R. Alan Harris, Ph.D.

Assistant Professor

(713) 798-2155

Email

rharris1@bcm.edu

Positions

Assistant Professor: Molecular and Human Genetics
Baylor College of Medicine
Houston, TX, US

Assistant Professor: Human Genome Sequencing Center
Baylor College of Medicine
Houston, Texas, United States

Addresses

Lab (Lab): Alkek Tower
Room: ALKT-N1419
Houston, TX, 77030
United States
Phone: (713) 798-2155
rharris1@bcm.edu

Education

Postdoctoral Training at Baylor College Of Medicine: 01/2009 - Houston, Texas, United States; Molecular and Human Genetics

PhD from Baylor College Of Medicine: 12/2007 - Houston, Texas, United States; Molecular and Human Genetics

MA from Kent State University: 05/1996 - Kent, Ohio, United States; Biological Anthropology

BA from Florida State University: 08/1990 - Tallahassee, Florida, United States; Anthropology, Geology

Professional Statement

My research integrates bioinformatics, genomics, and epigenomics to develop nonhuman primate disease models while investigating fundamental questions in primate evolution. Building on my interdisciplinary background, I pursue several interconnected research threads: (1) development and genomic characterization of nonhuman primate models for human diseases, with particular focus on rhesus macaque and marmoset (2) assembly and annotation of primate genomes to establish high-quality reference sequences for biomedical research (3) epigenomic regulation in development and disease, exploring DNA methylation patterns across a spectrum of human pathologies (4) development of computational tools for analyzing complex genomic and epigenomic datasets (5) primate comparative genomics to elucidate evolutionary mechanisms behind genomic structural changes, including work with the gibbon genome to understand chromosomal rearrangements.

