Nature Biotechnology / Sep 19, 2010

Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B. E., Fouse, S. D., Delaney, A., Zhao, Y., Olshen, A., Ballinger, T., Zhou, X., Forsberg, K. J., Gu, J., Echipare, L., O’Geen, H., Lister, R., Pelizzola, M., … Costello, J. F. (2010). Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology, 28(10), 1097–1105. https://doi.org/10.1038/nbt.1682

Genome Biology / Jan 01, 2012

Davies, M. N., Volta, M., Pidsley, R., Lunnon, K., Dixit, A., Lovestone, S., Coarfa, C., Harris, R. A., Milosavljevic, A., Troakes, C., Al-Sarraj, S., Dobson, R., Schalkwyk, L. C., & Mill, J. (2012). Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biology, 13(6), R43. https://doi.org/10.1186/gb-2012-13-6-r43

Cell / Dec 01, 2016

Stunnenberg, H. G., & Hirst, M. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell, 167(7), 1897. https://doi.org/10.1016/j.cell.2016.12.002

PLoS Genetics / Dec 23, 2010

Waterland, R. A., Kellermayer, R., Laritsky, E., Rayco-Solon, P., Harris, R. A., Travisano, M., Zhang, W., Torskaya, M. S., Zhang, J., Shen, L., Manary, M. J., & Prentice, A. M. (2010). Season of Conception in Rural Gambia Affects DNA Methylation at Putative Human Metastable Epialleles. PLoS Genetics, 6(12), e1001252. https://doi.org/10.1371/journal.pgen.1001252

PLoS Genetics / Dec 23, 2010

Waterland, R. A., Kellermayer, R., Laritsky, E., Rayco-Solon, P., Harris, R. A., Travisano, M., Zhang, W., Torskaya, M. S., Zhang, J., Shen, L., Manary, M. J., & Prentice, A. M. (2010). Season of Conception in Rural Gambia Affects DNA Methylation at Putative Human Metastable Epialleles. PLoS Genetics, 6(12), e1001252. https://doi.org/10.1371/journal.pgen.1001252

Nature Communications / May 20, 2014

Ma, J., Prince, A. L., Bader, D., Hu, M., Ganu, R., Baquero, K., Blundell, P., Alan Harris, R., Frias, A. E., Grove, K. L., & Aagaard, K. M. (2014). High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nature Communications, 5(1). https://doi.org/10.1038/ncomms4889

Nature / Sep 10, 2014

Carbone, L., Alan Harris, R., Gnerre, S., Veeramah, K. R., Lorente-Galdos, B., Huddleston, J., Meyer, T. J., Herrero, J., Roos, C., Aken, B., Anaclerio, F., Archidiacono, N., Baker, C., Barrell, D., Batzer, M. A., Beal, K., Blancher, A., Bohrson, C. L., Brameier, M., … Gibbs, R. A. (2014). Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195–201. https://doi.org/10.1038/nature13679

American Journal of Obstetrics and Gynecology / May 01, 2016

Prince, A. L., Ma, J., Kannan, P. S., Alvarez, M., Gisslen, T., Harris, R. A., Sweeney, E. L., Knox, C. L., Lambers, D. S., Jobe, A. H., Chougnet, C. A., Kallapur, S. G., & Aagaard, K. M. (2016). The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis. American Journal of Obstetrics and Gynecology, 214(5), 627.e1-627.e16. https://doi.org/10.1016/j.ajog.2016.01.193

Epigenetics / Nov 01, 2011

Suter, M., Ma, J., Harris, A. S., Patterson, L., Brown, K. A., Shope, C., Showalter, L., Abramovici, A., & Aagaard-Tillery, K. M. (2011). Maternal tobacco use modestly alters correlated epigenome-wide placental DNA methylation and gene expression. Epigenetics, 6(11), 1284–1294. https://doi.org/10.4161/epi.6.11.17819

Journal of Biological Chemistry / Sep 01, 2010

Polikepahad, S., Knight, J. M., Naghavi, A. O., Oplt, T., Creighton, C. J., Shaw, C., Benham, A. L., Kim, J., Soibam, B., Harris, R. A., Coarfa, C., Zariff, A., Milosavljevic, A., Batts, L. M., Kheradmand, F., Gunaratne, P. H., & Corry, D. B. (2010). Proinflammatory Role for let-7 MicroRNAS in Experimental Asthma. Journal of Biological Chemistry, 285(39), 30139–30149. https://doi.org/10.1074/jbc.m110.145698

Nature Genetics / Jul 20, 2014

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PLoS ONE / Feb 13, 2013

Munch, E. M., Harris, R. A., Mohammad, M., Benham, A. L., Pejerrey, S. M., Showalter, L., Hu, M., Shope, C. D., Maningat, P. D., Gunaratne, P. H., Haymond, M., & Aagaard, K. (2013). 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, 8(2), e50564. https://doi.org/10.1371/journal.pone.0050564

PLoS Genetics / Sep 04, 2009

Ma, L., Buchold, G. M., Greenbaum, M. P., Roy, A., Burns, K. H., Zhu, H., Han, D. Y., Harris, R. A., Coarfa, C., Gunaratne, P. H., Yan, W., & Matzuk, M. M. (2009). GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline. PLoS Genetics, 5(9), e1000635. https://doi.org/10.1371/journal.pgen.1000635

