 2004 Dec; 168(4):2349-61. View in: PubMed

  37. Genome-wide association study identifies ITGB3 as a QTL for whole blood serotonin. Eur J Hum Genet. 2004 Nov; 12(11):949-54. View in: PubMed

  38. Are common disease susceptibility alleles the same in outbred and founder populations? Eur J Hum Genet. 2004 Jul; 12(7):584-90. View in: PubMed

  39. Major loci influencing serum triglyceride levels on 2q14 and 9p21 localized by homozygosity-by-descent mapping in a large Hutterite pedigree. Hum Mol Genet. 2003 Jan 15; 12(2):137-44. View in: PubMed

  40. Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites. Am J Hum Genet. 2002 Apr; 70(4):920-34. View in: PubMed

  41. Detection of mis-specified relationships in inbred and outbred pedigrees. Genet Epidemiol. 2001; 21 Suppl 1:S36-41. View in: PubMed

  42. The importance of genealogy in determining genetic associations with complex traits. Am J Hum Genet. 2001 Nov; 69(5):1146-8. View in: PubMed

  43. The genetic dissection of complex traits in a founder population. Am J Hum Genet. 2001 Nov; 69(5):1068-79. View in: PubMed

  44. Broad and narrow heritabilities of quantitative traits in a founder population. Am J Hum Genet. 2001 May; 68(5):1302-7. View in: PubMed

  45. Estimation of variance components of quantitative traits in inbred populations. Am J Hum Genet. 2000 Feb; 66(2):629-50. View in: PubMed

  46. Genome-wide search for asthma susceptibility loci in a founder population. The Collaborative Study on the Genetics of Asthma. Hum Mol Genet. 1998 Sep; 7(9):1393-8. View in: PubMed