Andrew P Morgan, MD PhD
I am a clinical assistant professor of medicine at the University of North Carolina (starting July 2023) with a background in population genetics, evolution and bioinformatics.
Clinical
I completed residency in internal medicine and pediatrics at Duke University Hospital and now work as a hospitalist at the University of North Carolina.
Research interests
Mammalian genome evolution
The focus of my thesis was the evolution of the genome of the house mouse (Mus musculus). In particular I focused on the role of large duplications: these loci are highly variable beween species and contribute disproportionately to genetic variation within populations. I am interested in the population-genetic forces — recombination, mutation, selection and drift — that create and maintain this diversity.
I was supervised by Fernando Pardo-Manuel de Villena, whose lab anchors the UNC Systems Genetics research group.
Resources for mouse genetics
I also helped generate data and bioinformatics resources for two mouse reference populations for analysis of quantiative traits: the Collaborative Cross and Diversity Outbred stock.
I maintain a list of public whole-genome sequence datasets from wild mice to facilitate data-sharing and reuse by the research community.
Pathogen genomics
From 2018-2019 I was a visitor in the UNC Infectious Disease Epidemiology and Ecology Lab (IDEEL), studying population structure and selection in Plasmodium falciparum and Plasmodium vivax. I was supervised by Jonathan Juliano.
Publications and preprints
2023
Siebert A, Brake, MA, Verbeek SC, Johnston AJ, Morgan AP, Cleuren AC, Jurek AM, Schneider CD, Germain DM, Battistuzzi FU, Zhu G, Miller DR, Johnsen JM, Pardo-Manuel de Villena F, Rondina MT, Westrick R (2023) Identification of genomic loci regulating platelet plasminogen activator inhibitor-1 in mice. Journal of Thrombosis and Haemostasis in press.
Jones K, Morgan AP, Whang A, Feeney CD (2023) Fever, rash and abdominal pain in a 12-year-old boy. Pediatrics in Review, in press.
Rao P, Jordan KA, Burrows H, Morgan AP, Beck Dallaghan GL, Zwemer E (2023) Association between in-training exam scores and clinical exposure during the COVID-19 pandemic. Academic Pediatrics, in press.
Morgan AP, DeRaddo JS, Atkins C, Campbell MJ (2023) Streptococcal endarteritis associated with severe aortic coarctation. Progress in Pediatric Cardiology 70: 101657.
2022
Morgan AP*, Hughes JJ*, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, Pardo-Manuel de Villena F (2022) Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity 129: 183--194.
2021
Brazeau NF, Mitchell CL, Morgan AP, Deutsch-Feldman M, Watson OJ, Thwai KL, Gelabert P, van Dorp L, Keeler CY, Waltmann A, Emch M, Gartner V, Redelings B, Wray GA, Mwandagalirwa MK, Tshefu AK, Likwela JL, Edwards JK, Verity R, Parr JB, Meshnick SR, Juliano JJ (2021) The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo. Nature Communications 12: 4169.
Shrestha B, Shah Z, Morgan AP, Saingam P, Chaisatit C, Chaorattanakawee S, Praditpol C, Boonyalai N, Lertsethtakarn P, Wojnarski M, Deutsch-Feldman M, Adams M, Sea D, Chann S, Tyner SD, Lanteri CA, Spring MD, Saunders DL, Smith PL, Lon C, Gosi P, Sok S, Satharath P, Rekol H, Lek D, Vesely BA, Lin JT, Waters NC, Takala-Harrison S (2021) Distribution and Temporal Dynamics of Plasmodium falciparum Chloroquine Resistance Transporter Mutations Associated With Piperaquine Resistance in Northern Cambodia. Journal of Infectious Diseases 224: 1077--1085.
2020
Daughety MM, Morgan AP, Frost E, Kao C, Hwang J, Tobin R, Patel B, Fuller M, Welsby I, Ortel TL. (2020) COVID-19 associated coagulopathy: Thrombosis, hemorrhage and mortality rates with an escalated-dose thromboprophylaxis strategy. Thrombosis Research 196: 483--485.
10.1016/j.thromres.2020.10.004
Mukaj A, Pialek J, Fotopulosova V, Morgan AP, Odenthal-Hesse L, Parvanov ED, Forejt J. (2020) Prdm9 inter-subspecific interactions in hybrid male sterility of house mouse. Molecular Biology and Evolution 37: 3423--3438.
Verity R, Aydemir O, Brazeau NF, Watson OJ, Hathaway NJ, Mwandagalirwa MK, Marsh PW, Thwai K, Fulton T, Denton M, Morgan AP, Parr JB, Tumwebaze PK, Conrad M, Rosenthal PJ, Ishengoma DS, Ngondi J, Gutman J, Mulenga M, Norris DE, Moss WJ, Mensah BA, Myers-Hansen JL, Ghansah A, Tshefu AK, Ghani AC, Meshnick SR, Bailey JA, Juliano JJ (2020) The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC. Nature Communications 11: 2107.
Morgan AP*, Brazeau NF*, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Martensson A, Bjorkman A, Juliano JJ (2020) Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago. Malaria J 19: 47.
2019
Morgan AP, Bell TA, Crowley JJ, Pardo-Manuel de Villena F (2019) Instability of the pseudoautosomal boundary in house mice. Genetics 212: 469--487.
2018
Morgan AP*, Didion JP*, Hughes JJ, Searle JB, Jolley WJ, Campbell KJ, Threadgill DW, Pardo-Manuel de Villena F (2018) Genetic characterization of invasive house mouse populations on small islands. bioRxiv 10.1101/332064
2017
Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, Trinchieri G, Pardo-Manuel de Villena F, Yewdell JW, Rehermann B (2017) Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell 171: 1015--1028.
