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Tina Lindsay

Instructor in Genetics

    • 29618
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    19982022

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    • 2022

      Familial long-read sequencing increases yield of de novo mutations

      Noyes, M. D., Harvey, W. T., Porubsky, D., Sulovari, A., Li, R., Rose, N. R., Audano, P. A., Munson, K. M., Lewis, A. P., Hoekzema, K., Mantere, T., Graves-Lindsay, T. A., Sanders, A. D., Goodwin, S., Kramer, M., Mokrab, Y., Zody, M. C., Hoischen, A., Korbel, J. O., McCombie, W. R., & 1 othersEichler, E. E., Apr 7 2022, In: American journal of human genetics. 109, 4, p. 631-646 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      7 Scopus citations

    • Semi-automated assembly of high-quality diploid human reference genomes

      Human Pangenome Reference Consortium, Nov 17 2022, In: Nature. 611, 7936, p. 519-531 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      20 Scopus citations

    • The complete sequence of a human genome

      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., Caldas, G. V., & 80 othersChen, N. C., Cheng, H., Chin, C. S., Chow, W., de Lima, L. G., Dishuck, P. C., Durbin, R., Dvorkina, T., Fiddes, I. T., Formenti, G., Fulton, R. S., Fungtammasan, A., Garrison, E., Grady, P. G. S., Graves-Lindsay, T. A., Hall, I. M., Hansen, N. F., Hartley, G. A., Haukness, M., Howe, K., Hunkapiller, M. W., Jain, C., Jain, M., Jarvis, E. D., Kerpedjiev, P., Kirsche, M., Kolmogorov, M., Korlach, J., Kremitzki, M., Li, H., Maduro, V. V., Marschall, T., McCartney, A. M., McDaniel, J., Miller, D. E., Mullikin, J. C., Myers, E. W., Olson, N. D., Paten, B., Peluso, P., Pevzner, P. A., Porubsky, D., Potapova, T., Rogaev, E. I., Rosenfeld, J. A., Salzberg, S. L., Schneider, V. A., Sedlazeck, F. J., Shafin, K., Shew, C. J., Shumate, A., Sims, Y., Smit, A. F. A., Soto, D. C., Sovi, I., Storer, J. M., Streets, A., Sullivan, B. A., Thibaud-Nissen, F., Torrance, J., Wagner, J., Walenz, B. P., Wenger, A., Wood, J. M. D., Xiao, C., Yan, S. M., Young, A. C., Zarate, S., Surti, U., McCoy, R. C., Dennis, M. Y., Alexandrov, I. A., Gerton, J. L., O'Neill, R. J., Timp, W., Zook, J. M., Schatz, M. C., Eichler, E. E., Miga, K. H. & Phillippy, A. M., Apr 1 2022, In: Science. 376, 6588, p. 44-53 10 p.

      Research output: Contribution to journal › Article › peer-review

      372 Scopus citations
    • 2021

      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. D., 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. T. M., Moran, R. L., Peuß, R., & 8 othersRice, E. S., Riddle, M. R., Sifuentes-Romero, I., Stanhope, B. A., Tabin, C. J., Thakur, S., Yamamoto, Y. & Rohner, N., Dec 1 2021, In: Nature communications. 12, 1, 1447.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      32 Scopus citations

    • The structure, function and evolution of a complete human chromosome 8

      Logsdon, G. A., Vollger, M. R., Hsieh, P. H., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., de Lima, L. G., Dvorkina, T., Porubsky, D., Harvey, W. T., Mikheenko, A., Bzikadze, A. V., Kremitzki, M., Graves-Lindsay, T. A., Jain, C., Hoekzema, K., & 12 othersMurali, S. C., Munson, K. M., Baker, C., Sorensen, M., Lewis, A. M., Surti, U., Gerton, J. L., Larionov, V., Ventura, M., Miga, K. H., Phillippy, A. M. & Eichler, E. E., May 6 2021, In: Nature. 593, 7857, p. 101-107 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      106 Scopus citations
    • 2020

      A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

      Buckley, R. M., Davis, B. W., Brashear, W. A., Farias, F. H. G., Kuroki, K., Graves, T., Hillier, L. D. W., Kremitzki, M., Li, G., Middleton, R. P., Minx, P., Tomlinson, C., Lyons, L. A., Murphy, W. J. & Warren, W. C., Oct 22 2020, In: PLoS genetics. 16, 10, e1008926.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      44 Scopus citations

