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Bold indicates current/former lab members.
Preprints
*Carioscia, S. A., *Biddanda, A., Starostik, M. R., Tang, X., Hoffmann, E. R., McCoy, R. C. (2025). Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk. Nature, in press. *co-first author
Das, A., Biddanda, A., McCoy, R. C., Schatz, M. C. (2025). Assembling unmapped reads reveals hidden variation in South Asian genomes. bioRxiv, https://doi.org/10.1101/2025.05.14.653340
Lalli, J. L., Bortvin, A. N., †McCoy, R. C., †Werling, D. M. (2025). A T2T-CHM13 recombination
map and globally diverse haplotype reference panel improves phasing and imputation. bioRxiv, https://doi.org/10.1101/2025.02.24.639687. †co-corresponding author
DeGorter, M. K., Goddard, P. C., Karakoc, E., Kundu, S., Yan, S. M., Nachun, D., Abell, N., Aguirre, M., Carstensen, T., Chen, Z., Durrant, M., Dwaracherla, V. R., Feng, K., Gloudemans, M. J., Hunter, N., Moorthy, M. P. S., Pomilla, C., Rodrigues, K. B., Smith, C., Smith, K. S., Ungar, R. A., Balliu, B., Fellay, J., Flicek, P., McLaren, P. J., Henn, B., McCoy, R. C., Sugden, L., Kundaje, A., Sandu, M. S., Gurdasani, D., Montgomery, S. B. (2023). Transcriptomics and chromatin accessibility in multiple African population samples. bioRxiv, https://doi.org/10.1101/2023.11.04.564839.
Research Articles
2025
McDaniel, J. H., Patel, V., Olson, N. D., He, H. J., He, Z., Cole, K. D., Schmitt, A., Sikkink, K., Sedlazeck, F. J., Doddapaneni, H., Jhangiani, S. N., Muzny, D. M., Gingras, M. C., Mehta, H., Paulin, L. F., Hastie, A. R., Yu, H. C., Weigman, V., Rojas, A., Kennedy, K., Remington, J., Gonzalez, I., Sudkamp, M., Wiseman, K., Lajoie, B. R., Levy, S., Jain, M., Akeson, S., Narzisi, G., Steinsnyder, Z., Reeves, C., Shelton, J., Kingan, S. B., Lambert, C., Bayabyan, P., Wenger, A. M., McLaughlin, I. J., Adamson, A., Kingsley, C., Wescott, M., Kim, Y., Paten, B., Park, J., Violich, I., Miga, K. H., Gardner, J., McNulty, B., Rosen, G., McCoy, R. C., Brundu, F., Sayyari, E., Scheffler, K., Truong, S., Catreux, S., Hannah, L. C., Lipson, D., Benjamin, H., Iremadze, N., Soifer, I., Eacker, S., Wood, M., Cross, E., Husar, G., Gross, S., Vernich, M., Kolmogorov, M., Ahmad, T., Keskus, A., Bryant, A., Thibaud-Nissen, F., Trow, J., Proszynski, J., Hirschberg, J. W., Ryon, K., Mason, C. E., Wagner, J., Xiao, C., Liss, A. S., Zook, J. M. (2025). Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks. Scientific Data, 12, 1195.
Wang, D., Cearlock, A., Lane, K., Jan, I., McCoy, R. C., Yang, M. (2025). Chromosomal instability in human trophoblast stem cells and placentas. Nature Communications, 16, 3918.
Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J. M., Lin, J., Sequeira, A. N., Mangan, R. J., Hickey, G., Anez, G. M., Balachandran, P., Bankevich, A., Beck, C. R., Biddanda, A., Borchers, M., Bouffard, G. G., Brannan, E., Brooks, S. Y., Carbone, L., Carrel, L., Chan, A. P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G. H., de Gennaro, L., Gilbert, D., Green, R. E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R. S., Hartley, G. A., Harvey, W. T., Hiller, M., Hoekzema, K., Houck, M. L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A. P., Li, Q., Loftus, M., Loh, Y. H. E., Loucks, H., Ma, J., Mao, Y., Martinez, J. F. I., Masterson, P., McCoy, R. C., McGrath, B., McKinney, S., Meyer, B. S., Miga, K. H., Mohanty, S. K., Munson, K. M., Pal, K., Pennell, M., Pevzner, P. A., Porubsky, D., Potapova, T., Ringeling, F. R., Rocha, J. L., Ryder, O. A., Sacco, S., Saha, S., Sasaki, T., Schatz, M. C., Schork, N. J., Shanks, C., Smeds, L., Son, D. R., Steiner, C., Sweeten, A. P., Tassia, M. G., Thibaud-Nissen, F., Torres-Gonzalez, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S. A., Zhu, Y., Jarvis, E. D., Gerton, J. L., Rivas-Gonzalez, I., Paten, B., Szpiech, Z. A., Huber, C. D., Lenz, T. L., Konkel, M. K., Yi, S. V., Canzar, S., Watson, C. T., Sudmant, P. H., Molloy, E., Garrison, E., Lowe, C. B., Ventura, M., O’Neill, R. J., Koren, S., Makova, K. D., Phillippy, A. M. Eichler, E. E. (2025). Complete sequencing of ape genomes. Nature, 641, 401–418.
Liang, S., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J.M., Mao, Y., Chen, L. (2025). A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome. Genome Biology, 26, 32.
2024
Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Yan, S. M., Wojcik, G. L., Battle, A., McCoy, R. C. (2024). Sources of gene expression variation in a globally diverse human cohort. Nature, 632, 122-130.
Xiang, G., He, X., Giardine, B. M., Weaver, K. J., Taylor, D. J., McCoy, R. C., Jansen, C., Keller, C. A., Wixom, A., Cockburn, A., Miller, A., Qi, Q., He, Y., Li, Y., Lichtenberg, J., Heuston, E. F., Anderson, S. M., Luan, J., Vermunt, M. W., Yue, F., Sauria, M. E. G., Schatz., M. C., Taylor, J., Gottgens, B., Hughes, J. R., Higgs, D. R., Weiss, M. J., Cheng, Y., Blobel, G. A., Bodine, D., Zhang, Y., Li, Q., Mahony, S., Hardison, R. C. (2024). Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Research, 34, 1089-1105.
Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechova, M., …, Biddanda, A., …, McCoy, R. C., …, Tassia, M. G., …, Eichler, E., Phillippy, A. M. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature, 630, 401–411.
Hadyniak, S. E., Eldred, K. C., Brenerman, B., Hussey, K. A., McCoy, R. C., Sauria, M. E. G., Kuchenbeker, J. A., Neitz, M., Neitz, J., Taylor, J., Johnston, R. J. (2024). Retinoic acid signaling regulates spatiotemporal specification of human green and red cones. PLoS Biology, 22, e3002464.
Ariad, D., Madjunkova, S., Madjunkov, M., Chen, S., Abramov, R., Librach, C., McCoy, R. C. (2024). Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Research, 34, 70-84.
2023
Sun, S., Aboelenain, M., Ariad, D., Haywood, M. E., Wageman, C. R., Duke, M., Bag, A., Viotti, M., Katz-Jaffe, M., McCoy, R. C., Schindler, K., Xing, J. (2023). A method of identifying risk genes using ultra-low coverage whole-genome sequencing – insights into embryo aneuploidy. American Journal of Human Genetics, 10, 2092-2102.
McCoy, R. C., Summers, M. C., McCollin, A., Ottolini, C. S., Ahuja, K., Handyside, A. H. (2023). Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Medicine, 15, 77.
*Rhie, A., *Nurk, S., *Cechova, M., *Hoyt, S., *Taylor, D., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., McNulty, B. M., Bzikadze, A. V., Chen, N.-C., Chin, C.-S. Diekhans, M., Formenti, G., Flicek, P., …, McCoy, R. C., …, Eichler, E. E., O’Neill, R., Schatz, M. C., Miga, K. H., Makova, K. D., Phillippy, A. M. (2023). The complete sequence of a human Y chromosome. Nature, 621, 344–354. *co-first author
Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Vollger, M. R., Chen, N.-C., Taylor, D. J., Harvey, W. T., Logsdon, G. A., Meng, D., Shi, J., McCoy, R. C., Schatz, M. C., Li, W., Eichler, E. E., Lu, Q., Mao, Y. (2023). Characterization of large-scale genomic differences in the first complete human genome. Genome Biology, 24, 157.