The FASEB Journal / Sep 14, 2012

Suter, M. A., Chen, A., Burdine, M. S., Choudhury, M., Harris, R. A., Lane, R. H., Friedman, J. E., Grove, K. L., Tackett, A. J., & Aagaard, K. M. (2012). A maternal high‐fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates. The FASEB Journal, 26(12), 5106–5114. Portico. https://doi.org/10.1096/fj.12-212878

MHR: Basic science of reproductive medicine / Mar 09, 2010

Ahn, H. W., Morin, R. D., Zhao, H., Harris, R. A., Coarfa, C., Chen, Z.-J., Milosavljevic, A., Marra, M. A., & Rajkovic, A. (2010). MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. MHR: Basic Science of Reproductive Medicine, 16(7), 463–471. https://doi.org/10.1093/molehr/gaq017

Human Molecular Genetics / Feb 04, 2011

Schaible, T. D., Harris, R. A., Dowd, S. E., Smith, C. W., & Kellermayer, R. (2011). Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes. Human Molecular Genetics, 20(9), 1687–1696. https://doi.org/10.1093/hmg/ddr044

Genome Research / Dec 03, 2008

Hampton, O. A., Den Hollander, P., Miller, C. A., Delgado, D. A., Li, J., Coarfa, C., Harris, R. A., Richards, S., Scherer, S. E., Muzny, D. M., Gibbs, R. A., Lee, A. V., & Milosavljevic, A. (2008). 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 Research, 19(2), 167–177. https://doi.org/10.1101/gr.080259.108

The FASEB Journal / Jan 12, 2011

Kellermayer, R., Dowd, S. E., Harris, R. A., Balasa, A., Schaible, T. D., Wolcott, R. D., Tatevian, N., Szigeti, R., Li, Z., Versalovic, J., & Smith, C. W. (2011). Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll‐like receptor 2‐knockout mice. The FASEB Journal, 25(5), 1449–1460. Portico. https://doi.org/10.1096/fj.10-172205

Science Advances / Jan 04, 2019

Rogers, J., Raveendran, M., Harris, R. A., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., … Kothe, M. (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1). https://doi.org/10.1126/sciadv.aau6947

Science Advances / Jan 04, 2019

Rogers, J., Raveendran, M., Harris, R. A., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., … Kothe, M. (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1). https://doi.org/10.1126/sciadv.aau6947

Journal of Crohn's and Colitis / Sep 28, 2015

McDermott, E., Ryan, E. J., Tosetto, M., Gibson, D., Burrage, J., Keegan, D., Byrne, K., Crowe, E., Sexton, G., Malone, K., Harris, R. A., Kellermayer, R., Mill, J., Cullen, G., Doherty, G. A., Mulcahy, H., & Murphy, T. M. (2015). DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis. Journal of Crohn’s and Colitis, 10(1), 77–86. https://doi.org/10.1093/ecco-jcc/jjv176

The American Journal of Human Genetics / May 01, 2016

Mbarek, H., Steinberg, S., Nyholt, D. R., Gordon, S. D., Miller, M. B., McRae, A. F., Hottenga, J. J., Day, F. R., Willemsen, G., de Geus, E. J., Davies, G. E., Martin, H. C., Penninx, B. W., Jansen, R., McAloney, K., Vink, J. M., Kaprio, J., Plomin, R., Spector, T. D., … Boomsma, D. I. (2016). Identification of Common Genetic Variants Influencing Spontaneous Dizygotic Twinning and Female Fertility. The American Journal of Human Genetics, 98(5), 898–908. https://doi.org/10.1016/j.ajhg.2016.03.008

The American Journal of Human Genetics / May 01, 2016

Mbarek, H., Steinberg, S., Nyholt, D. R., Gordon, S. D., Miller, M. B., McRae, A. F., Hottenga, J. J., Day, F. R., Willemsen, G., de Geus, E. J., Davies, G. E., Martin, H. C., Penninx, B. W., Jansen, R., McAloney, K., Vink, J. M., Kaprio, J., Plomin, R., Spector, T. D., … Boomsma, D. I. (2016). Identification of Common Genetic Variants Influencing Spontaneous Dizygotic Twinning and Female Fertility. The American Journal of Human Genetics, 98(5), 898–908. https://doi.org/10.1016/j.ajhg.2016.03.008

Scientific Reports / Jan 27, 2017

Aagaard, K. M., Lahon, A., Suter, M. A., Arya, R. P., Seferovic, M. D., Vogt, M. B., Hu, M., Stossi, F., Mancini, M. A., Harris, R. A., Kahr, M., Eppes, C., Rac, M., Belfort, M. A., Park, C. S., Lacorazza, D., & Rico-Hesse, R. (2017). Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication. Scientific Reports, 7(1). https://doi.org/10.1038/srep41389

Nature Communications / Feb 18, 2015

Elliott, G., Hong, C., Xing, X., Zhou, X., Li, D., Coarfa, C., Bell, R. J. A., Maire, C. L., Ligon, K. L., Sigaroudinia, M., Gascard, P., Tlsty, T. D., Harris, R. A., Schalkwyk, L. C., Bilenky, M., Mill, J., Farnham, P. J., Kellis, M., Marra, M. A., … Costello, J. F. (2015). Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications, 6(1). https://doi.org/10.1038/ncomms7363

