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Mark A. Abney

TitleResearch Associate Professor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    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.


    Collapse Biography 
    Collapse education and training
    University of California San Diego, San DiegoB.S.06/1989Physics
    University of Chicago, ChicagoPh.D.08/1996Physics

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Abney M, ElSherbiny A. Kinpute: using identity by descent to improve genotype imputation. Bioinformatics. 2019 Nov 01; 35(21):4321-4326. PMID: 30918937.
      View in: PubMed
    2. Gonzales NM, Seo J, Hernandez Cordero AI, St Pierre CL, Gregory JS, Distler MG, Abney M, Canzar S, Lionikas A, Palmer AA. Genome wide association analysis in a mouse advanced intercross line. Nat Commun. 2018 12 04; 9(1):5162. PMID: 30514929.
      View in: PubMed
    3. Papachristou C, Ober C, Abney M. 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. PMID: 27980640.
      View in: PubMed
    4. Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W, Okada Y, Stancáková A, Faul JD, Zhao W, Bartz TM, Concas MP, Franceschini N, Enroth S, Vitart V, Trompet S, Guo X, Chasman DI, O'Connel JR, Corre T, Nongmaithem SS, Chen Y, Mangino M, Ruggiero D, Traglia M, Farmaki AE, Kacprowski T, Bjonnes A, van der Spek A, Wu Y, Giri AK, Yanek LR, Wang L, Hofer E, Rietveld CA, McLeod O, Cornelis MC, Pattaro C, Verweij N, Baumbach C, Abdellaoui A, Warren HR, Vuckovic D, Mei H, Bouchard C, Perry JRB, Cappellani S, Mirza SS, Benton MC, Broeckel U, Medland SE, Lind PA, Malerba G, Drong A, Yengo L, Bielak LF, Zhi D, van der Most PJ, Shriner D, Mägi R, Hemani G, Karaderi T, Wang Z, Liu T, Demuth I, Zhao JH, Meng W, Lataniotis L, van der Laan SW, Bradfield JP, Wood AR, Bonnefond A, Ahluwalia TS, Hall LM, Salvi E, Yazar S, Carstensen L, de Haan HG, Abney M, Afzal U, Allison MA, Amin N, Asselbergs FW, Bakker SJL, Barr RG, Baumeister SE, Benjamin DJ, Bergmann S, Boerwinkle E, Bottinger EP, Campbell A, Chakravarti A, Chan Y, Chanock SJ, Chen C, Chen YI, Collins FS, Connell J, Correa A, Cupples LA, Smith GD, Davies G, Dörr M, Ehret G, Ellis SB, Feenstra B, Feitosa MF, Ford I, Fox CS, Frayling TM, Friedrich N, Geller F, Scotland G, Gillham-Nasenya I, Gottesman O, Graff M, Grodstein F, Gu C, Haley C, Hammond CJ, Harris SE, Harris TB, Hastie ND, Heard-Costa NL, Heikkilä K, Hocking LJ, Homuth G, Hottenga JJ, Huang J, Huffman JE, Hysi PG, Ikram MA, Ingelsson E, Joensuu A, Johansson Å, Jousilahti P, Jukema JW, Kähönen M, Kamatani Y, Kanoni S, Kerr SM, Khan NM, Koellinger P, Koistinen HA, Kooner MK, Kubo M, Kuusisto J, Lahti J, Launer LJ, Lea RA, Lehne B, Lehtimäki T, Liewald DCM, Lind L, Loh M, Lokki ML, London SJ, Loomis SJ, Loukola A, Lu Y, Lumley T, Lundqvist A, Männistö S, Marques-Vidal P, Masciullo C, Matchan A, Mathias RA, Matsuda K, Meigs JB, Meisinger