Search results

  • 2009

    Recurring mutations found by sequencing an acute myeloid leukemia genome

    Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Locke, D. P., Magrini, V. J., Abbott, R. M., Vickery, T. L., Reed, J. S., Robinson, J. S., Wylie, T., Smith, S. M. & Carmichael, L. & 38 others, Eldred, J. M., Harris, C. C., Walker, J., Peck, J. B., Du, F., Dukes, A. F., Sanderson, G. E., Brummett, A. M., Clark, E., McMichael, J. F., Meyer, R. J., Schindler, J. K., Pohl, C. S., Wallis, J. W., Shi, X., Lin, L., Schmidt, H., Tang, Y., Haipek, C., Wiechert, M. E., Ivy, J. V., Kalicki, J., Elliott, G., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M. A., Baty, J., Heath, S., Shannon, W. D., Nagarajan, R., Link, D. C., Walter, M. J., Graubert, T. A., DiPersio, J. F., Wilson, R. K. & Ley, T. J., Sep 10 2009, In: New England Journal of Medicine. 361, 11, p. 1058-1066 9 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1898 Scopus citations
  • VarScan: Variant detection in massively parallel sequencing of individual and pooled samples

    Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K. & Ding, L., 2009, In: Bioinformatics. 25, 17, p. 2283-2285 3 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    979 Scopus citations
  • 2008

    DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

    Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D., Dunford-Shore, B. H., McGrath, S., Hickenbotham, M., Cook, L., Abbott, R., Larson, D. E., Koboldt, D. C., Pohl, C., Smith, S., Hawkins, A., Abbott, S., Locke, D. & Hillier, L. W. & 28 others, Miner, T., Fulton, L., Magrini, V., Wylie, T., Glasscock, J., Conyers, J., Sander, N., Shi, X., Osborne, J. R., Minx, P., Gordon, D., Chinwalla, A., Zhao, Y., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M., Baty, J., Ivanovich, J., Heath, S., Shannon, W. D., Nagarajan, R., Walter, M. J., Link, D. C., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., Nov 6 2008, In: Nature. 456, 7218, p. 66-72 7 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1054 Scopus citations
  • Genome analysis of the platypus reveals unique signatures of evolution

    Warren, W. C., Hillier, L. D. W., Marshall Graves, J. A., Birney, E., Ponting, C. P., Grützner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A. T., Yang, S. P., Heger, A., Locke, D. P., Miethke, P., Waters, P. D., Veyrunes, F., Fulton, L., Fulton, B., Graves, T. & Wallis, J. & 82 others, Puente, X. S., López-Otín, C., Ordóñez, G. R., Eichler, E. E., Chen, L., Cheng, Z., Deakin, J. E., Alsop, A., Thompson, K., Kirby, P., Papenfuss, A. T., Wakefield, M. J., Olender, T., Lancet, D., Huttley, G. A., Smit, A. F. A., Pask, A., Temple-Smith, P., Batzer, M. A., Walker, J. A., Konkel, M. K., Harris, R. S., Whittington, C. M., Wong, E. S. W., Gemmell, N. J., Buschiazzo, E., Vargas Jentzsch, I. M., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Ole Kriegs, J., Brosius, J., Murchison, E. P., Sachidanandam, R., Smith, C., Hannon, G. J., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lefèvre, C. M., Sharp, J. A., Nicholas, K. R., Ray, D. A., Kube, M., Reinhardt, R., Pringle, T. H., Taylor, J., Jones, R. C., Nixon, B., Dacheux, J. L., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, M. N., Pohl, C. S., Smith, S. M., Hou, S., Renfree, M. B., Mardis, E. R. & Wilson, R. K., May 8 2008, In: Nature. 453, 7192, p. 175-183 9 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    548 Scopus citations
  • Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183))

    Warren, W. C., Hillier, L. D. W., Marshall Graves, J. A., Birney, E., Ponting, C. P., Grützner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A. T., Yang, S. P., Heger, A., Locke, D. P., Miethke, P., Waters, P. D., Veyrunes, F., Fulton, L., Fulton, B., Graves, T. & Wallis, J. & 84 others, Puente, X. S., López-Otín, C., Ordó̃ez, G. R., Eichler, E. E., Chen, L., Cheng, Z., Deakin, J. E., Alsop, A., Thompson, K., Kirby, P., Papenfuss, A. T., Wakefield, M. J., Olender, T., Lancet, D., Huttley, G. A., Smit, A. F. A., Pask, A., Temple-Smith, P., Batzer, M. A., Walker, J. A., Konkel, M. K., Harris, R. S., Whittington, C. M., Wong, E. S. W., Gemmell, N. J., Buschiazzo, E., Vargas Jentzsch, I. M., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Kriegs, J. O., Brosius, J., Murchison, E. P., Sachidanandam, R., Smith, C., Hannon, G. J., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lefèvre, C. M., Sharp, J. A., Nicholas, K. R., Ray, D. A., Kube, M., Reinhardt, R., Pringle, T. H., Taylor, J., Jones, R. C., Nixon, B., Dacheux, J. L., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, M. N., Pohl, C. S., Smith, S. M., Hou, S., Nefedov, M., De Jong, P. J., Renfree, M. B., Mardis, E. R. & Wilson, R. K., Sep 2008, In: Nature. 455, 7210, p. 256 1 p.