Websites

Google Scholar

Pubmed Bibliography

Selected Publications

Harris RA, Tardif SD, Vinar T, Wildman DE, Rutherford J, Rogers J, Worley KC, Aagaard KM. " Evolutionary genetics and implications of small size and twinning in callitrichine primates " Proc Natl Acad Sci. 2014 ; 111 : 1467-72.
Pubmed PMID: 24379383.
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung . " Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications " Nat Biotechnol. 2010 Oct ; 28 (10) : 1097-105.
Pubmed PMID: 20852635.
Harris RA, Rogers J, Milosavljevic A. " Human-specific changes of genome structure detected by genomic triangulation " Science. 2007 Apr 13; 316 (5822) : 235-7.
Pubmed PMID: 17431168.
Harris RA, Nagy-Szakal D, Mir SA, Frank E, Szigeti R, Kaplan JL, Bronsky J, Opekun A, Ferry GD, Winter H, Kellermayer R. " DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis " Epigenetics. 2014 ;
Pubmed PMID: 24937444.
Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. " Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability " PLoS Genet. 2013 Feb ; 9 (2) : e1003333.
Pubmed PMID: 23468659.
*Munch EM, *Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K *These authors contributed equally. " Transcriptome profiling of microRNA by next-gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk " PLoS ONE. 2013 ; 8 (2) : e50564.
Pubmed PMID: 23418415.
Harris RA, Nagy-Szakal D, Kellermayer R. " Human metastable epiallele candidates link to common disorders " Epigenetics. 2013 Feb 1; 8 (2) : 157-63.
Pubmed PMID: 23321599.
Harris RA, Nagy-Szakal D, Pedersen N, Opekun A, Bronsky J, Munkholm P, Jespersgaard C, Andersen P, Melegh B, Ferry G, Jess T, Kellermayer R. " Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases " Inflamm Bowel Dis. 2012 Dec ; 18 (12) : 2334-41.
Pubmed PMID: 22467598.
Harris RA, Ferrari F, Ben-Shachar S, Wang X, Saade G, Van Den Veyver I, Facchinetti F, Aagaard-Tillery K. " Genome-wide array-based copy number profiling in human placentas from unexplained stillbirths " Prenat Diagn. 2011 Oct ; 31 (10) : 932-44.
Pubmed PMID: 21732394.
Carbone L, Harris RA, et al.. " Gibbon genome and the fast karyotype evolution of small apes. " Nature. 2014 ; 513 : 195-201.
Suter MA, Chen A, Burdine MS, Choudhury M, Harris RA, Lane RH, Friedman JE, Grove KL, Tackett AJ, Aagaard KM. " A maternal high-fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates " FASEB J. 2012 Dec ; 26 (12) : 5106-14.
Pubmed PMID: 22982377.
Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. " A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome " Genome Res. 2009 Feb ; 19 (2) : 167-77.
Pubmed PMID: 19056696.
Fawcett GL, Raveendran M, Deiros DR, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J. " Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta) " BMC Genomics. 2011 ; 12 : 311.
Pubmed PMID: 21668978.
Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW. " Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice " FASEB J. 2011 May ; 25 (5) : 1449-60.
Pubmed PMID: 21228220.
Rhesus Macaque Genome Sequencing and Analysis Consortium. " Evolutionary and biomedical insights from the rhesus macaque genome " Science. 2007 Apr 13; 316 (5822) : 222-34.
Pubmed PMID: 17431167.
Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM. " GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline " PLoS Genet. 2009 Sep ; 5 (9) : e1000635.
Pubmed PMID: 19730684.
Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. " Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome " PLoS Genet. 2012 May ; 8 (5) : e1002692.
Pubmed PMID: 22615578.
Suter MA, Sangi-Haghpeykar H, Showalter L, Shope C, Hu M, Brown K, Williams S, Harris RA, Grove KL, Lane RH, Aagaard KM. " Maternal high-fat diet modulates the fetal thyroid axis and thyroid gene expression in a nonhuman primate model " Mol Endocrinol. 2012 Dec ; 26 (12) : 2071-80.
Pubmed PMID: 23015752.
Schaible TD, Harris RA, Dowd SE, Smith CW, Kellermayer R. " Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes " Hum Mol Genet. 2011 May 1; 20 (9) : 1687-96.
Pubmed PMID: 21296867.
Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A. " Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing " BMC Bioinformatics. 2010 ; 11 : 572.
Pubmed PMID: 21092284.
Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GM, Gibbs RA. " Pooled genomic indexing of rhesus macaque " Genome Res. 2005 Feb ; 15 (2) : 292-301.
Pubmed PMID: 15687293.
Waterland RA, Kellermayer R, Laritsky E, Rayco-Solon P, Harris RA, Travisano M, Zhang W, Torskaya MS, Zhang J, Shen L, Manary MJ, Prentice AM. " Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles " PLoS Genet. 2010 ; 6 (12) : e1001252.
Pubmed PMID: 21203497.
Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavl. " The DNA sequence, annotation and analysis of human chromosome 3 " Nature. 2006 Apr 27; 440 (7088) : 1194-8.
Pubmed PMID: 16641997.
Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT,. " The finished DNA sequence of human chromosome 12 " Nature. 2006 Mar 16; 440 (7082) : 346-51.
Pubmed PMID: 16541075.
Majewski T, Lee S, Jeong J, Yoon DS, Kram A, Kim MS, Tuziak T, Bondaruk J, Lee S, Park WS, Tang KS, Chung W, Shen L, Ahmed SS, Johnston DA, Grossman HB, Dinney CP, Zhou JH, Harris RA, Snyder C, Filipek S, Narod SA, Watson P, Lynch HT, Gazdar A, Bar-Eli M,. " Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy " Lab Invest. 2008 Jul ; 88 (7) : 694-721.
Pubmed PMID: 18458673.
The Marmoset Genome Sequencing and Analysis Consortium. " The common marmoset genome provides insight into primate biology and evolution " Nat Genet. 2014 ;
Pubmed PMID: 25038751.
Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA. " Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing " Nucleic Acids Res. 2014 ; 42 : e43.
Pubmed PMID: 24391148.
Ma J, Prince AL, Bader D, Hu M, Ganu R, Baquero K, Blundell P, Harris RA, Frias AE, Grove KL, Aagaard KM. " High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model " Nat Commun. 2014 ; 5 (3889)
Pubmed PMID: 24846660.
Suter MA, Ma J, Vuguin PM, Hartil K, Fiallo A, Harris RA, Charron MJ, Aagaard KM. " In utero exposure to a maternal high-fat diet alters the epigenetic histone code in a murine model " Am J Obstet Gynecol. 2014 ; 210 : 463.e1-463.e11.
Pubmed PMID: 24793723.
Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DI, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. " Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons " Genome Biol Evol. 2012 ; 4 : 648-658.
Pubmed PMID: 22593550.
Davies M, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J. " Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood " Genome Biology. 2012 ; 13 : R43.
Pubmed PMID: 22703893.
Suter M, Ma J, Harris RA, Patterson L, Brown K, Shope C, Hu M, Showalter L, Abramovici A, Aagaard-Tillery K. " Maternal tobacco use modestly alters correlated epigenome-wide placental DNA methylation and gene expression " Epigenetics. 2011 ; 6 : 1284-1294.
Pubmed PMID: 21937876.
Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. " Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution " PLoS Genet. 2009 ; 5 : e1000538.
Pubmed PMID: 19557196.
Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. " MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing " Mol Hum Reprod. ; 16 : 463-471.
Pubmed PMID: 20215419.
Raveendran M, Tardif S, Ross CN, Austad SN, Harris RA, Milosavljevic A, Rogers J. " Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method " Am J Primatol. 2008 ; 70 : 906-10.
Pubmed PMID: 18561252.
Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB. " Pro-inflammatory role for let-7 microRNAs in experimental asthma " J Biol Chem. 2010 ; 285 : 30139-30149.
Pubmed PMID: 20630862.
Carbone L, Vessere GM, ten Hallers BFH, Zhu B, Osoegawa K, Mootnick A, Kofler A, Wienberg J, Rogers J, Humphray S, Scott C, Harris RA, Milosavljevic A, de Jong PJ. " A high-resolution map of synteny disruptions in gibbon and human genomes " PLoS Genet. 2006 ; 2 : e223.
Pubmed PMID: 17196042.
Raveendran M, Harris RA, Milosavljevic A, Johnson Z, Shelledy W, Cameron J, Rogers J. " Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates " Genomics. 2006 ; 88 : 706-710.
Pubmed PMID: 17010566.
Ganu RS, Harris RA, Collins K, Aagaard KM. " Early Origins of Adult Disease: Approaches for Investigating the Programmable Epigenome in Humans, Nonhuman Primates, and Rodents " ILAR J. 2012 ; 53 : 306-321.
Pubmed PMID: 23744969.
Ganu RS, Harris RA, Collins K, Aagaard KM. " Maternal diet: a modulator for epigenomic regulation during development in nonhuman primates and humans " Int J Obes Suppl. 2012 ; 2 : S14-S18.
Pubmed PMID: 25018872.
Aagaard-Tillery KM, Suter MA, Harris RA, Abramovici A, Cantu J. " Epigenetics and reproduction and the developmental origins of health and disease. " Anim Reprod. 2010 ; 7 : 103-116.
Harris RA, Milosavljevic A. " Human-specific changes of genome structure. " Encyclopedia of Life Sciences. 2008 ;