PLoS Genetics / Jun 26, 2009

Carbone, L., Harris, R. A., Vessere, G. M., Mootnick, A. R., Humphray, S., Rogers, J., Kim, S. K., Wall, J. D., Martin, D., Jurka, J., Milosavljevic, A., & de Jong, P. J. (2009). Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution. PLoS Genetics, 5(6), e1000538. https://doi.org/10.1371/journal.pgen.1000538

Science / Dec 18, 2020

Warren, W. C., Harris, R. A., Haukness, M., Fiddes, I. T., Murali, S. C., Fernandes, J., Dishuck, P. C., Storer, J. M., Raveendran, M., Hillier, L. W., Porubsky, D., Mao, Y., Gordon, D., Vollger, M. R., Lewis, A. P., Munson, K. M., DeVogelaere, E., Armstrong, J., Diekhans, M., … Eichler, E. E. (2020). Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science, 370(6523). https://doi.org/10.1126/science.abc6617

PLoS Genetics / May 17, 2012

Li, J., Harris, R. A., Cheung, S. W., Coarfa, C., Jeong, M., Goodell, M. A., White, L. D., Patel, A., Kang, S.-H., Shaw, C., Chinault, A. C., Gambin, T., Gambin, A., Lupski, J. R., & Milosavljevic, A. (2012). Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome. PLoS Genetics, 8(5), e1002692. https://doi.org/10.1371/journal.pgen.1002692

Genome Research / Oct 17, 2016

Xue, C., Raveendran, M., Harris, R. A., Fawcett, G. L., Liu, X., White, S., Dahdouli, M., Rio Deiros, D., Below, J. E., Salerno, W., Cox, L., Fan, G., Ferguson, B., Horvath, J., Johnson, Z., Kanthaswamy, S., Kubisch, H. M., Liu, D., Platt, M., … Rogers, J. (2016). The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Research, 26(12), 1651–1662. https://doi.org/10.1101/gr.204255.116

Inflammatory Bowel Diseases / Dec 01, 2012

Harris, A. R., Nagy-Szakal, D., Pedersen, N., Opekun, A., Bronsky, J., Munkholm, P., Jespersgaard, C., Andersen, P., Melegh, B., Ferry, G., Jess, T., & Kellermayer, R. (2012). Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflammatory Bowel Diseases, 18(12), 2334–2341. https://doi.org/10.1002/ibd.22956

Current Biology / Oct 01, 2018

Thomas, G. W. C., Wang, R. J., Puri, A., Harris, R. A., Raveendran, M., Hughes, D. S. T., Murali, S. C., Williams, L. E., Doddapaneni, H., Muzny, D. M., Gibbs, R. A., Abee, C. R., Galinski, M. R., Worley, K. C., Rogers, J., Radivojac, P., & Hahn, M. W. (2018). Reproductive Longevity Predicts Mutation Rates in Primates. Current Biology, 28(19), 3193-3197.e5. https://doi.org/10.1016/j.cub.2018.08.050

American Journal of Gastroenterology / Apr 01, 2015

Kellermayer, R., Nagy-Szakal, D., Harris, A. R., Luna, R. A., Pitashny, M., Schady, D., Mir, S. A. V., Lopez, M. E., Gilger, M. A., Belmont, J., Hollister, E. B., & Versalovic, J. (2015). Serial Fecal Microbiota Transplantation Alters Mucosal Gene Expression in Pediatric Ulcerative Colitis. American Journal of Gastroenterology, 110(4), 604–606. https://doi.org/10.1038/ajg.2015.19

Nature Communications / Feb 18, 2015

Amin, V., Harris, R. A., Onuchic, V., Jackson, A. R., Charnecki, T., Paithankar, S., Lakshmi Subramanian, S., Riehle, K., Coarfa, C., & Milosavljevic, A. (2015). Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. Nature Communications, 6(1). https://doi.org/10.1038/ncomms7370

Science / Sep 28, 2018

Onuchic, V., Lurie, E., Carrero, I., Pawliczek, P., Patel, R. Y., Rozowsky, J., Galeev, T., Huang, Z., Altshuler, R. C., Zhang, Z., Harris, R. A., Coarfa, C., Ashmore, L., Bertol, J. W., Fakhouri, W. D., Yu, F., Kellis, M., Gerstein, M., & Milosavljevic, A. (2018). Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science, 361(6409). https://doi.org/10.1126/science.aar3146

Nature / Mar 15, 2006

Smith, L. M. (2006). The manifold faces of DNA. Nature, 440(7082), 283–284. https://doi.org/10.1038/440283a

American Journal of Obstetrics and Gynecology / May 01, 2014

Suter, M. A., Ma, J., Vuguin, P. M., Hartil, K., Fiallo, A., Harris, R. A., Charron, M. J., & Aagaard, K. M. (2014). In utero exposure to a maternal high-fat diet alters the epigenetic histone code in a murine model. American Journal of Obstetrics and Gynecology, 210(5), 463.e1-463.e11. https://doi.org/10.1016/j.ajog.2014.01.045

