Jonathan Shortt, PhD

Assistant Research Professor, Biomedical Informatics

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Graduate School
  • PhD, University of Colorado Denver (2018)
Undergraduate School
  • BS, Brigham Young University (UT) (2008)
Department
Biomedical Informatics

Professional Titles

  • Research Instructor

Publications

  • Schneider K, Chowdhury M, Tepper M, Khan J, Shortt JA, Gignoux C, Layer R. GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts. bioRxiv. 2024 Nov 3. PubMed PMID: 39554195
  • Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet. 2024 Jan 4;111(1):11-23. PubMed PMID: 38181729
  • Pozdeyev N, Dighe M, Barrio M, Raeburn C, Smith H, Fisher M, Chavan S, Rafaels N, Shortt JA, Lin M, Leu MG, Clark T, Marshall C, Haugen BR, Subramanian D, Crooks K, Gignoux C, Cohen T. Thyroid Cancer Polygenic Risk Score Improves Classification of Thyroid Nodules as Benign or Malignant. J Clin Endocrinol Metab. 2024 Jan 18;109(2):402-412. PubMed PMID: 37683082
  • O'Brien KA, Gu W, Houck JA, Holzner LMW, Yung HW, Armstrong JL, Sowton AP, Baxter R, Darwin PM, Toledo-Jaldin L, Lazo-Vega L, Moreno-Aramayo AE, Miranda-Garrido V, Shortt JA, Matarazzo CJ, Yasini H, Burton GJ, Moore LG, Simonson TS, Murray AJ, Julian CG. Genomic Selection Signals in Andean Highlanders Reveal Adaptive Placental Metabolic Phenotypes That Are Disrupted in Preeclampsia. Hypertension. 2024 Feb;81(2):319-329. PubMed PMID: 38018457
  • Kullo IJ, Conomos MP, Nelson SC, Adebamowo SN, Choudhury A, Conti D, Fullerton SM, Gogarten SM, Heavner B, Hornsby WE, Kenny EE, Khan A, Khera AV, Li Y, Martin I, Mercader JM, Ng M, Raffield LM, Reiner A, Rowley R, Schaid D, Stilp A, Wiley K, Wilson R, Witte JS, Natarajan P. The PRIMED Consortium: Reducing disparities in polygenic risk assessment. Am J Hum Genet. 2024 Dec 5;111(12):2594-2606. PubMed PMID: 39561770
  • Lo Faro V, Bhattacharya A, Zhou W, Zhou D, Wang Y, Läll K, Kanai M, Lopera-Maya E, Straub P, Pawar P, Tao R, Zhong X, Namba S, Sanna S, Nolte IM, Okada Y, Ingold N, MacGregor S, Snieder H, Surakka I, Shortt J, Gignoux C, Rafaels N, Crooks K, Verma A, Verma SS, Guare L, Rader DJ, Willer C, Martin AR, Brantley MA Jr, Gamazon ER, Jansonius NM, Joos K, Cox NJ, Hirbo J. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation. Cell Rep Med. 2024 Feb 20;5(2):101430. PubMed PMID: 38382466
  • Hou K, Gogarten S, Kim J, Hua X, Dias JA, Sun Q, Wang Y, Tan T, Atkinson EG, Martin A, Shortt J, Hirbo J, Li Y, Pasaniuc B, Zhang H. Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Bioinformatics. 2024 Mar 29;40(4). PubMed PMID: 38490256
  • Kanai M, Elzur R, Zhou W, Daly MJ, Finucane HK. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution. Cell Genom. 2022 Dec 14;2(12). PubMed PMID: 36643910
  • . A first update on mapping the human genetic architecture of COVID-19. Nature. 2022 Aug;608(7921):E1-E10. PubMed PMID: 35922517
  • Johnson RK, Marker KM, Mayer D, Shortt J, Kao D, Barnes KC, Lowery JT, Gignoux CR. COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine: Observational Study. JMIR Public Health Surveill. 2022 Jun 13;8(6):e37327. PubMed PMID: 35486493
  • Harrison GF, Leaton LA, Harrison EA, Kichula KM, Viken MK, Shortt J, Gignoux CR, Lie BA, Vukcevic D, Leslie S, Norman PJ. Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Comput Biol. 2022 Feb;18(2):e1009059. PubMed PMID: 35192601
  • D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Rep. 2022 Jun 14;39(11):110968. PubMed PMID: 35705058