C, Meitinger T, Menni C, Mentch FD, Mihailov E, Milani L, Montasser ME, Montgomery GW, Morrison A, Myers RH, Nadukuru R, Navarro P, Nelis M, Nieminen MS, Nolte IM, O'Connor GT, Ogunniyi A, Padmanabhan S, Palmas WR, Pankow JS, Patarcic I, Pavani F, Peyser PA, Pietilainen K, Poulter N, Prokopenko I, Ralhan S, Redmond P, Rich SS, Rissanen H, Robino A, Rose LM, Rose R, Sala C, Salako B, Salomaa V, Sarin AP, Saxena R, Schmidt H, Scott LJ, Scott WR, Sennblad B, Seshadri S, Sever P, Shrestha S, Smith BH, Smith JA, Soranzo N, Sotoodehnia N, Southam L, Stanton AV, Stathopoulou MG, Strauch K, Strawbridge RJ, Suderman MJ, Tandon N, Tang ST, Taylor KD, Tayo BO, Töglhofer AM, Tomaszewski M, Tšernikova N, Tuomilehto J, Uitterlinden AG, Vaidya D, van Hylckama Vlieg A, van Setten J, Vasankari T, Vedantam S, Vlachopoulou E, Vozzi D, Vuoksimaa E, Waldenberger M, Ware EB, Wentworth-Shields W, Whitfield JB, Wild S, Willemsen G, Yajnik CS, Yao J, Zaza G, Zhu X, Project TBJ, Salem RM, Melbye M, Bisgaard H, Samani NJ, Cusi D, Mackey DA, Cooper RS, Froguel P, Pasterkamp G, Grant SFA, Hakonarson H, Ferrucci L, Scott RA, Morris AD, Palmer CNA, Dedoussis G, Deloukas P, Bertram L, Lindenberger U, Berndt SI, Lindgren CM, Timpson NJ, Tönjes A, Munroe PB, Sørensen TIA, Rotimi CN, Arnett DK, Oldehinkel AJ, Kardia SLR, Balkau B, Gambaro G, Morris AP, Eriksson JG, Wright MJ, Martin NG, Hunt SC, Starr JM, Deary IJ, Griffiths LR, Tiemeier H, Pirastu N, Kaprio J, Wareham NJ, Pérusse L, Wilson JG, Girotto G, Caulfield MJ, Raitakari O, Boomsma DI, Gieger C, van der Harst P, Hicks AA, Kraft P, Sinisalo J, Knekt P, Johannesson M, Magnusson PKE, Hamsten A, Schmidt R, Borecki IB, Vartiainen E, Becker DM, Bharadwaj D, Mohlke KL, Boehnke M, van Duijn CM, Sanghera DK, Teumer A, Zeggini E, Metspalu A, Gasparini P, Ulivi S, Ober C, Toniolo D, Rudan I, Porteous DJ, Ciullo M, Spector TD, Hayward C, Dupuis J, Loos RJF, Wright AF, Chandak GR, Vollenweider P, Shuldiner A, Ridker PM, Rotter JI, Sattar N, Gyllensten U, North KE, Pirastu M, Psaty BM, Weir DR, Laakso M, Gudnason V, Takahashi A, et al. Directional dominance on stature and cognition in diverse human populations. Nature. 2015 Jul 23; 523(7561):459-462. PMID: 26131930.
      View in: PubMed
    5. Bakken AJ, Schoof SC, Bickerton M, Kamminga KL, Jenrette JC, Malone S, Abney MA, Herbert DA, Reisig D, Kuhar TP, Walgenbach JF. 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. PMID: 26314046.
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    6. Abney M. Permutation testing in the presence of polygenic variation. Genet Epidemiol. 2015 May; 39(4):249-58. PMID: 25758362.
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    7. Livne OE, Han L, Alkorta-Aranburu G, Wentworth-Sheilds W, Abney M, Ober C, Nicolae DL. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population. PLoS Comput Biol. 2015 Mar; 11(3):e1004139. PMID: 25735005.