    • Precise breakpoint detection in a patient with 9p– syndrome

      Ng, J., Sams, E., Baldridge, D., Kremitzki, M., Wegner, D. J., Lindsay, T., Fulton, R., Cole, F. S. & Turner, T. N., Feb 2020, In: Cold Spring Harbor molecular case studies. 6, 3, a005348.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations

    • Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

      Hughes, J. F., Skaletsky, H., Pyntikova, T., Koutseva, N., Raudsepp, T., Brown, L. G., Bellott, D. W., Cho, T. J., Dugan-Rocha, S., Khan, Z., Kremitzki, C., Fronick, C., Graves-Lindsay, T. A., Fulton, L., Warren, W. C., Wilson, R. K., Owens, E., Womack, J. E., Murphy, W. J., Muzny, D. M., & 4 othersWorley, K. C., Chowdhary, B. P., Gibbs, R. A. & Page, D. C., Nov 18 2020, In: Genome research. 31, 12, p. 1716-1726 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      17 Scopus citations

    • Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

      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. D. W., Porubsky, D., Mao, Y., Gordon, D., Vollger, M. R., Lewis, A. P., Munson, K. M., Devogelaere, E., Armstrong, J., Diekhans, M., Walker, J. A., & 40 othersTomlinson, C., Graves-Lindsay, T. A., Kremitzki, M., Salama, S. R., Audano, P. A., Escalona9, M., Maurer, N. W., Antonacci, F., Mercuri, L., Maggiolini, F. A. M., Catacchio, C. R., Underwood, J. G., O'Connor, D. H., Sanders, A. D., Korbel, J. O., Ferguson, B., Kubisch, H. M., Picker, L., Kalin, N. H., Rosene, D., Levine, J., Abbott, D. H., Gray25, S. B., Sanchez, M. M., Kovacs-Balint, Z. A., Kemnitz, J. W., Thomasy, S. M., Roberts, J. A., Kinnally, E. L., Capitanio, J. P., Skene, J. H. P., Platt, M., Cole, S. A., Green, R. E., Ventura, M., Wiseman, R. W., Paten, B., Batzer, M. A., Rogers, J. & Eichler, E. E., Dec 18 2020, In: Science. 370, 6523, eabc6617.

      Research output: Contribution to journal › Article › peer-review

      43 Scopus citations

    • Telomere-to-telomere assembly of a complete human X chromosome

      Miga, K. H., Koren, S., Rhie, A., Vollger, M. R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G. A., Schneider, V. A., Potapova, T., Wood, J., Chow, W., Armstrong, J., Fredrickson, J., Pak, E., Tigyi, K., Kremitzki, M., Markovic, C., & 33 othersMaduro, V., Dutra, A., Bouffard, G. G., Chang, A. M., Hansen, N. F., Wilfert, A. B., Thibaud-Nissen, F., Schmitt, A. D., Belton, J. M., Selvaraj, S., Dennis, M. Y., Soto, D. C., Sahasrabudhe, R., Kaya, G., Quick, J., Loman, N. J., Holmes, N., Loose, M., Surti, U., Risques, R. A., Graves Lindsay, T. A., Fulton, R., Hall, I., Paten, B., Howe, K., Timp, W., Young, A., Mullikin, J. C., Pevzner, P. A., Gerton, J. L., Sullivan, B. A., Eichler, E. E. & Phillippy, A. M., Sep 3 2020, In: Nature. 585, 7823, p. 79-84 6 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      312 Scopus citations
    • 2019

      Characterizing the Major Structural Variant Alleles of the Human Genome

      Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. M. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., Warren, W. C., Magrini, V., McGrath, S. D., Li, Y. I., Wilson, R. K. & Eichler, E. E., Jan 24 2019, In: Cell. 176, 3, p. 663-675.e19

      Research output: Contribution to journal › Article › peer-review

      Open Access
      225 Scopus citations

    • Long-read sequence and assembly of segmental duplications

      Vollger, M. R., Dishuck, P. C., Sorensen, M., Welch, A. M. E., Dang, V., Dougherty, M. L., Graves-Lindsay, T. A., Wilson, R. K., Chaisson, M. J. P. & Eichler, E. E., Jan 1 2019, In: Nature Methods. 16, 1, p. 88-94 7 p.