  • Zhou W, Kanai M, Wu K, Rasheed H, Tsuo K, Hirbo J, Wang Y, Bhattacharya A, Zhao H, Namba S, Surakka I, Wolford B, Lo Faro V, Lopera-Maya E, Läll K, Favé M, Partanen J, Chapman S, Karjalainen J, Kurki M, Maasha M, Brumpton B, Chavan S, Chen T, Daya M, Ding Y, Feng Y, Guare L, Gignoux C, Graham S, Hornsby W, Ingold N, Ismail S, Johnson R, Laisk T, Lin K, Lv J, Millwood I, Moreno-Grau S, Nam K, Palta P, Pandit A, Preuss M, Saad C, Setia-Verma S, Thorsteinsdottir U, Uzunovic J, Verma A, Zawistowski M, Zhong X, Afifi N, Al-Dabhani K, Al Thani A, Bradford Y, Campbell A, Crooks K, de Bock G, Damrauer S, Douville N, Finer S, Fritsche L, Fthenou E, Gonzalez-Arroyo G, Griffiths C, Guo Y, Hunt K, Ioannidis A, Jansonius N, Konuma T, Lee M, Lopez-Pineda A, Matsuda Y, Marioni R, Moatamed B, Nava-Aguilar M, Numakura K, Patil S, Rafaels N, Richmond A, Rojas-Muñoz A, Shortt J, Straub P, Tao R, Vanderwerff B, Vernekar M, Veturi Y, Barnes K, Boezen M, Chen Z, Chen C, Cho J, Smith G, Finucane H, Franke L, Gamazon E, Ganna A, Gaunt T, Ge T, Huang H, Huffman J, Katsanis N, Koskela J, Lajonchere C, Law M, Li L, Lindgren C, Loos R, MacGregor S, Matsuda K, Olsen C, Porteous D, Shavit J, Snieder H, Takano T, Trembath R, Vonk J, Whiteman D, Wicks S, Wijmenga C, Wright J, Zheng J, Zhou X, Awadalla P, Boehnke M, Bustamante C, Cox N, Fatumo S, Geschwind D, Hayward C, Hveem K, Kenny E, Lee S, Lin Y, Mbarek H, Mägi R, Martin H, Medland S, Okada Y, Palotie A, Pasaniuc B, Rader D, Ritchie M, Sanna S, Smoller J, Stefansson K, van Heel D, Walters R, Zöllner S, Martin A, Willer C, Daly M, Neale B. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease. Cell Genomics. 2022/10; 2(10):100192.
  • Shortt JA, Timm LE, Hales NR, Nikolakis ZL, Schield DR, Perry BW, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts. Sci Rep. 2021 Mar 25;11(1):6884. PubMed PMID: 33767307
  • Deng Z, Zhen J, Harrison GF, Zhang G, Chen R, Sun G, Yu Q, Nemat-Gorgani N, Guethlein LA, He L, Tang M, Gao X, Cai S, Palmer WH, Shortt JA, Gignoux CR, Carrington M, Zou H, Parham P, Hong W, Norman PJ. Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians. Mol Biol Evol. 2021 May 19;38(6):2582-2596. PubMed PMID: 33616658
  • Stanislawski MA, Lange LA, Raffield LM, Zakai NA, Meyer M, Ferrier K, Szeto MD, Leavitt C, Shortt JA, Thornton TA, Tracy RP, Auer PL, Reiner AP, Lange EM, Olson NC. Soluble CD14 Levels in the Jackson Heart Study: Associations With Cardiovascular Disease Risk and Genetic Variants. Arterioscler Thromb Vasc Biol. 2021 Jun;41(6):e369-e378. PubMed PMID: 33910371
  • Lazorwitz A, Aquilante CL, Shortt JA, Sheeder J, Teal S, Gignoux CR. Applicability of ancestral genotyping in pharmacogenomic research with hormonal contraception. Clin Transl Sci. 2021 Sep;14(5):1713-1718. PubMed PMID: 33650294
  • Warshauer EM, Brown A, Fuentes I, Shortt J, Gignoux C, Montinaro F, Metspalu M, Youssefian L, Vahidnezhad H, Jacków J, Christiano AM, Uitto J, Fajardo-Ramírez ÓR, Salas-Alanis JC, McGrath JA, Consuegra L, Rivera C, Maier PA, Runfeldt G, Behar DM, Skorecki K, Sprecher E, Palisson F, Norris DA, Bruckner AL, Kogut I, Bilousova G, Roop DR. Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry. Am J Med Genet A. 2021 Nov;185(11):3390-3400. PubMed PMID: 34435747
  • . Mapping the human genetic architecture of COVID-19. Nature. 2021 Dec;600(7889):472-477. PubMed PMID: 34237774
  • Shortt JA, Ruggiero RP, Cox C, Wacholder AC, Pollock DD. Finding and extending ancient simple sequence repeat-derived regions in the human genome. Mob DNA. 2020;11:11. PubMed PMID: 32095164
  • Leaton LA, Shortt J, Kichula KM, Tao S, Nemat-Gorgani N, Mentzer AJ, Oppenheimer SJ, Deng Z, Hollenbach JA, Gignoux CR, Guethlein LA, Parham P, Carrington M, Norman PJ. Conservation, Extensive Heterozygosity, and Convergence of Signaling Potential All Indicate a Critical Role for KIR3DL3 in Higher Primates. Front Immunol. 2019;10:24. PubMed PMID: 30745901
  • Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nat Commun. 2018 Jul 17;9(1):2774. PubMed PMID: 30018307


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