Publications

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Filters: Author is R. Alan Harris  [Clear All Filters]
2023
Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S, Eichler EE, Levine JE, Rogers J. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (). Genes (Basel). 2023 ;14(12).
2021
Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CChuen, Lim WKhong, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKai-How, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol. 2021 ;83(6):e23255.
2020
Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol. 2020 ;20(1):33.
2023
Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 ;24(1):23.
2018
Schmidtke D, Lempp C, Dubicanac M, Radespiel U, Zimmermann E, Baumgärtner W, Kästner S, Meier M, Balkema-Buschmann A, Harris RA, Raveendran M, Muzny DM, Worley KC, Rogers J. Spontaneous Spongiform Brainstem Degeneration in a Young Mouse Lemur () with Conspicuous Behavioral, Motor, Growth, and Ocular Pathologies. Comp Med. 2018 ;68(6):489-495.
2023
Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci. 2023 ;24(13).
2020
Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LDW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CRita, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, H Kubisch M, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHPate, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science. 2020 ;370(6523).
2018
Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive Longevity Predicts Mutation Rates in Primates. Curr Biol. 2018 ;28(19):3193-3197.e5.
2020
Xue C, Rustagi N, Liu X, Raveendran M, Harris RA, Venkata MGorentla, Rogers J, Yu F. Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS One. 2020 ;15(8):e0236285.
Vanderpool D, Minh BQuang, Lanfear R, Hughes D, Murali S, Harris RA, Raveendran M, Muzny DM, Hibbins MS, Williamson RJ, Gibbs RA, Worley KC, Rogers J, Hahn MW. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol. 2020 ;18(12):e3000954.
2021
Petty LE, Phillippi-Falkenstein K, H Kubisch M, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour. 2021 ;21(4):1333-1346.
2020
Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res. 2020 ;30(6):826-834.
2021
Thomas GWC, Wang RJ, Nguyen J, Harris RA, Raveendran M, Rogers J, Hahn MW. Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. Mol Biol Evol. 2021 ;38(4):1460-1471.
2019
Moshiri A, Chen R, Kim S, Harris RA, Li Y, Raveendran M, Davis S, Liang Q, Pomerantz O, Wang J, Garzel L, Cameron A, Yiu G, J Stout T, Huang Y, Murphy CJ, Roberts J, Gopalakrishna KN, Boyd K, Artemyev NO, Rogers J, Thomasy SM. A nonhuman primate model of inherited retinal disease. J Clin Invest. 2019 ;129(2):863-874.
2021
Tapmeier TT, Rahmioglu N, Lin J, De Leo B, Obendorf M, Raveendran M, Fischer OM, Bafligil C, Guo M, Harris RA, Hess-Stumpp H, Laux-Biehlmann A, Lowy E, Lunter G, Malzahn J, Martin NG, Martinez FO, Manek S, Mesch S, Montgomery GW, Morris AP, Nagel J, Simmons HA, Brocklebank D, Shang C, Treloar S, Wells G, Becker CM, Oppermann U, Zollner TM, Kennedy SH, Kemnitz JW, Rogers J, Zondervan KT. Neuropeptide S receptor 1 is a nonhormonal treatment target in endometriosis. Sci Transl Med. 2021 ;13(608).
Smith LM, Ladner JT, Hodara VL, Parodi LM, Harris RA, Callery JE, Lai Z, Zou Y, Raveedran M, Rogers J, Giavedoni LD. Multiplexed Simian Immunodeficiency Virus-Specific Paired RNA-Guided Cas9 Nickases Inactivate Proviral DNA. J Virol. 2021 ;95(23):e0088221.
2018
Dray BK, Raveendran M, Harris RA, Benavides F, Gray SB, Perez CJ, McArthur MJ, Williams LE, Baze WB, Doddapaneni H, Muzny DM, Abee CR, Rogers J. Mismatch repair gene mutations lead to lynch syndrome colorectal cancer in rhesus macaques. Genes Cancer. 2018 ;9(3-4):142-152.
2019
Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O'Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics. 2019 ;71(8-9):531-544.
2023
Harris RA, Archer KJ, Goodarzi MO, York TP, Rogers J, Dunaif A, McAllister JM, Strauss JF. Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome. Gene. 2023 ;852:147062.
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Amaral JValsecchi, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MHeide, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKai-How. The landscape of tolerated genetic variation in humans and primates. Science. 2023 ;380(6648):eabn8153.
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Amaral JValsecchi, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MHeide, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Farh KKai-How. The landscape of tolerated genetic variation in humans and primates. bioRxiv. 2023 ;.
2021
Fox AS, Harris RA, Del Rosso L, Raveendran M, Kamboj S, Kinnally EL, Capitanio JP, Rogers J. Infant inhibited temperament in primates predicts adult behavior, is heritable, and is associated with anxiety-relevant genetic variation. Mol Psychiatry. 2021 ;26(11):6609-6618.
2024
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MHeide, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Bonet TMarques, Farh KKai-How. Identification of constrained sequence elements across 239 primate genomes. Nature. 2024 ;625(7996):735-742.
2007
Harris RA, Rogers J, Milosavljevic A. Human-specific changes of genome structure detected by genomic triangulation. Science. 2007 ;316(5822):235-7.
2022
Gunter C, Harris RA, Kovacs-Balint Z, Raveendran M, Michopoulos V, Bachevalier J, Raper J, Sanchez MM, Rogers J. Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study. Autism Res. 2022 ;15(3):447-463.