      Research output: Contribution to journal › Article › peer-review

      70 Scopus citations
    • 2018

      High-resolution comparative analysis of great ape genomes

      Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., Munson, K. M., Hastie, A. R., Diekhans, M., Hormozdiari, F., Lorusso, N., Hoekzema, K., Qiu, R., Clark, K., Raja, A., Welch, A. M. E., & 24 othersSorensen, M., Baker, C., Fulton, R. S., Armstrong, J., Graves-Lindsay, T. A., Denli, A. M., Hoppe, E. R., Hsieh, P. H., Hill, C. M., Pang, A. W. C., Lee, J., Lam, E. T., Dutcher, S. K., Gage, F. H., Warren, W. C., Shendure, J., Haussler, D., Schneider, V. A., Cao, H., Ventura, M., Wilson, R. K., Paten, B., Pollen, A. & Eichler, E. E., Jun 8 2018, In: Science. 360, 6393, eaar6343.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      181 Scopus citations

    • Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family

      Cantsilieris, S., Nelson, B. J., Huddleston, J., Baker, C., Harshman, L., Penewit, K., Munson, K. M., Sorensen, M., Welch, A. M. E., Dang, V., Grassmann, F., Richardson, A. J., Guymer, R. H., Graves-Lindsay, T. A., Wilson, R. K., Weber, B. H. F., Baird, P. N., Allikmets, R. & Eichler, E. E., May 8 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 19, p. E4433-E4442

      Research output: Contribution to journal › Article › peer-review

      Open Access
      32 Scopus citations
    • 2017

      A new chicken genome assembly provides insight into avian genome structure

      Warren, W. C., Hillier, L. D. W., Tomlinson, C., Minx, P., Kremitzki, M., Graves, T., Markovic, C., Bouk, N., Pruitt, K. D., Thibaud-Nissen, F., Schneider, V., Mansour, T. A., Brown, C. T., Zimin, A., Hawken, R., Abrahamsen, M., Pyrkosz, A. B., Morisson, M., Fillon, V., Vignal, A., & 12 othersChow, W., Howe, K., Fulton, J. E., Miller, M. M., Lovell, P., Mello, C. V., Wirthlin, M., Mason, A. S., Kuo, R., Burt, D. W., Dodgson, J. B. & Cheng, H. H., 2017, In: G3: Genes, Genomes, Genetics. 7, 1, p. 109-117 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      146 Scopus citations

    • Avian W and mammalian y chromosomes convergently retained dosage-sensitive regulators

      Bellott, D. W., Skaletsky, H., Cho, T. J., Brown, L., Locke, D., Chen, N., Galkina, S., Pyntikova, T., Koutseva, N., Graves, T., Kremitzki, C., Warren, W. C., Clark, A. G., Gaginskaya, E., Wilson, R. K. & Page, D. C., Mar 1 2017, In: Nature Genetics. 49, 3, p. 387-394 8 p.

      Research output: Contribution to journal › Article › peer-review

      90 Scopus citations

    • Discovery and genotyping of structural variation from long-read haploid genome sequence data

      Huddleston, J., Chaisson, M. J. P., Steinberg, K. M., Warren, W., Hoekzema, K., Gordon, D., Graves-Lindsay, T. A., Munson, K. M., Kronenberg, Z. N., Vives, L., Peluso, P., Boitano, M., Chin, C. S., Korlach, J., Wilson, R. K. & Eichler, E. E., May 2017, In: Genome research. 27, 5, p. 677-685 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      202 Scopus citations

    • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

      Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H. C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., Fulton, R. S., Kremitzki, M., Magrini, V., Markovic, C., McGrath, S., Steinberg, K. M., Auger, K., Chow, W., Collins, J., Harden, G., & 18 othersHubbard, T., Pelan, S., Simpson, J. T., Threadgold, G., Torrance, J., Wood, J. M., Clarke, L., Koren, S., Boitano, M., Peluso, P., Li, H., Chin, C. S., Phillippy, A. M., Durbin, R., Wilson, R. K., Flicek, P., Eichler, E. E. & Church, D. M., May 2017, In: Genome research. 27, 5, p. 849-864 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      380 Scopus citations

    • The evolution and population diversity of human-specific segmental duplications

      Dennis, M. Y., Harshman, L., Nelson, B. J., Penn, O., Cantsilieris, S., Huddleston, J., Antonacci, F., Penewit, K., Denman, L., Raja, A., Baker, C., Mark, K., Malig, M., Janke, N., Espinoza, C., Stessman, H. A. F., Nuttle, X., Hoekzema, K., Lindsay-Graves, T. A., Wilson, R. K., & 1 othersEichler, E. E., Feb 17 2017, In: Nature Ecology and Evolution. 1, 3, 0069.