Morgan AP, Pardo-Manuel de Villena F (2017) Sequence and structural diversity of mouse Y chromosomes. Molecular Biology and Evolution 34: 3186--3204.
Makhanova N, Morgan AP, Kayashima Y, Makhanov A, Hiller S, Zhilicheva S, Xu L, Pardo-Manuel de Villena F, Maeda N (2017) Genetic architecture of atherosclerosis dissected by QTL analyses in three F2 intercrosses of apolipoprotein E-null mice on C57BL6/J, DBA/2J and 129S6/SvEvTac backgrounds. PLoS One 12: e0182882.
Gralinski LE, Menachery VD, Morgan AP, Totura AL, Beall A, Kocher J, Plante J, Harrison-Shostak DC, Schafer A, Pardo-Manuel de Villena F, Ferris MT, Baric RS (2017) Allelic variation in the Toll-like receptor adaptor protein Ticam2 contributes to SARS-coronavirus pathogenesis in mice. G3 7: 1653--1663.
Morgan AP, Gatti DM, Najarian M, Keane TM, Pack AI, Mott R, Churcill GA, Pardo-Manuel de Villena (2017) Structural variation shapes the landscape of recombination in mouse. Genetics 206: 603--619.
10.1534/genetics.116.197988 | data @ Zenodo
Srivastava A*, Morgan AP*, Najarian M*, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, Giusti-Rodriguez P, Ferris MT, Sullivan PF, Miller DR, Bell TA, McMillan L, Churchill GA, Pardo-Manuel de Villena F (2017) The genomes of the mouse Collaborative Cross. Genetics 206: 537--556.
10.1534/genetics.116.198838 | resources @ UNC
Shorter JR, Odet F, Aylor DL, Pan W, Kao CY, Fu CP, Morgan AP, Greenstein S, Bell TA, Stevans AM, Feathers RW, Patel S, Cates SE, Shaw GD, Ahmed S, Miller DR, Chesler EJ, McMillian L, O’Brien DA, Pardo-Manuel de Villena F (2017) Male infertility is responsible for nearly half of the strain extinction observed in the Collaborative Cross. Genetics 206: 557--572.
2016
Morgan AP*, Didion JP*, Doran AG, Holt JM, McMillan L, Keane TM, Pardo-Manuel de Villena F (2016) Whole genome sequence of two wild-derived Mus musculus domesticus inbred strains, LEWES/EiJ and ZALENDE/EiJ, with different diploid numbers. G3 6: 4211--4216
10.1534/g3.116.034751 | data @ ENA: PRJEB15190
Chesler EJ, Gatti DM, Morgan AP, Strobel M, Trepanier L, Oberbeck D, McWeeney S, Hitzemann R, Ferris M, McMullan R, Clayshulte A, Bell TA, Pardo-Manuel de Villena F, Churchill GA (2016) Diversity Outbred Mice at 21: Maintaining allelic variation in the face of selection. G3 6: 3893--3902.
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AMF, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, Pardo-Manuel de Villena F (2016) The evolutionary fates of a large segmental duplication in mouse. Genetics 204: 267--285.
Didion JP*, Morgan AP*, Yadgary L, Bell TA, McMullan RC, Ortiz de Solorzano L, Britton-Davidian J, Bult CJ, Campbell KJ, Castiglia R, Ching YH, Chunco AJ, Crowley JJ, Chesler EJ, Förster DW, French JE, Gabriel SI, Gatti DM, Garland T Jr, Giagia-Athanasopoulou EB, Giménez MD, Grize SA, Gündüz İ, Holmes A, Hauffe HC, Herman JS, Holt JM, Hua K, Jolley WJ, Lindholm AK, López-Fuster MJ, Mitsainas G, da Luz Mathias M, McMillan L, Ramalhinho MD, Rehermann B, Rosshart SP, Searle JB, Shiao MS, Solano E, Svenson KL, Thomas-Laemont P, Threadgill DW, Ventura J, Weinstock GM, Pomp D, Churchill GA, Pardo-Manuel de Villena F (2016) R2d2 drives selfish sweeps in the house mouse. Molecular Biology and Evolution 33: 1381--1395.
2015
Morgan AP*, Fu CP*, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F (2015) The Mouse Universal Genotyping Array: from substrains to subspecies. G3 6: 263--297.
10.1534/g3.115.022087 | data @ Dryad | resources @ UNC
Morgan AP. (2015) argyle: an R package for analysis of Illumina genotyping arrays. G3 6: 281--286.
10.1534/g3.115.023739 | code @ Github
Morgan AP, Welsh CE (2015) Informatics resources for the Collaborative Cross and related mouse populations. Mammalian Genome 26: 521--539.
Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F (2015) Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nature Genetics 47: 353--360.
Didion JP, Morgan AP, Clayshulte AM, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T Jr, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O'Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F (2015) A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genetics 11: e1004850.
2014
Liu EY*, Morgan AP*, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F (2015) High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics 197: 91--106.
10.1534/genetics.114.161653 | genetic map converter @ Jax
Rogala AR, Morgan AP, Christensen AM, Gooch TJ, Bell TA, Miller DR, Godfrey VL, de Villena FP (2014) The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mammalian Genome 25: 95--108.
Morgan AP*, Crowley JJ*, Nonneman RJ, Quackenbush CR, Miller CN, Ryan AK, Bogue MA, Paredes SH, Yourstone S, Carroll IM, Kawula TH, Bower MA, Sartor RB, Sullivan PF (2014) The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse. PLoS One 9: e115225.