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    8. Parker CC, Carbonetto P, Sokoloff G, Park YJ, Abney M, Palmer AA. High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice. Genetics. 2014 Sep; 198(1):103-16. PMID: 25236452.
      View in: PubMed
    9. Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One. 2014; 9(8):e104396. PMID: 25116239.
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    10. Cheng R, Parker CC, Abney M, Palmer AA. 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. PMID: 23979941.
      View in: PubMed
    11. Yao TC, Du G, Han L, Sun Y, Hu D, Yang JJ, Mathias R, Roth LA, Rafaels N, Thompson EE, Loisel DA, Anderson R, Eng C, Arruabarrena Orbegozo M, Young M, Klocksieben JM, Anderson E, Shanovich K, Lester LA, Williams LK, Barnes KC, Burchard EG, Nicolae DL, Abney M, Ober C. Genome-wide association study of lung function phenotypes in a founder population. J Allergy Clin Immunol. 2014 Jan; 133(1):248-55.e1-10. PMID: 23932459.
      View in: PubMed
    12. Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O'Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE. Estimating the human mutation rate using autozygosity in a founder population. Nat Genet. 2012 Nov; 44(11):1277-81. PMID: 23001126.
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    13. Han L, Abney M. Using identity by descent estimation with dense genotype data to detect positive selection. Eur J Hum Genet. 2013 Feb; 21(2):205-11. PMID: 22781100.
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    14. Stanhope SA, Abney M. 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. PMID: 22522135.
      View in: PubMed
    15. Motika CA, Papachristou C, Abney M, Lester LA, Ober C. Rising prevalence of asthma is sex-specific in a US farming population. J Allergy Clin Immunol. 2011 Oct; 128(4):774-9. PMID: 21840584.
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    16. Cheng R, Abney M, Palmer AA, Skol AD. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet. 2011 Jul 27; 12:66. PMID: 21794153.
      View in: PubMed
    17. Han L, Abney M. Identity by descent estimation with dense genome-wide genotype data. Genet Epidemiol. 2011 Sep; 35(6):557-67. PMID: 21769932.
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    18. Parker CC, Cheng R, Sokoloff G, Lim JE, Skol AD, Abney M, Palmer AA. 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. PMID: 21761260.
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    19. Papachristou C, Ober C, Abney M. Genetic variance components estimation for binary traits using multiple related individuals. Genet Epidemiol. 2011 Jul; 35(5):291-302. PMID: 21465547.
      View in: PubMed
    20. Kosova G, Pickrell JK, Kelley JL, McArdle PF, Shuldiner AR, Abney M, Ober C. 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. PMID: 20532200.
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    21. Cheng R, Lim JE, Samocha KE, Sokoloff G, Abney M, Skol AD, Palmer AA. 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. PMID: 20439773.
      View in: PubMed
    22. Kosova G, Abney M, Ober C. 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. PMID: 19822755.
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    23. Abney M. A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics. 2009 Jun 15; 25(12):1561-3. PMID: 19359355.
      View in: PubMed
    24. Ober C, Nord AS, Thompson EE, Pan L, Tan Z, Cusanovich D, Sun Y, Nicolae R, Edelstein C, Schneider DH, Billstrand C, Pfaffinger D, Phillips N, Anderson RL, Philips B, Rajagopalan R, Hatsukami TS, Rieder MJ, Heagerty PJ, Nickerson DA, Abney M, Marcovina S, Jarvik GP, Scanu AM, Nicolae DL. Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q. J Lipid Res. 2009 May; 50(5):798-806. PMID: 19124843.
      View in: PubMed
    25. Abney M. Identity-by-descent estimation and mapping of qualitative traits in large, complex pedigrees. Genetics. 2008 Jul; 179(3):1577-90. PMID: 18622032.
      View in: PubMed
    26. Papachristou C, Abney M, Lin S. Confidence intervals for putative quantitative trait loci - development and applications of new linkage methods. BMC Proc. 2007; 1 Suppl 1:S91. PMID: 18466595.