Journal of Clinical Investigation / Jan 22, 2019

Moshiri, A., Chen, R., Kim, S., Harris, R. A., Li, Y., Raveendran, M., Davis, S., Liang, Q., Pomerantz, O., Wang, J., Garzel, L., Cameron, A., Yiu, G., Stout, J. T., Huang, Y., Murphy, C. J., Roberts, J., Gopalakrishna, K. N., Boyd, K., … Thomasy, S. M. (2019). A nonhuman primate model of inherited retinal disease. Journal of Clinical Investigation, 129(2), 863–874. https://doi.org/10.1172/jci123980

Proceedings of the National Academy of Sciences / Dec 30, 2013

Harris, R. A., Tardif, S. D., Vinar, T., Wildman, D. E., Rutherford, J. N., Rogers, J., Worley, K. C., & Aagaard, K. M. (2013). Evolutionary genetics and implications of small size and twinning in callitrichine primates. Proceedings of the National Academy of Sciences, 111(4), 1467–1472. https://doi.org/10.1073/pnas.1316037111

ILAR Journal / Dec 01, 2012

Ganu, R. S., Harris, R. A., Collins, K., & Aagaard, K. M. (2012). Early Origins of Adult Disease: Approaches for Investigating the Programmable Epigenome in Humans, Nonhuman Primates, and Rodents. ILAR Journal, 53(3–4), 306–321. https://doi.org/10.1093/ilar.53.3-4.306

Laboratory Investigation / Jul 01, 2008

Majewski, T., Lee, S., Jeong, J., Yoon, D.-S., Kram, A., Kim, M.-S., Tuziak, T., Bondaruk, J., Lee, S., Park, W.-S., Tang, K. S., Chung, W., Shen, L., Ahmed, S. S., Johnston, D. A., Grossman, H. B., Dinney, C. P., Zhou, J.-H., Harris, R. A., … Czerniak, B. (2008). Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. Laboratory Investigation, 88(7), 694–721. https://doi.org/10.1038/labinvest.2008.27

Epigenetics / Jun 17, 2014

Harris, R. A., Nagy-Szakal, D., Mir, S. A., Frank, E., Szigeti, R., Kaplan, J. L., Bronsky, J., Opekun, A., Ferry, G. D., Winter, H., & Kellermayer, R. (2014). DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis. Epigenetics, 9(8), 1131–1137. https://doi.org/10.4161/epi.29446

Nucleic Acids Research / Jan 03, 2014

Kunde-Ramamoorthy, G., Coarfa, C., Laritsky, E., Kessler, N. J., Harris, R. A., Xu, M., Chen, R., Shen, L., Milosavljevic, A., & Waterland, R. A. (2014). Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Research, 42(6), e43–e43. https://doi.org/10.1093/nar/gkt1325

Nature / Apr 01, 2006

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PLOS Biology / Dec 03, 2020

Vanderpool, D., Minh, B. Q., Lanfear, R., Hughes, D., Murali, S., Harris, R. A., Raveendran, M., Muzny, D. M., Hibbins, M. S., Williamson, R. J., Gibbs, R. A., Worley, K. C., Rogers, J., & Hahn, M. W. (2020). Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLOS Biology, 18(12), e3000954. https://doi.org/10.1371/journal.pbio.3000954

Nature / Jan 01, 2018

Palesch, D., Bosinger, S. E., Tharp, G. K., Vanderford, T. H., Paiardini, M., Chahroudi, A., Johnson, Z. P., Kirchhoff, F., Hahn, B. H., Norgren, R. B., Patel, N. B., Sodora, D. L., Dawoud, R. A., Stewart, C.-B., Seepo, S. M., Harris, R. A., Liu, Y., Raveendran, M., Han, Y., … Silvestri, G. (2018). Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host. Nature, 553(7686), 77–81. https://doi.org/10.1038/nature25140

Epigenetics / Feb 01, 2013

Harris, R. A., Nagy-Szakal, D., & Kellermayer, R. (2013). Human metastable epiallele candidates link to common disorders. Epigenetics, 8(2), 157–163. https://doi.org/10.4161/epi.23438

Genome Biology and Evolution / Jan 01, 2012

Carbone, L., Harris, R. A., Mootnick, A. R., Milosavljevic, A., Martin, D. I. K., Rocchi, M., Capozzi, O., Archidiacono, N., Konkel, M. K., Walker, J. A., Batzer, M. A., & de Jong, P. J. (2012). Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons. Genome Biology and Evolution, 4(7), 648–658. https://doi.org/10.1093/gbe/evs048

BMC Bioinformatics / Nov 23, 2010

Coarfa, C., Yu, F., Miller, C. A., Chen, Z., Harris, R. A., & Milosavljevic, A. (2010). 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, 11(1). https://doi.org/10.1186/1471-2105-11-572

PLoS Genetics / Jan 01, 2005

Carbone, L., Vessere, G. M., ten Hallers, B. F. H., Zhu, B., Osoegawa, K., Mootnick, A., Kofler, A., Wienberg, J., Rogers, J., Humpray, S., Scott, C., Harris, A. R., Milosavljevic, A., & de Jong, P. J. (2005). A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes. PLoS Genetics, preprint(2006), e223. https://doi.org/10.1371/journal.pgen.0020223.eor