      Research output: Contribution to journal › Article › peer-review

      78 Scopus citations
    • 2016

      A genomic case study of mixed fibrolamellar hepatocellular carcinoma

      Griffith, O. L., M.Griffith, K.Krysiak, V.Magrini, A.Ramu, Z.L.Skidmore, J.Kunisaki, R.Austin, S.McGrath, J.Zhang, R.Demeter, T.Graves, J.M.Eldred, J.Walker, D.E.Larson, C.A.Maher, Y.Lin, W.Chapman, A.Mahadevan, R.Miksad, & 3 othersI.Nasser, D.W.Hanto & E.R.Mardis, Jun 18 2016, In: Annals of Oncology. 27, 6, p. 1148-1154 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      15 Scopus citations

    • Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

      Mohajeri, K., Cantsilieris, S., Huddleston, J., Nelson, B. J., Coe, B. P., Campbell, C. D., Baker, C., Harshman, L., Munson, K. M., Kronenberg, Z. N., Kremitzki, M., Raja, A., Catacchio, C. R., Graves, T. A., Wilson, R. K., Ventura, M. & Eichler, E. E., Nov 2016, In: Genome research. 26, 11, p. 1453-1467 15 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      25 Scopus citations
    • 2015

      Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

      Watson, C. T., Steinberg, K. M., Graves, T. A., Warren, R. L., Malig, M., Schein, J., Wilson, R. K., Holt, R. A., Eichler, E. E. & Breden, F., Jan 24 2015, In: Genes and Immunity. 16, 1, p. 24-34 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      25 Scopus citations

    • The genome of the vervet (Chlorocebus æthiops sabæus)

      Warren, W. C., Jasinska, A. J., García-Pérez, R., Svardal, H., Tomlinson, C., Rocchi, M., Archidiacono, N., Capozzi, O., Minx, P., Montague, M. J., Kyung, K., Hillier, L. D. W., Kremitzki, M., Graves, T., Chiang, C., Hughes, J., Tran, N., Huang, Y., Ramensky, V., Choi, O. W., & 38 othersJung, Y. J., Schmitt, C. A., Juretic, N., Wasserscheid, J., Turner, T. R., Wiseman, R. W., Tuscher, J. J., Karl, J. A., Schmitz, J. E., Zahn, R., O'Connor, D. H., Redmond, E., Nisbett, A., Jacquelin, B., Müller-Trutwin, M. C., Brenchley, J. M., Dione, M., Antonio, M., Schroth, G. P., Kaplan, J. R., Jorgensen, M. J., Thomas, G. W. C., Hahn, M. W., Raney, B. J., Aken, B., Nag, R., Schmitz, J., Churakov, G., Noll, A., Stanyon, R., Webb, D., Thibaud-Nissen, F., Nordborg, M., Marques-Bonet, T., Dewar, K., Weinstock, G. M., Wilson, R. K. & Freimer, N. B., Dec 2015, In: Genome research. 25, 12, p. 1921-1933 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      59 Scopus citations
    • 2014

      Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome

      O'Bleness, M., Searles, V. B., Dickens, C. M., Astling, D., Albracht, D., Mak, A. C. Y., Lai, Y. Y. Y., Lin, C., Chu, C., Graves, T., Kwok, P. Y., Wilson, R. K. & Sikela, J. M., May 20 2014, In: BMC genomics. 15, 1, 387.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      34 Scopus citations

    • Mammalian y chromosomes retain widely expressed dosage-sensitive regulators

      Bellott, D. W., Hughes, J. F., Skaletsky, H., Brown, L. G., Pyntikova, T., Cho, T. J., Koutseva, N., Zaghlul, S., Graves, T., Rock, S., Kremitzki, C., Fulton, R. S., Dugan, S., Ding, Y., Morton, D., Khan, Z., Lewis, L., Buhay, C., Wang, Q., Watt, J., & 9 othersHolder, M., Lee, S., Nazareth, L., Rozen, S., Muzny, D. M., Warren, W. C., Gibbs, R. A., Wilson, R. K. & Page, D. C., 2014, In: Nature. 508, 7497, p. 494-499 6 p.

      Research output: Contribution to journal › Article › peer-review

      406 Scopus citations

    • Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

      Antonacci, F., Dennis, M. Y., Huddleston, J., Sudmant, P. H., Steinberg, K. M., Rosenfeld, J. A., Miroballo, M., Graves, T. A., Vives, L., Malig, M., Denman, L., Raja, A., Stuart, A., Tang, J., Munson, B., Shaffer, L. G., Amemiya, C. T., Wilson, R. K. & Eichler, E. E., Dec 11 2014, In: Nature Genetics. 46, 12, p. 1293-1302 10 p.

