Publications

Here are links to my publications. If you cannot access something that's paywalled, feel free to contact me and I can share it with you. Note birth name Rice. A * denotes equal contribution.

• 2026
  • Gene conversion empowers natural selection in a clonal fish species Edward S. Ricemeyer*, Nathan K. Schaefer*, Kang Du, Irene da Cruz, Susanne Kneitz, Rafael D. Acemel, Darío G. Lupiáñez, Rachel A. Carroll, Rosie Drinkwater, Manfred Schartl & Wesley C. Warren (2026). Nature, in press.
    Nature
• 2025
  • Beyond FoxP3 – Identification of a chicken regulatory T cell signature. Naumann, I., Ricemeyer, E. S., Elleder, D., Plachy, J., von La Roche, D., Vučinić, K., Göbel, T. W., Kaspers, B., Früh, S. P., & Härtle, S. (2025). European Journal of Immunity, 55(12), e70106.
    European Journal of ImmunityPDF
  • Genomic resources for comparative analyses of obligate avian brood parasitism. Carroll, R. A., Ricemeyer, E. S., Hillier, L. W., DaCosta, J. M., Osipova, E., Smith, S., Joardar, V., Jamie, G., Martinez Suarez, J. G., Marques-Bonet, T., Manthey, J. D., Fuxjager, M. J., Lynch, K. S., Jarvis, E., Joarder, V., Thibaud-Nissen, F., Spottiswoode, C. N., Sackton, T. B., Balakrishnan, C. N., Sorenson, M. D., & Warren, W. C. (2025). Journal of Heredity, esaf087.
    Journal of HeredityPDF
  • Comparative multi-omics evaluation of the tumor microenvironment in canine and human hepatocellular carcinoma. Nussbaum, Y. I., Bryan, J. N., Li, G., Rodney, A., Culp, W. T. N., Dickinson, P. J., Koutoulas, A., Megquier, K., An, H., Kramer, S. T., Ricemeyer, E. S., Mitchem, J. B., & Warren, W. C. (2025). Veterinary Oncology, 2, 25.
    Veterinary Oncology PDF
  • Mitochondrial introgression with potential functional effects in North American yak. Treffer, L. K., Schroeder, R. L., Ricemeyer, E. S., Kalbfleisch, T., Fuller, A. M., & Petersen, J. L. (2025). Ecology and Evolution, 15(10), e72362.
    Ecology and Evolution PDF
  • Agptools: a utility suite for editing genome assemblies. Ricemeyer, E. S., Carroll, R. A., & Warren, W. C. (2025). Bioinformatics, 41(7), btaf388.
    Bioinformatics PDF
• 2024
  • A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken. Sculley, E. R.*, Ricemeyer, E. S.*, Carroll, R. A., Driver, J., Smith, J., Kaufman, J., Hearn, C., Balic, A., Chen, P., Lamont, S., Kramer, S., Drechsler, Y, Cheng, H., & Warren, W. C. (2024). bioRxiv 2024.08.05.606414.
    bioRxiv
  • Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. Warren, W. C., Rice, E. S., X, M., Roback, E., Keene, A., Smith, F., Ogeh, D., Haggerty, L., Carroll, R. A., McGaugh, S., & Rohner, N. (2024). G3: Genes, Genomes, Genetics, 14(8).
    G3 PDF
  • A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Carroll, R. A., Rice, E. S., Lyons, L. A., Coghill, L., Swanson, W. F., Terio, K. A., Boyd, T., & Warren, W. C. (2024). Scientific Reports, 14, 8073.
    Scientific ReportsPDF
• 2023
  • A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. Rice, E. S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J. R., Bardou, P., Blackmon, H., Fedrigo, O., Fiddaman, S. R., Formenti, G., Frantz, L., Gilbert, M. T. P., Hearn, C. J., Jarvis, E. D., Klopp, C., Marcos, S., Velez-Irizarry, D., Xu, L., & Warren, W. C. (2023). BMC Biology, 21, 267.
    BMC Biology PDF
  • Single-haplotype comparative genomics reveals the role of structural innovations during cat evolution. Bredemeyer, K. R., Hillier, L., Harris, A. J., Hughes, G. M., Foley, N. M., Lawless, C., Carroll, R. A., Storer, J. M., Batzer, M. A., Rice, E. S., Davis, B. W., Raudsepp, T., O’Brien, S. J., Lyons, L. A., Warren, W. C., & Murphy, W. J. (2023). Nature Genetics, 55, 1953-1963.