      View in: PubMed
    27. McArdle PF, Dytch H, O'Connell JR, Shuldiner AR, Mitchell BD, Abney M. 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. PMID: 17908314.
      View in: PubMed
    28. Pan L, Ober C, Abney M. Heritability estimation of sex-specific effects on human quantitative traits. Genet Epidemiol. 2007 May; 31(4):338-47. PMID: 17323368.
      View in: PubMed
    29. Weiss LA, Pan L, Abney M, Ober C. The sex-specific genetic architecture of quantitative traits in humans. Nat Genet. 2006 Feb; 38(2):218-22. PMID: 16429159.
      View in: PubMed
    30. Kurina LM, Weiss LA, Graves SW, Parry R, Williams GH, Abney M, Ober C. 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. PMID: 15941864.
      View in: PubMed
    31. Weiss LA, Abney M, Parry R, Scanu AM, Cook EH, Ober C. 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. PMID: 15834589.
      View in: PubMed
    32. Weiss LA, Abney M, Cook EH, Ober C. Sex-specific genetic architecture of whole blood serotonin levels. Am J Hum Genet. 2005 Jan; 76(1):33-41. PMID: 15526234.
      View in: PubMed
    33. Weiss LA, Veenstra-Vanderweele J, Newman DL, Kim SJ, Dytch H, McPeek MS, Cheng S, Ober C, Cook EH, Abney M. Genome-wide association study identifies ITGB3 as a QTL for whole blood serotonin. Eur J Hum Genet. 2004 Nov; 12(11):949-54. PMID: 15292919.
      View in: PubMed
    34. Bourgain C, Abney M, Schneider D, Ober C, McPeek MS. Testing for Hardy-Weinberg equilibrium in samples with related individuals. Genetics. 2004 Dec; 168(4):2349-61. PMID: 15371359.
      View in: PubMed
    35. Newman DL, Hoffjan S, Bourgain C, Abney M, Nicolae RI, Profits ET, Grow MA, Walker K, Steiner L, Parry R, Reynolds R, McPeek MS, Cheng S, Ober C. Are common disease susceptibility alleles the same in outbred and founder populations? Eur J Hum Genet. 2004 Jul; 12(7):584-90. PMID: 15100713.
      View in: PubMed
    36. Newman DL, Abney M, Dytch H, Parry R, McPeek MS, Ober C. 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. PMID: 12499394.
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    37. Abney M, Ober C, McPeek MS. 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. PMID: 11880950.
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    38. Newman DL, Abney M, McPeek MS, Ober C, Cox NJ. The importance of genealogy in determining genetic associations with complex traits. Am J Hum Genet. 2001 Nov; 69(5):1146-8. PMID: 11590549.
      View in: PubMed
    39. Ober C, Abney M, McPeek MS. The genetic dissection of complex traits in a founder population. Am J Hum Genet. 2001 Nov; 69(5):1068-79. PMID: 11590547.
      View in: PubMed
    40. Abney M, McPeek MS, Ober C. Broad and narrow heritabilities of quantitative traits in a founder population. Am J Hum Genet. 2001 May; 68(5):1302-7. PMID: 11309690.
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    41. Sun L, Abney M, McPeek MS. Detection of mis-specified relationships in inbred and outbred pedigrees. Genet Epidemiol. 2001; 21 Suppl 1:S36-41. PMID: 11793699.
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    42. Abney M, McPeek MS, Ober C. Estimation of variance components of quantitative traits in inbred populations. Am J Hum Genet. 2000 Feb; 66(2):629-50. PMID: 10677322.
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    43. Ober C, Cox NJ, Abney M, Di Rienzo A, Lander ES, Changyaleket B, Gidley H, Kurtz B, Lee J, Nance M, Pettersson A, Prescott J, Richardson A, Schlenker E, Summerhill E, Willadsen S, Parry R. 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. PMID: 9700192.
      View in: PubMed
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