Molecular Endocrinology / Dec 01, 2012

Suter, M. A., Sangi-Haghpeykar, H., Showalter, L., Shope, C., Hu, M., Brown, K., Williams, S., Harris, R. A., Grove, K. L., Lane, R. H., & Aagaard, K. M. (2012). Maternal High-Fat Diet Modulates the Fetal Thyroid Axis and Thyroid Gene Expression in a Nonhuman Primate Model. Molecular Endocrinology, 26(12), 2071–2080. https://doi.org/10.1210/me.2012-1214

BMC Biology / Nov 16, 2017

Larsen, P. A., Harris, R. A., Liu, Y., Murali, S. C., Campbell, C. R., Brown, A. D., Sullivan, B. A., Shelton, J., Brown, S. J., Raveendran, M., Dudchenko, O., Machol, I., Durand, N. C., Shamim, M. S., Aiden, E. L., Muzny, D. M., Gibbs, R. A., Yoder, A. D., Rogers, J., & Worley, K. C. (2017). Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biology, 15(1). https://doi.org/10.1186/s12915-017-0439-6

Science / Jun 02, 2023

Fiziev, P. P., McRae, J., Ulirsch, J. C., Dron, J. S., Hamp, T., Yang, Y., Wainschtein, P., Ni, Z., Schraiber, J. G., Gao, H., Cable, D., Field, Y., Aguet, F., Fasnacht, M., Metwally, A., Rogers, J., Marques-Bonet, T., Rehm, H. L., O’Donnell-Luria, A., … Farh, K. K.-H. (2023). Rare penetrant mutations confer severe risk of common diseases. Science, 380(6648). https://doi.org/10.1126/science.abo1131

Science / Jun 02, 2023

Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., de Vries, D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A., … Marques Bonet, T. (2023). A global catalog of whole-genome diversity from 233 primate species. Science, 380(6648), 906–913. https://doi.org/10.1126/science.abn7829

Genome Research / May 27, 2020

Wang, R. J., Thomas, G. W. C., Raveendran, M., Harris, R. A., Doddapaneni, H., Muzny, D. M., Capitanio, J. P., Radivojac, P., Rogers, J., & Hahn, M. W. (2020). Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Research, 30(6), 826–834. https://doi.org/10.1101/gr.255174.119

Science / Apr 13, 2007

Harris, R. A., Rogers, J., & Milosavljevic, A. (2007). Human-Specific Changes of Genome Structure Detected by Genomic Triangulation. Science, 316(5822), 235–237. https://doi.org/10.1126/science.1139477

BMC Genomics / Jun 13, 2011

Fawcett, G. L., Raveendran, M., Deiros, D. R., Chen, D., Yu, F., Harris, R. A., Ren, Y., Muzny, D. M., Reid, J. G., Wheeler, D. A., Worley, K. C., Shelton, S. E., Kalin, N. H., Milosavljevic, A., Gibbs, R., & Rogers, J. (2011). Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics, 12(1). https://doi.org/10.1186/1471-2164-12-311

Prenatal Diagnosis / Jul 05, 2011

Harris, R. A., Ferrari, F., Ben‐Shachar, S., Wang, X., Saade, G., Van Den Veyver, I., Facchinetti, F., & Aagaard‐Tillery, K. (2011). Genome‐wide array‐based copy number profiling in human placentas from unexplained stillbirths. Prenatal Diagnosis, 31(10), 932–944. Portico. https://doi.org/10.1002/pd.2817

Scientific Reports / Nov 04, 2016

Harris, R. A., Alcott, C. E., Sullivan, E. L., Takahashi, D., McCurdy, C. E., Comstock, S., Baquero, K., Blundell, P., Frias, A. E., Kahr, M., Suter, M., Wesolowski, S., Friedman, J. E., Grove, K. L., & Aagaard, K. M. (2016). Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model. Scientific Reports, 6(1). https://doi.org/10.1038/srep36123

Science Translational Medicine / Aug 25, 2021

Tapmeier, T. T., Rahmioglu, N., Lin, J., De Leo, B., Obendorf, M., Raveendran, M., Fischer, O. M., Bafligil, C., Guo, M., Harris, R. A., Hess-Stumpp, H., Laux-Biehlmann, A., Lowy, E., Lunter, G., Malzahn, J., Martin, N. G., Martinez, F. O., Manek, S., Mesch, S., … Zondervan, K. T. (2021). Neuropeptide S receptor 1 is a nonhormonal treatment target in endometriosis. Science Translational Medicine, 13(608). https://doi.org/10.1126/scitranslmed.abd6469

PLOS Genetics / Dec 07, 2015

Yuan, B., Liu, P., Gupta, A., Beck, C. R., Tejomurtula, A., Campbell, I. M., Gambin, T., Simmons, A. D., Withers, M. A., Harris, R. A., Rogers, J., Schwartz, D. C., & Lupski, J. R. (2015). Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLOS Genetics, 11(12), e1005686. https://doi.org/10.1371/journal.pgen.1005686

International Journal of Obesity Supplements / Dec 01, 2012

Ganu, R. S., Harris, R. A., Collins, K., & Aagaard, K. M. (2012). Maternal diet: a modulator for epigenomic regulation during development in nonhuman primates and humans. International Journal of Obesity Supplements, 2(S2), S14–S18. https://doi.org/10.1038/ijosup.2012.16

