Edward Stallknecht Rice

I am a computational biologist living in Munich. I use bioinformatics to study evolutionary, molecular, and organismal biology.

• Curriculum Vitae
• Google Scholar

Here are links to my publications:

• 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. (in review). bioRxiv, 2023.11.16.567450.
  [Preprint]
• A novel 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. (in review). bioRxiv, 2022.11.17.516921.
  [bioRxiv]
• 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, in press.
  [Preprint]
• 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 Genetics][pdf]
• 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, in press.
  [ 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 Research][pdf]
• 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 Reports][pdf]
• 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.
  [Cells][pdf]
• 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 Genomics][pdf]
• 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 Communications][pdf]
• 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.
  [Science][pdf]
• 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]
• 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.
  [GigaScience][pdf]
• New approaches for genome assembly and scaffolding
  Rice, E. S. & Green, R. E. (2019) Annual Review of Animal Biosciences, 7, 17-40.
  [Annual Reviews] [pdf]
• 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.
  † these authors contributed equally to this work
  [Communications Biology][pdf]
• 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.
  [Science] [pdf]
• 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 Research] [pdf]
• 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 Research] [pdf]
• 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.
  [Bioinformatics] [pdf]