Giraldo, D., Rankin-Turner, S., Corver, A., Tauxe, G. M., Gao, A. L., Jackson, D. M., Simubali, L., Book, C., Stevenson, J. C., Thuma, P. E., McCoy, R. C., Gordus, A., Mburu, M. M., Simulundu, E., McMeniman, C. J. (2023). Human scent guides mosquito thermotaxis and host selection under naturalistic conditions. Current Biology, 33, 2367-2382.e7.
*DeBoy, E. A., *Tassia, M. G., Schratz, K. E., Yan, S. M., Cosner, Z. L., McNally, E. J., Gable, D. L., Xiang, Z., Lombard, D. B., Antonarakis, E. S., Gocke, C. D., McCoy, R. C., Armanios, M. (2023), Familial clonal hematopoiesis in a long telomere syndrome. New England Journal of Medicine, 388, 2422-2433. *co-first author
2022
*Carioscia, S. A., *Weaver, K. J., Bortvin, A. N., Pan, H., Ariad, D., Bell, A. D., McCoy, R. C. (2022). A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm. eLife, 11, e76383. *co-first author
Griffin, D. K., Brezina, P. R., Tobler, K., Silvestri, G., McCoy, R. C., Anchan, R., Benner, A., Cutting, G. R., Kearns, W. G. (2022). The human embryonic genome is karyotypically complex, with chromosomally abnormal cells preferentially located away from the developing fetus. Human Reproduction, 38, 180-188.
*Aganezov, S., *Yan, S. M., *Soto, D. C., *Kirsche, M., *Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Meredith, M., Martin, S., Koren, S., Rosenfeld, J. A., Paten, B., Layer, R., Chin, C., Sedlazeck, F. J., Hansen, N. F., Miller, D. E., Phillippy, A., Miga, K., †McCoy, R. C., †Dennis, M. Y., †Zook, J. M., †Schatz, M. C. (2022). A complete reference genome improves analysis of human genetic variation. Science, 375, eabl3533. *co-first author; †co-corresponding author
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., …, Yan, S. M., …, McCoy, R. C., …, Eichler, E. E., Miga, K. H., Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376, eabj6987.
2021
Ariad, D., Yan, S. M., Victor, A. R., Barnes, F. L., Zouves, C. G., Viotti, M., McCoy, R. C. (2021). Haplotype-aware inference of human chromosome abnormalities. PNAS, 118, e2109307118.
Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10, e67615.
Ranallo-Benavidez, T. R., Lemmon, Z. H., Soyk, S., Aganezov, S., Salerno, W. J., McCoy, R. C., Lippman, Z. B., Schatz, M. C., Sedlazeck, F. J. (2021). Optimized sample selection for cost-efficient long-read population sequencing. Genome Research, 31, 910-918.
2020
Tyc, K. M., McCoy, R. C., Schindler, K., Xing, J. (2020). Mathematical modeling of human oocyte aneuploidy. PNAS, 117, 10455-10464.
Sharma, R., Singh, P., McCoy, R. C., Lenz, S. M., Donovan, K., Ochoa, M. T., Mayra Silva-Miranda, I. E., Jurado-Santa Cruz, F., Balagon, M. F., Stryjewska, B., Scollard, D. M., Pena, M. T., Lahiri, R., Williams, D. L., Truman, R. W.,Adams, L. B. (2020). Isolation of Mycobacterium lepromatosis and Development of Molecular Diagnostic Assays to Distinguish M. leprae and M. lepromatosis. Clinical Infectious Diseases, 71(8), e262-e269.