Journal of Immunology Research / Jan 01, 2016

Harris, R. A., Shah, R., Hollister, E. B., Tronstad, R. R., Hovdenak, N., Szigeti, R., Versalovic, J., & Kellermayer, R. (2016). Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents. Journal of Immunology Research, 2016, 1–7. https://doi.org/10.1155/2016/9170162

Molecular Biology and Evolution / Jun 30, 2022

Wang, R. J., Raveendran, M., Harris, R. A., Murphy, W. J., Lyons, L. A., Rogers, J., & Hahn, M. W. (2022). De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations. Molecular Biology and Evolution, 39(7). https://doi.org/10.1093/molbev/msac147

Genomics / Dec 01, 2006

Raveendran, M., Harris, R. A., Milosavljevic, A., Johnson, Z., Shelledy, W., Cameron, J., & Rogers, J. (2006). Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates. Genomics, 88(6), 706–710. https://doi.org/10.1016/j.ygeno.2006.08.009

The FASEB Journal / Aug 01, 2015

Nagy-Szakal, D., Mir, S. A. V., Harris, R. A., Dowd, S. E., Yamada, T., Lacorazza, H. D., Tatevian, N., Smith, C. W., de Zoeten, E. F., Klein, J., & Kellermayer, R. (2015). Loss of n-6 fatty acid induced pediatric obesity protects against acute murine colitis. The FASEB Journal, 29(8), 3151–3159. https://doi.org/10.1096/fj.14-267690

Genes & Cancer / Apr 28, 2018

Dray, B. K., Raveendran, M., Harris, R. A., Benavides, F., Gray, S. B., Perez, C. J., McArthur, M. J., Williams, L. E., Baze, W. B., Doddapaneni, H., Muzny, D. M., Abee, C. R., & Rogers, J. (2018). Mismatch repair gene mutations lead to lynch syndrome colorectal cancer in rhesus macaques. Genes & Cancer, 9(3–4), 142–152. https://doi.org/10.18632/genesandcancer.170

Immunogenetics / Mar 25, 2017

Prall, T. M., Graham, M. E., Karl, J. A., Wiseman, R. W., Ericsen, A. J., Raveendran, M., Alan Harris, R., Muzny, D. M., Gibbs, R. A., Rogers, J., & O’Connor, D. H. (2017). Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics, 69(5), 325–339. https://doi.org/10.1007/s00251-017-0977-7

Genome Research / Feb 01, 2005

Milosavljevic, A., Harris, R. A., Sodergren, E. J., Jackson, A. R., Kalafus, K. J., Hodgson, A., Cree, A., Dai, W., Csuros, M., Zhu, B., de Jong, P. J., Weinstock, G. M., & Gibbs, R. A. (2005). Pooled genomic indexing of rhesus macaque. Genome Research, 15(2), 292–301. https://doi.org/10.1101/gr.3162505

Nov 01, 2020

Fox, A., Harris, R., Del Rosso, L., Raveendran, M., Kamboj, S., Kinnally, E., Capitanio, J., & Rogers, J. (2020). Infant Inhibited Temperament in Primates Predicts Adult Behavior, is Heritable, and is Associated with Anxiety-Relevant Genetic Variation. https://doi.org/10.1101/2020.10.30.361477

BMC Evolutionary Biology / Feb 27, 2020

Harris, R. A., Raveendran, M., Worley, K. C., & Rogers, J. (2020). Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evolutionary Biology, 20(1). https://doi.org/10.1186/s12862-020-1595-9

Medical and Health Genomics / Jan 01, 2016

Kumar, D. (2016). The Human Genome. In Medical and Health Genomics (pp. 1–13). Elsevier. https://doi.org/10.1016/b978-0-12-420196-5.00001-0

American Journal of Perinatology / Sep 02, 2015

Racusin, D., Villarreal, S., Antony, K., Harris, R., Mastrobattista, J., Lee, W., Shamshirsaz, A., Belfort, M., & Aagaard, K. (2015). Role of Maternal Serum Alpha-Fetoprotein and Ultrasonography in Contemporary Detection of Spina Bifida. American Journal of Perinatology, 32(14), 1287–1291. https://doi.org/10.1055/s-0035-1562930

Immunogenetics / Jul 18, 2019

Caskey, J. R., Wiseman, R. W., Karl, J. A., Baker, D. A., Lee, T., Maddox, R. J., Raveendran, M., Harris, R. A., Hu, J., Muzny, D. M., Rogers, J., & O’Connor, D. H. (2019). MHC genotyping from rhesus macaque exome sequences. Immunogenetics, 71(8–9), 531–544. https://doi.org/10.1007/s00251-019-01125-w

Autism Research / Jan 29, 2022

Gunter, C., Harris, R. A., Kovacs‐Balint, Z., Raveendran, M., Michopoulos, V., Bachevalier, J., Raper, J., Sanchez, M. M., & Rogers, J. (2022). Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study. Autism Research, 15(3), 447–463. Portico. https://doi.org/10.1002/aur.2675

Science Advances / Apr 23, 2021

Guevara, E. E., Webster, T. H., Lawler, R. R., Bradley, B. J., Greene, L. K., Ranaivonasy, J., Ratsirarson, J., Harris, R. A., Liu, Y., Murali, S., Raveendran, M., Hughes, D. S. T., Muzny, D. M., Yoder, A. D., Worley, K. C., & Rogers, J. (2021). Comparative genomic analysis of sifakas ( Propithecus ) reveals selection for folivory and high heterozygosity despite endangered status. Science Advances, 7(17). https://doi.org/10.1126/sciadv.abd2274