    Nature GeneticsPDF
  • Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Warren, W. C., Fedrigo, O., Tracey, A., Mason, A. S., Formenti, G., Perini, F., Wu, Z., Murphy, T., Schneider, V., Stiers, K., Rice, E. S., Coghill, L. M., Anthony, N., Okimoto, R., Carroll, R. A., Mountcastle, J., Balacco, J., Haase, B., Yang, C., Zhang, G., Smith, J., Drechsler, Y, Cheng, H., Howe, K., & Jarvis, E. (2023). Cytogenetic and Genome Research, 162(8-9), 407–416.
    Cytogenetic and Genome Research PDF
  • High resolution genomes of multiple Xiphophorus species provide new insight into microevolution, hybrid incompatibility, epistasis and disease. Lu, Y.*, Rice, E. S.*, Du, K., Kneitz, S., Naville, M., Dechaud, C., Volff, J., Boswell, M., Boswell, W., Hillier, L., Tomlinson, C., Kremitzki, M., Walter, R., Schartl, M., & Warren, W. C. (2023). Genome Research, 33, 557-571.
    Genome ResearchPDF
  • A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference. Puritz, J. B., Guo, X., Hare, M., He, Y., Hillier, L., Jin, S., Liu, M., Lotterhos, K., Minx, P., Modak, T., Proestou, D., Rice, E. S., Tomlison, C., Warren, W. C., Witkop, E., Zhao, H., & Gomez-Chiarri, M. (2023). Molecular Ecology Resources, 2023(00):1-18.
    Molecular Ecology Resources PDF
  • The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus. Warren, W. C., Rice, E. S., Meyer, A., Hearn, C. J., Steep, A., Hunt, H. D., Monson, M. S., Lamont, S. J, Cheng, H. H. (2023). Scientific Reports, 13, 5355.
    Scientific ReportsPDF
• 2022
  • Discordant genome assemblies drastically alter the interpretation of single-cell RNA sequencing data which can be mitigated by a novel integration method. Potts, H. G., Lemieux, M. E., Rice, E. S., Warren, W.C., Choudhury, R. P., & Mommersteeg, M.T.M. (2022). Cells, 11, 608.
    CellsPDF
• 2021
  • Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. Edwards, R. J., Field, M. A., Ferguson, J. M., Dudchenko, O., Keilwagen, J., Rosen, B. D., Johnson, G. S., Rice, E. S., Hillier, L., Hammond, J. M., Towarnicki, S. G., Omer, A., Skvortsova, K., Bogdanovic, O., Zammit, R. A., Lieberman Aiden, E., Warren, W. C., & Ballard, J. W. O. (2021). BMC Genomics, 22, 188.
    BMC GenomicsPDF
  • A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Warren, W. C., Boggs, T. E., Borowsky, R., Carlson, B. M., Ferrufino, E., Gross, J. B., Hillier, L., Hu, Z., Keene, A. C., Kenzior, A., Kowalko, J. E., Tomlinson, C., Kremitzki, M., Lemieux, M. E., Graves-Lindsay, T., McGaugh, S. E., Miller, J. T., Mommersteeg, M., Moran, R. L., Peuß, R., Rice, E. S., Riddle, M. R., Sifuentes-Romero, I., Stanhope, B. A., Tabin, C. J., Thakur, S., Yoshiyuki, Y. & Rohner, N. (2021). Nature Communications, 12, 1447.
    Nature CommunicationsPDF
  • Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. Trujillo, C. A., Rice, E. S., Schaefer, N. K., Chaim, I. A., Wheeler, E. C., Madrigal, A. A., Buchanan, J., Preissl, S., Wang, A., Negraes, P. D., Szeto, R., Herai, R. H., Huseynov, A., Ferraz, M. S. A., da S. Borges, F., Kihara, A. H., Byrne, A., Marin, M., Vollmers, C., Brooks, A. N., Lautz, J. D., Semendeferi, K., Shapiro, B. A., Yeo, G. W., Smith, S. E. P., Green, R. E., & Muotri, A. R. (2021). Science, 371(6530), eaax2537.
    SciencePDF
  • Transcriptomic changes of murine visceral fat exposed to intermittent hypoxia at single cell resolution. Khalyfa, A., Warren, W. C., Andrade, J., Bottoms, C. A., Rice, E. S., Cortese, R., Kheirandish-Gozal, L., & Gozal, D. (2021). Int. J. Mol. Sci., 22, 261.