2019
Gruhn, J. R., Zielinska, A. P., Shukla, V., Blanshard, R., Capalbo, A., Cimadomo, D., Nikiforov, D., Chan, A. C., Newnham, L. J., Vogel, I., Scarica, C., Krapchev, M., Taylor, D., Kristensen, S. G., Cheng, J., Ernst, E., Bjørn, A. B., Colmorn, L. B., Blayney, M., Elder, K., Liss, J., Hartshorne, G., Grøndahl, M. L., Rienzi, L., Ubaldi, F., McCoy, R. C., Lukaszuk, K., Andersen, C. Y., Schuh, M., Hoffmann, E. R. (2019). Chromosome errors in human eggs shape natural fertility over reproductive life span. Science, 365(6460), 1466-1469.
Victor, A. R., Tyndall, J. C., Brake, A. J., Lepkowski, L. T., Murphy, A., Griffin, D. K., McCoy, R. C., Barnes, F. L., Zouves, C. G., Viotti, M. (2019). One hundred mosaic embryos transferred prospectively in a single clinic: exploring when and why they result in healthy pregnancies. Fertility & Sterility, 111(2), 280-293.
Victor, A. R., Griffin, D. K., Brake, A. J., Tyndall, J. C., Murphy, A., Lepkowsky, L. T., Lal, A., Zouves, C. G., Barnes, F. L., McCoy, R. C., Viotti, M. (2019). Assessment of aneuploidy concordance between clinical trophectoderm biopsy and blastocyst. Human Reproduction, 34(1), 181-192.
2018
Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B, Robinson, M., Barbieri, C., Fu, W., Purnomo, G. A., Sudoyo, H., Barbujani, G., Visscher, P. M., Akey, J. M., Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science, 361(6401), 511-516.
Press, M. O., McCoy, R. C., Hall, A. N., Akey, J. M., Queitsch, C. (2018). Short tandem repeats with massive variation and functional consequences across strains of Arabidopsis thaliana. Genome Research, 28, 1169-1178.
*McCoy, R. C., *Newnham, L. J., Ottolini, C. S., Hoffmann, E. R., Chatzimeletiou, K., Cornejo, O. E., Zhan, Q., Zaninovic, N., Rosenwaks, Z., Petrov, D. A., Demko, Z. P., Sigurjonsson, S., Handyside, A. H. (2018). Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos. Human Molecular Genetics, 27(14), 2573–2585. *co-first author
Kort, J. D., McCoy, R. C., Demko, Z. P., Lathi, R. B. (2018). Are blastocyst aneuploidy rates different between fertile and infertile populations? Journal of Assisted Reproduction and Genetics, 35(3), 403–408.
2017
2016
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., Scheinfeldt, L. B., Merriwether, D. A., Koki, G., Friedlaender, J. S., Wakefield, J., Pääbo, S., Akey, J. M. (2016). Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, 352(6282), 235-239.
Demko, Z. P., Simon, A. L., McCoy, R. C., Petrov, D. A., Rabinowitz, M. (2016). Effects of maternal age on euploidy in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening. Fertility & Sterility, 105(5), 1307-1313.
2015
McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Petrov, D. A. (2015). Evidence of selection against complex mitotic-origin aneuploidy during preimplantation development. PLoS Genetics, 11(10), e1005601.
McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Fraser, H. B., Petrov, D. A. (2015). Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science, 348(6231), 235-238.
2014
Ahola, V., Lehtonen, R., Somervou, P., Salmela, L., Koskinen, P., Rastas, P., Välimäki, L. P., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E., Ferguson, L., Luo, S., Cao, Z., de Jong, M., Duplouy, A., Smolander, O., McCoy, R. C., Qian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J., Joshi, A., Salojärvi, J., Wheat, C., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkänen, E., Ylinen, J., Waterhouse, R., Turunen, M., Vähärautio, A., Ojanen, S., Schulman, A., Taipale, M., Lawson, D., Ukkonen, E., Mäkinen, V., Goldsmith, M., Holm, L., Auvinen, P., Frilander, M., Hanski, I. (2014). The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications, 5.
McCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., Fiston-Lavier, A. S. (2014). Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE, 9(9), e106689.
McCoy, R. C., Garud, N. R., Kelley, J. L., Boggs, C. L., Petrov, D. A. (2014). Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population. Molecular Ecology, 23(1), 136-150.
Review Articles
2025
*Moya, N. D., *Yan, S. M., †McCoy, R. C., †Andersen, E. C. (2025), The long and short of hyperdivergent regions. Trends in Genetics, 41, 303-314. *co-first author; †co-corresponding author
2024
*Taylor, D. J., *Eizenga, J. M., *Li, Q., Das, A., Jenike, K. M., Kenny, E. E., Miga, K. H., †Monlong, J., †McCoy, R. C., †Paten, B., †Schatz, M. C. (2024), Beyond the Human Genome Project: Applications and opportunities for complete genomes and pangenomes. Annual Review of Genomics and Human Genetics, 25, 77-104. *co-first author; †co-corresponding author
2023
Muter, J., Lynch, V. J., McCoy, R. C., Brosens, J. J. (2023). Human embryo implantation. Development, 150, dev201507.
2022
Brosens, J. J., Bennett, P. R., Abrahams, V., Ramhorst, R., Coomarasamy, A., Quenby, S., Lucas, E. S., McCoy, R. C. (2022). Maternal selection of human embryos in early gestation: insights from recurrent miscarriage. Seminars in Cell and Developmental Biology, 131, 14-24.
2021
Quenby, S., Gallos, I. D., Dhillon-Smith, R. K., Podesek, M., Stephenson, M. D., Fisher, J., Brosens, J. J., Brewin, J., Ramhorst, R., Lucas, E. S., McCoy, R. C., Anderson, R., Daher, S., Regan, L., Al-Memar, M., Bourne, T., MacIntyre, D. A., Rai, R., Christiansen, O. B., Sugiura-Ogasawara, M., Odendaal, J., Devall, A. J., Bennett, P. R., Petrou, S., Coomarasamy, A. (2021). Miscarriage matters: the epidemiological, physical, psychological, and economic costs of early pregnancy loss. The Lancet, 397, 1658-1667.
Wartosch, L., Schindler, K., Schuh, M., Gruhn, J. R., Hoffmann, E. R., McCoy, R. C., Xing, J. (2021). Origins and mechanisms leading to aneuploidy in human eggs. Prenatal Diagnosis, 41, 620-630.
Levy, B., Hoffmann, E. R., McCoy, R. C., Grati, F. R. (2021). Chromosomal mosaicism: origins and clinical implications in preimplantation and prenatal diagnosis. Prenatal Diagnosis, 41, 631-641.
2020
2017
2024
Carioscia, S., McCoy, R. C. (2024), A rare genetic variant biases maternal meiotic recombination toward risk of pregnancy loss. Nature Structural & Molecular Biology, 31, 584–585.
2021
Viotti, M., McCoy, R. C., Griffin, D. K., Spinella, F., Greco, E., Madjunkov, M., Madjunkova, S., Librach, C. L., Victor, A. R., Barnes, F. L., Zouves, C. G. (2021), Let the data do the talking: The Need To Consider Mosaicism During Embryo Selection. Fertility & Sterility, 116, 1212–1219.
2019
Yan, S. M., McCoy, R. C. (2019). Functional divergence among hominins. Nature Ecology & Evolution, 3, 1507-1508.
McCoy, R. C., Kort, J. D. (2019). Quantifying the transcriptional impacts of aneuploidy in human blastocysts. Fertility & Sterility, 111(5), 888-889.
2017
McCoy, R. C., Akey, J. M. (2017). Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation. Genome Biology, 18, 139.
Adashi, E. Y., McCoy, R. C. (2017). Technology versus biology: the limits of pre-implantation genetic screening. EMBO Reports, e201743941.
2016
McCoy, R. C., Akey, J. M. (2016). Patterns of deleterious variation between human populations reveal an unbalanced load. PNAS, 113(4), 809-811.
McCoy Lab 