Molecular Biology and Evolution / Nov 23, 2020

Thomas, G. W. C., Wang, R. J., Nguyen, J., Alan Harris, R., Raveendran, M., Rogers, J., & Hahn, M. W. (2020). Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. Molecular Biology and Evolution, 38(4), 1460–1471. https://doi.org/10.1093/molbev/msaa303

American Journal of Primatology / Jun 16, 2008

Raveendran, M., Tardif, S., Ross, C. N., Austad, S. N., Harris, R. A., Milosavljevic, A., & Rogers, J. (2008). Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost‐ and time‐efficient method. American Journal of Primatology, 70(9), 906–910. Portico. https://doi.org/10.1002/ajp.20581

Science / Jun 02, 2023

Sørensen, E. F., Harris, R. A., Zhang, L., Raveendran, M., Kuderna, L. F. K., Walker, J. A., Storer, J. M., Kuhlwilm, M., Fontsere, C., Seshadri, L., Bergey, C. M., Burrell, A. S., Bergman, J., Phillips-Conroy, J. E., Shiferaw, F., Chiou, K. L., Chuma, I. S., Keyyu, J. D., Fischer, J., … Rogers, J. (2023). Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science, 380(6648). https://doi.org/10.1126/science.abn8153

Gene / Feb 01, 2023

Alan Harris, R., Archer, K. J., Goodarzi, M. O., York, T. P., Rogers, J., Dunaif, A., McAllister, J. M., & Strauss, J. F. (2023). Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome. Gene, 852, 147062. https://doi.org/10.1016/j.gene.2022.147062

American Journal of Obstetrics and Gynecology / Sep 01, 2016

Pew, B. K., Harris, R. A., Sbrana, E., Guaman, M. C., Shope, C., Chen, R., Meloche, S., & Aagaard, K. (2016). Structural and transcriptomic response to antenatal corticosteroids in an Erk3-null mouse model of respiratory distress. American Journal of Obstetrics and Gynecology, 215(3), 384.e1-384.e89. https://doi.org/10.1016/j.ajog.2016.04.043

PLOS Genetics / Apr 21, 2022

Ozirmak Lermi, N., Gray, S. B., Bowen, C. M., Reyes-Uribe, L., Dray, B. K., Deng, N., Harris, R. A., Raveendran, M., Benavides, F., Hodo, C. L., Taggart, M. W., Colbert Maresso, K., Sinha, K. M., Rogers, J., & Vilar, E. (2022). Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLOS Genetics, 18(4), e1010163. https://doi.org/10.1371/journal.pgen.1010163

American Journal of Perinatology Reports / Jan 01, 2020

Antony, K. M., Kazembe, P. N., Pace, R. M., Levison, J., Phiri, H., Chiudzu, G., Harris, R. A., Chirwa, R., Nyondo, M., Marko, E., Chigayo, A., Nanthuru, D., Banda, B., Twyman, N., Ramin, S. M., Raine, S. P., Belfort, M. A., & Aagaard, K. M. (2020). Population-Based Estimation of the Preterm Birth Rate in Lilongwe, Malawi: Making Every Birth Count. American Journal of Perinatology Reports, 10(01), e78–e86. https://doi.org/10.1055/s-0040-1708491

Feb 03, 2021

Melin, A. D., Orkin, J. D., Janiak, M. C., Valenzuela, A., Kuderna, L., Marrone, F., Ramangason, H., Horvath, J. E., Roos, C., Kitchener, A. C., Khor, C. C., Lim, W. K., Lee, J. G. H., Tan, P., Umapathy, G., Raveendran, M., Harris, R. A., Gut, I., Gut, M., … Higham, J. P. (2021). Variation in predicted COVID-19 risk among lemurs and lorises. https://doi.org/10.1101/2021.02.03.429540

PLOS Genetics / May 11, 2020

Brasó-Vives, M., Povolotskaya, I. S., Hartasánchez, D. A., Farré, X., Fernandez-Callejo, M., Raveendran, M., Harris, R. A., Rosene, D. L., Lorente-Galdos, B., Navarro, A., Marques-Bonet, T., Rogers, J., & Juan, D. (2020). Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLOS Genetics, 16(5), e1008742. https://doi.org/10.1371/journal.pgen.1008742

Genome Biology and Evolution / Sep 29, 2022

Wang, R. J., Peña-Garcia, Y., Bibby, M. G., Raveendran, M., Harris, R. A., Jansen, H. T., Robbins, C. T., Rogers, J., Kelley, J. L., & Hahn, M. W. (2022). Examining the Effects of Hibernation on Germline Mutation Rates in Grizzly Bears. Genome Biology and Evolution, 14(10). https://doi.org/10.1093/gbe/evac148

PLOS ONE / Aug 25, 2020

Xue, C., Rustagi, N., Liu, X., Raveendran, M., Harris, R. A., Venkata, M. G., Rogers, J., & Yu, F. (2020). Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLOS ONE, 15(8), e0236285. https://doi.org/10.1371/journal.pone.0236285