      Research output: Contribution to journal › Article › peer-review

      73 Scopus citations

    • Reconstructing complex regions of genomes using long-read sequencing technology

      Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., Hon, L., Sudmant, P. H., Graves, T. A., Alkan, C., Dennis, M. Y., Wilson, R. K., Turner, S. W., Korlach, J. & Eichler, E. E., Apr 2014, In: Genome research. 24, 4, p. 688-696 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      181 Scopus citations

    • Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes

      Soh, Y. Q. S., Alföldi, J., Pyntikova, T., Brown, L. G., Graves, T., Minx, P. J., Fulton, R. S., Kremitzki, C., Koutseva, N., Mueller, J. L., Rozen, S., Hughes, J. F., Owens, E., Womack, J. E., Murphy, W. J., Cao, Q., De Jong, P., Warren, W. C., Wilson, R. K., Skaletsky, H., & 1 othersPage, D. C., Nov 6 2014, In: Cell. 159, 4, p. 800-813 14 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      203 Scopus citations

    • Single haplotype assembly of the human genome from a hydatidiform mole

      Steinberg, K. M., Schneider, V. A., Graves-Lindsay, T. A., Fulton, R. S., Agarwala, R., Huddleston, J., Shiryev, S. A., Morgulis, A., Surti, U., Warren, W. C., Church, D. M., Eichler, E. E. & Wilson, R. K., Dec 1 2014, In: Genome research. 24, 12, p. 2066-2076 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      83 Scopus citations

    • Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline

      Stong, N., Deng, Z., Gupta, R., Hu, S., Paul, S., Weiner, A. K., Eichler, E. E., Graves, T., Fronick, C. C., Courtney, L., Wilson, R. K., Lieberman, P. M., Davuluri, R. V. & Riethman, H., Jun 2014, In: Genome research. 24, 6, p. 1039-1050 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      47 Scopus citations

    • The common marmoset genome provides insight into primate biology and evolution

      Worley, K. C., Warren, W. C., Rogers, J., Locke, D., Muzny, D. M., Mardis, E. R., Weinstock, G. M., Tardif, S. D., Aagaard, K. M., Archidiacono, N., Arul Rayan, N., Batzer, M. A., Beal, K., Brejova, B., Capozzi, O., Capuano, S. B., Casola, C., Chandrabose, M. M., Cree, A., Diep Dao, M., & 91 othersDe Jong, P. J., Cruz-Herrera del Rosario, R., Delehaunty, K. D., Dinh, H. H., Eichler, E. E., Fitzgerald, S., Flicek, P., Fontenot, C. C., Fowler, R. G., Fronick, C., Fulton, L. A., Fulton, R. S., Gabisi, R. A., Gerlach, D., Graves, T. A., Gunaratne, P. H., Hahn, M. W., Haig, D., Han, Y., Harris, R. A., Herrero, J., Hillier, L. D. W., Hubley, R., Hughes, J. F., Hume, J., Jhangiani, S. N., Jorde, L. B., Joshi, V., Karakor, E., Konkel, M. K., Kosiol, C., LKovar, C., Kriventseva, E. V., Lee, S. L., Lewis, L. R., Liu, Y. S., Lopez, J., Lopez-Otin, C., Lorente-Galdos, B., Mansfield, K. G., Marques-Bonet, T., Minx, P., Misceo, D., Moncrieff, J. S., Morgan, M. B., Nazareth, L. V., Newsham, I., Nguyen, N. B., Okwuonu, G. O., Prabhakar, S., Perales, L., Pu, L. L., Puente, X. S., Quesada, V., Ranck, M. C., Raney, B. J., Raveendran, M., Deiros, D. R., Rocchi, M., Rodriguez, D., Ross, C., Ruffier, M., Ruiz, S. J., Sajjadian, S., Santibanez, J., Schrider, D. R., Searle, S., Skaletsky, H., Soibam, B., Smit, A. F. A., Tennakoon, J. B., Tomaska, L., Ullmer, B., Vejnar, C. E., Ventura, M., Vilella, A. J., Vinar, T., Vogel, J. H., Walker, J. A., Wang, Q., Warner, C. M., Wildman, D. E., Witherspoon, D. J., Wright, R. A., Wu, Y., Xiao, W., Xing, J., Zdobnov, E. M., Zhu, B., Gibbs, R. A. & Wilson, R. K., Aug 2014, In: Nature Genetics. 46, 8, p. 850-857 8 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      170 Scopus citations
    • 2013

      Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation

      Watson, C. T., Steinberg, K. M., Huddleston, J., Warren, R. L., Malig, M., Schein, J., Willsey, A. J., Joy, J. B., Scott, J. K., Graves, T. A., Wilson, R. K., Holt, R. A., Eichler, E. E. & Breden, F., Apr 4 2013, In: American journal of human genetics. 92, 4, p. 530-546 17 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      157 Scopus citations

    • Genomic pathology of sle-associated copy-number variation at the FCGR2C/FCGR3B/FCGR2B locus

      Mueller, M., Barros, P., Witherden, A. S., Roberts, A. L., Zhang, Z., Schaschl, H., Yu, C. Y., Hurles, M. E., Schaffner, C., Floto, R. A., Game, L., Steinberg, K. M., Wilson, R. K., Graves, T. A., Eichler, E. E., Cook, H. T., Vyse, T. J. & Aitman, T. J., Jan 10 2013, In: American journal of human genetics. 92, 1, p. 28-40 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      47 Scopus citations

    • Independent specialization of the human and mouse X chromosomes for the male germ line

      Mueller, J. L., Skaletsky, H., Brown, L. G., Zaghlul, S., Rock, S., Graves, T., Auger, K., Warren, W. C., Wilson, R. K. & Page, D. C., Sep 2013, In: Nature Genetics. 45, 9, p. 1083-1087 5 p.

      Research output: Contribution to journal › Article › peer-review

      119 Scopus citations

    • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

      Bradley Shaffer, H., Minx, P., Warren, D. E., Shedlock, A. M., Thomson, R. C., Valenzuela, N., Abramyan, J., Amemiya, C. T., Badenhorst, D., Biggar, K. K., Borchert, G. M., Botka, C. W., Bowden, R. M., Braun, E. L., Bronikowski, A. M., Bruneau, B. G., Buck, L. T., Capel, B., Castoe, T. A., Czerwinski, M., & 39 othersDelehaunty, K. D., Edwards, S. V., Fronick, C. C., Fujita, M. K., Fulton, L., Graves, T. A., Green, R. E., Haerty, W., Hariharan, R., Hernandez, O., Hillier, L. D. W., Holloway, A. K., Janes, D., Janzen, F. J., Kandoth, C., Kong, L., de Koning, A. P. J., Li, Y., Literman, R., McGaugh, S. E., Mork, L., O'Laughlin, M., Paitz, R. T., Pollock, D. D., Ponting, C. P., Radhakrishnan, S., Raney, B. J., Richman, J. M., St John, J., Schwartz, T., Sethuraman, A., Spinks, P. Q., Storey, K. B., Thane, N., Vinar, T., Zimmerman, L. M., Warren, W. C., Mardis, E. R. & Wilson, R. K., Mar 28 2013, In: Genome biology. 14, 3, R28.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      234 Scopus citations
    • 2012

      Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication

      Dennis, M. Y., Nuttle, X., Sudmant, P. H., Antonacci, F., Graves, T. A., Nefedov, M., Rosenfeld, J. A., Sajjadian, S., Malig, M., Kotkiewicz, H., Curry, C. J., Shafer, S., Shaffer, L. G., De Jong, P. J., Wilson, R. K. & Eichler, E. E., May 11 2012, In: Cell. 149, 4, p. 912-922 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      170 Scopus citations

    • Insights into hominid evolution from the gorilla genome sequence

      Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, S. H., Schwalie, P. C., Tang, Y. A., Ward, M. C., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, L. N., Ayub, Q., & 51 othersBall, E. V., Beal, K., Bradley, B. J., Chen, Y., Clee, C. M., Fitzgerald, S., Graves, T. A., Gu, Y., Heath, P., Heger, A., Karakoc, E., Kolb-Kokocinski, A., Laird, G. K., Lunter, G., Meader, S., Mort, M., Mullikin, J. C., Munch, K., O'Connor, T. D., Phillips, A. D., Prado-Martinez, J., Rogers, A. S., Sajjadian, S., Schmidt, D., Shaw, K., Simpson, J. T., Stenson, P. D., Turner, D. J., Vigilant, L., Vilella, A. J., Whitener, W., Zhu, B., Cooper, D. N., De Jong, P., Dermitzakis, E. T., Eichler, E. E., Flicek, P., Goldman, N., Mundy, N. I., Ning, Z., Odom, D. T., Ponting, C. P., Quail, M. A., Ryder, O. A., Searle, S. M., Warren, W. C., Wilson, R. K., Schierup, M. H., Rogers, J., Tyler-Smith, C. & Durbin, R., Mar 8 2012, In: Nature. 483, 7388, p. 169-175 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      483 Scopus citations

    • Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing

      Itsara, A., Vissers, L. E. L. M., Steinberg, K. M., Meyer, K. J., Zody, M. C., Koolen, D. A., De Ligt, J., Cuppen, E., Baker, C., Lee, C., Graves, T. A., Wilson, R. K., Jenkins, R. B., Veltman, J. A. & Eichler, E. E., Apr 6 2012, In: American journal of human genetics. 90, 4, p. 599-613 15 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      19 Scopus citations

    • Strict evolutionary conservation followed rapid gene loss on human and rhesus y chromosomes

      Hughes, J. F., Skaletsky, H., Brown, L. G., Pyntikova, T., Graves, T., Fulton, R. S., Dugan, S., Ding, Y., Buhay, C. J., Kremitzki, C., Wang, Q., Shen, H., Holder, M., Villasana, D., Nazareth, L. V., Cree, A., Courtney, L., Veizer, J., Kotkiewicz, H., Cho, T. J., & 7 othersKoutseva, N., Rozen, S., Muzny, D. M., Warren, W. C., Gibbs, R. A., Wilson, R. K. & Page, D. C., Mar 1 2012, In: Nature. 483, 7387, p. 82-87 6 p.

      Research output: Contribution to journal › Article › peer-review

      181 Scopus citations

    • The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

      Ventura, M., Catacchio, C. R., Sajjadian, S., Vives, L., Sudmant, P. H., Marques-Bonet, T., Graves, T. A., Wilson, R. K. & Eichler, E. E., Jun 2012, In: Genome research. 22, 6, p. 1036-1049 14 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      25 Scopus citations
    • 2011

      A high-resolution map of human evolutionary constraint using 29 mammals

      Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Alföldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., & 66 othersDi Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, M. J., Jaffe, D. B., Jungreis, I., Kent, W. J., Kostka, D., Lara, M., Martins, A. L., Massingham, T., Moltke, I., Raney, B. J., Rasmussen, M. D., Robinson, J., Stark, A., Vilella, A. J., Wen, J., Xie, X., Zody, M. C., Worley, K. C., Kovar, C. L., Muzny, D. M., Gibbs, R. A., Warren, W. C., Mardis, E. R., Weinstock, G. M., Wilson, R. K., Birney, E., Margulies, E. H., Herrero, J., Green, E. D., Haussler, D., Siepel, A., Goldman, N., Pollard, K. S., Pedersen, J. S., Lander, E. S., Kellis, M., Baldwin, J., Bloom, T., Chin, C. W., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Cree, A., Dihn, H. H., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, L. R., Nazareth, L. V., Okwuonu, G., Santibanez, J., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P. & Sodergren, E., Oct 27 2011, In: Nature. 478, 7370, p. 476-482 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      354 Scopus citations

    • Comparative and demographic analysis of orang-utan genomes

      Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., Yang, S. P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., & 81 othersGraves, T. A., Markovic, C., Cree, A., Dinh, H. H., Hume, J., Kovar, C. L., Fowler, G. R., Lunter, G., Meader, S., Heger, A., Ponting, C. P., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J. M., Eichler, E. E., White, S., Searle, S., Vilella, A. J., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darré, F., Farré, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Valle, G. D., Purgato, S., Rocchi, M., Konkel, M. K., Walker, J. A., Ullmer, B., Batzer, M. A., Smit, A. F. A., Hubley, R., Casola, C., Schrider, D. R., Hahn, M. W., Quesada, V., Puente, X. S., Ordõez, G. R., Ĺpez-Otín, C., Vinar, T., Brejova, B., Ratan, A., Harris, R. S., Miller, W., Kosiol, C., Lawson, H. A., Taliwal, V., Martins, A. L., Siepel, A., Roychoudhury, A., Ma, X., Degenhardt, J., Bustamante, C. D., Gutenkunst, R. N., Mailund, T., Dutheil, J. Y., Hobolth, A., Schierup, M. H., Ryder, O. A., Yoshinaga, Y., De Jong, P. J., Weinstock, G. M., Rogers, J., Mardis, E. R., Gibbs, R. A. & Wilson, R. K., Jan 27 2011, In: Nature. 469, 7331, p. 529-533 5 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      381 Scopus citations

    • Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

      Ventura, M., Catacchio, C. R., Alkan, C., Marques-Bonet, T., Sajjadian, S., Graves, T. A., Hormozdiari, F., Navarro, A., Malig, M., Baker, C., Lee, C., Turner, E. H., Chen, L., Kidd, J. M., Archidiacono, N., Shendure, J., Wilson, R. K. & Eichler, E. E., Oct 2011, In: Genome research. 21, 10, p. 1640-1649 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      53 Scopus citations

    • Modernizing reference genome assemblies

      Church, D. M., Schneider, V. A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H. C., Agarwala, R., McLaren, W. M., Ritchie, G. R. S., Albracht, D., Kremitzki, M., Rock, S., Kotkiewicz, H., Kremitzki, C., Wollam, A., Trani, L., Fulton, L., Fulton, R., Matthews, L., & 19 othersWhitehead, S., Chow, W., Torrance, J., Dunn, M., Harden, G., Threadgold, G., Wood, J., Collins, J., Heath, P., Griffiths, G., Pelan, S., Grafham, D., Eichler, E. E., Weinstock, G., Mardis, E. R., Wilson, R. K., Howe, K., Flicek, P. & Hubbard, T., Jul 2011, In: PLoS biology. 9, 7, e1001091.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      294 Scopus citations
    • 2010

      A human genome structural variation sequencing resource reveals insights into mutational mechanisms

      Kidd, J. M., Graves, T., Newman, T. L., Fulton, R., Hayden, H. S., Malig, M., Kallicki, J., Kaul, R., Wilson, R. K. & Eichler, E. E., Nov 24 2010, In: Cell. 143, 5, p. 837-847 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      208 Scopus citations

    • A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

      Antonacci, F., Kidd, J. M., Marques-Bonet, T., Teague, B., Ventura, M., Girirajan, S., Alkan, C., Campbell, C. D., Vives, L., Malig, M., Rosenfeld, J. A., Ballif, B. C., Shaffer, L. G., Graves, T. A., Wilson, R. K., Schwartz, D. C. & Eichler, E. E., Sep 2010, In: Nature Genetics. 42, 9, p. 745-751 7 p.

      Research output: Contribution to journal › Article › peer-review

      32 Scopus citations

    • Characterization of missing human genome sequences and copy-number polymorphic insertions

      Kidd, J. M., Sampas, N., Antonacci, F., Graves, T., Fulton, R., Hayden, H. S., Alkan, C., Malig, M., Ventura, M., Giannuzzi, G., Kallicki, J., Anderson, P., Tsalenko, A., Yamada, N. A., Tsang, P., Kaul, R., Wilson, R. K., Bruhn, L. & Eichler, E. E., May 2010, In: Nature Methods. 7, 5, p. 365-371 7 p.

      Research output: Contribution to journal › Article › peer-review

      36 Scopus citations

    • Chimpanzee and human y chromosomes are remarkably divergent in structure and gene content

      Hughes, J. F., Skaletsky, H., Pyntikova, T., Graves, T. A., Van Daalen, S. K. M., Minx, P. J., Fulton, R. S., McGrath, S. D., Locke, D. P., Friedman, C., Trask, B. J., Mardis, E. R., Warren, W. C., Repping, S., Rozen, S., Wilson, R. K. & Page, D. C., Jan 28 2010, In: Nature. 463, 7280, p. 536-539 4 p.

      Research output: Contribution to journal › Article › peer-review

      276 Scopus citations

    • Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

      Bellott, D. W., Skaletsky, H., Pyntikova, T., Mardis, E. R., Graves, T., Kremitzki, C., Brown, L. G., Rozen, S., Warren, W. C., Wilson, R. K. & Page, D. C., Jul 29 2010, In: Nature. 466, 7306, p. 612-616 5 p.

      Research output: Contribution to journal › Article › peer-review

      82 Scopus citations

    • Gene duplication and fragmentation in the zebra finch major histocompatibility complex

      Balakrishnan, C. N., Ekblom, R., Völker, M., Westerdahl, H., Godinez, R., Kotkiewicz, H., Burt, D. W., Graves, T., Griffin, D. K., Warren, W. C. & Edwards, S. V., Apr 1 2010, In: BMC Biology. 8, 29.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      111 Scopus citations