    Int. J. Mol. Sci.PDF
• 2020
  • Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T.S., Hardy, T., Hackett, P.H., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., & Smith, T.P.L. (2020) GigaScience, 9(4), giaa029.
    GigaSciencePDF
• 2019
  • New approaches for genome assembly and scaffolding Rice, E. S. & Green, R. E. (2019) Annual Review of Animal Biosciences, 7, 17-40.
    Annual ReviewsPDF
• 2018
  • Improved reference genome for the domestic horse increases assembly contiguity and composition. Kalbfleisch, T.S.*, Rice, E. S.*, DePriest, Jr., M. S., Walenz, B. P., Hestand, M. S., Vermeesch, J. R., O'Connell, B.L, Fiddes, I. T., Vershinina, A. O., Saremi, N. F., Petersen, J. L., Finno, C. J., Bellone, R. R., McCue, M. E., Brooks, S. A., Bailey, E., Orlando, L., Green, R. E., Miller, D. C., Antczak, D. F., MacLeod, J. N. (2018) Communications Biology, 1(1), 197.

    Communications BiologyPDF
• 2017
  • Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Murray, G. G. R., Soares, A. E. R., Novak, B. J., Schaefer, N. K., Cahill, J. A., Baker, A. J, Demboski, J. R., Doll, A., Fonseca, R. R. D., Fulton, T. L., Gilbert, M. T. P., Heintzman, P. D., Letts, B., McIntosh, G., O'Connell, B., Peck, M., Pipes, M., Rice, E. S., Santos, K. M., Sohrweide, A. G., Vohr, S. H., Corbett-Detig, R. B., Green, R. E., & Shapiro, B. (2017) Science, 358(6365), 951-954.
    SciencePDF
  • Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Rice, E. S., Kohno, S., St. John, J., Pham, S., Howard, J., Lareau, L. F., O'Connell, B. L., Hickey, G., Armstrong, J., Deran, A., Fiddes, I., Platt, R. N. II, Gresham, C., McCarthy, F., Kern, C., Haan, D., Phan, T., Schmidt, C., Sanford, J. R., Ray, D. A., Paten, B., Guillette, L. J. Jr., & Green, R.E. (2017). Genome Research, 27(5), 686-696.

    Genome ResearchPDF
• earlier
  • A 4,103 marker integrated physical and comparative map of the horse genome. Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M. L., Goh, G., Seabury, C. M., Brinkmeyer-Langford, C., Lee, E. J., Agarwala, R., Rice, E. S., Schäffer, A. A., Skow, L. C., Tozaki, T., Yasue, H., Penedo, M. C., Lyons, L. A., Khazanehdari, K. A., Binns, M. M., MacLeod, J. N., Distl, O., Guérin, G., Leeb, T., Mickelson, J. R., & Chowdhary, B. P. (2008). Cytogenetic and Genome Research, 122(1), 28-36.
    Cytogenetic and Genome ResearchPDF
  • rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Schäffer, A. A., Rice, E. S., Cook, W., & Agarwala, R. (2007). Bioinformatics, 23(9), 1156-1158.
    BioinformaticsPDF