Nature / Nov 29, 2023

Kuderna, L. F. K., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., Cox, A. J., Gao, H., Kumar, A., Aguet, F., Christmas, M. J., Clawson, H., Haeussler, M., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., … Farh, K. K.-H. (2023). Identification of constrained sequence elements across 239 primate genomes. Nature, 625(7996), 735–742. https://doi.org/10.1038/s41586-023-06798-8

Molecular Ecology Resources / Jan 27, 2021

Petty, L. E., Phillippi‐Falkenstein, K., Kubisch, H. M., Raveendran, M., Harris, R. A., Vallender, E. J., Huff, C. D., Bohm, R. P., Rogers, J., & Below, J. E. (2021). Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Molecular Ecology Resources, 21(4), 1333–1346. Portico. https://doi.org/10.1111/1755-0998.13317

GigaScience / Jan 01, 2022

Harris, R. A., Raveendran, M., Lyfoung, D. T., Sedlazeck, F. J., Mahmoud, M., Prall, T. M., Karl, J. A., Doddapaneni, H., Meng, Q., Han, Y., Muzny, D., Wiseman, R. W., O’Connor, D. H., & Rogers, J. (2022). Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster,Mesocricetus auratus. GigaScience, 11. https://doi.org/10.1093/gigascience/giac039

American Journal of Perinatology Reports / Jul 01, 2019

Antony, K. M., Kazembe, P. N., Pace, R. M., Levison, J., Mlotha-Namarika, J., Phiri, H., Chiudzu, G., Harris, R. A., Aagaard, J., Twyman, N., Ramin, S. M., Raine, S. P., Belfort, M. A., & Aagaard, K. M. (2019). Population-Based Estimation of Dental Caries and Periodontal Disease Rates of Gravid and Recently Postpartum Women in Lilongwe, Malawi. American Journal of Perinatology Reports, 09(03), e268–e274. https://doi.org/10.1055/s-0039-1695003

Comparative Medicine / Dec 01, 2018

Schmidtke, D., Lempp, C., Dubicanac, M., Radespiel, U., Zimmermann, E., Baumgärtner, W., Kästner, S., Meier, M., Balkema-Buschmann, A., Harris, R. A., Raveendran, M., Muzny, D. M., Worley, K. C., & Rogers, J. (2018). Spontaneous Spongiform Brainstem Degeneration in a Young Mouse Lemur (Microcebus murinus) with Conspicuous Behavioral, Motor, Growth, and Ocular Pathologies. Comparative Medicine, 68(6), 489–495. https://doi.org/10.30802/aalas-cm-18-000019

Journal of Animal Science / Sep 01, 2016

Liu, Y., Murali, S. C., Harris, R. A., English, A. C., Qin, X., Skinner, E., Richards, S., Rogers, J., Han, Y., Vee, V., Wang, M., Meng, Q., Heaton, M. P., Smith, T. P. L., Dalrymple, B. P., Kijas, J., Cockett, N. E., Boerwinkle, E. A., Muzny, D. M., … Worley, K. C. (2016). P1009 Sheep reference genome sequence updates: Texel improvements and Rambouillet progress. Journal of Animal Science, 94(suppl_4), 18–19. https://doi.org/10.2527/jas2016.94supplement418b

Gastroenterology / May 01, 2014

Kellermayer, R., Nagy-Szakal, D., Harris, R. A., Hollister, E. B., Mir, S., Luna, R. A., Pitashny, M., Schady, D., Lopez, M. E., Gilger, M. A., & Versalovic, J. (2014). Tu1192 Clinical, Epigenetic, and Metagenomic Responses to Serial Fecal Microbiome Transplants in Pediatric Ulcerative Colitis. Gastroenterology, 146(5), S-780. https://doi.org/10.1016/s0016-5085(14)62813-4

PLoS Genetics / Feb 28, 2013

Harris, R. A., Shaw, C., Li, J., Cheung, S. W., Coarfa, C., Jeong, M., Goodell, M. A., White, L. D., Patel, A., Kang, S.-H., Chinault, A. C., Gambin, T., Gambin, A., Lupski, J. R., & Milosavljevic, A. (2013). Confounding by Repetitive Elements and CpG Islands Does Not Explain the Association between Hypomethylation and Genomic Instability. PLoS Genetics, 9(2), e1003333. https://doi.org/10.1371/journal.pgen.1003333

Gastroenterology / May 01, 2014

Kellermayer, R., Nagy-Szakal, D., Harris, R. A., Hollister, E. B., Mir, S., Luna, R. A., Pitashny, M., Schady, D., Lopez, M. E., Gilger, M. A., & Versalovic, J. (2014). Tu1192 Clinical, Epigenetic, and Metagenomic Responses to Serial Fecal Microbiome Transplants in Pediatric Ulcerative Colitis. Gastroenterology, 146(5), S-780. https://doi.org/10.1016/s0016-5085(14)62813-4

Developments in Primatology: Progress and Prospects / Jan 01, 2023

Rogers, J., Harris, R. A., Raveendran, M., Williams, L., & Worley, K. C. (2023). A Reference Genome Assembly and Initial Polymorphism Data for Aotus nancymaae. In Owl Monkeys (pp. 251–264). Springer International Publishing. https://doi.org/10.1007/978-3-031-13555-2_8