    Research output: Contribution to journalComment/debate

    Open Access
    9 Scopus citations
  • NemaPath: Online exploration of KEGG-based metabolic pathways for nematodes

    Wylie, T., Martin, J., Abubucker, S., Yin, Y., Messina, D., Wang, Z., McCarter, J. P. & Mitreva, M., Nov 4 2008, In: BMC genomics. 9, 525.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    21 Scopus citations
  • Whole-genome sequencing and variant discovery in C. elegans

    Hillier, L. D. W., Marth, G. T., Quinlan, A. R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J. I., Hickenbotham, M., Huang, W., Magrini, V. J., Richt, R. J., Sander, S. N., Stewart, D. A., Stromberg, M., Tsung, E. F., Wylie, T., Schedl, T., Wilson, R. K. & Mardis, E. R., Feb 2008, In: Nature Methods. 5, 2, p. 183-188 6 p.

    Research output: Contribution to journalArticlepeer-review

    349 Scopus citations
  • 2007

    Evolutionary and biomedical insights from the rhesus macaque genome

    Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E. & Siepel, A. & 156 others, Sikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Li, Z., Liu, Y. S., Moore, S. M., Muzny, D., Nazareth, L. V., Dinh, N. N., Okwuonu, G. O., Pai, G., Parker, D., Paul, H. A., Pfannkoch, C., Pohl, C. S., Rogers, Y. H., Ruiz, S. J., Sabo, A., Santibanez, J., Schneider, B. W., Smith, S. M., Sodergren, E., Svatek, A. F., Utterback, T. R., Vattathil, S., Warren, W., White, C. S., Chinwalla, A. T., Feng, Y., Halpern, A. L., Hillier, L. D. W., Huang, X., Minx, P., Nelson, J. O., Pepin, K. H., Qin, X., Sutton, G. G., Venter, E., Walenz, B. P., Wallis, J. W., Worley, K. C., Yang, S. P., Jones, S. M., Marra, M. A., Rocchi, M., Schein, J. E., Baertsch, R., Clarke, L., Csürös, M., Glasscock, J., Harris, R. A., Havlak, P., Jackson, A. R., Jiang, H., Liu, Y., Messina, D. N., Shen, Y., Song, H. X. Z., Wylie, T., Zhang, L., Birney, E., Han, K., Konkel, M. K., Lee, J., Smit, A. F. A., Ullmer, B., Wang, H., Xing, J., Burhans, R., Cheng, Z., Karro, J. E., Ma, J., Raney, B., She, X., Cox, M. J., Demuth, J. P., Dumas, L. J., Han, S. G., Hopkins, J., Karimpour-Fard, A., Kim, Y. H., Pollack, J. R., Vinar, T., Addo-Quaye, C., Degenhardt, J., Denby, A., Hubisz, M. J., Indap, A., Kosiol, C., Lahn, B. T., Lawson, H. A., Marklein, A., Nielsen, R., Vallender, E. J., Clark, A. G., Ferguson, B., Hernandez, R. D., Hirani, K., Kehrer-Sawatzki, H., Kolb, J., Patil, S., Pu, L. L., Ren, Y., Smith, D. G., Wheeler, D. A., Schenck, I., Ball, E. V., Chen, R., Cooper, D. N., Giardine, B., Hsu, F., Kent, W. J., Lesk, A., Nelson, D. L., O'Brien, W. E., Prüfer, K., Stenson, P. D., Wallace, J. C., Ke, H., Liu, X. M., Wang, P., Xiang, A. P., Yang, F., Barber, G. P., Haussler, D., Karolchik, D., Kern, A. D., Kuhn, R. M., Smith, K. E. & Zwieg, A. S., Apr 13 2007, In: Science. 316, 5822, p. 222-234 13 p.

    Research output: Contribution to journalReview articlepeer-review

    1087 Scopus citations
  • 2006

    Codon usage patterns in Nematoda: Analysis based on over 25 million codons in thirty-two species

    Mitreva, M., Wendl, M. C., Martin, J., Wylie, T., Yin, Y., Larson, A., Parkinson, J., Waterston, R. H. & McCarter, J. P., Aug 14 2006, In: Genome biology. 7, 8, R75.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    52 Scopus citations
  • 2005

    Investigating hookworm genomes by comparative analysis of two Ancylostoma species

    Mitreva, M., McCarter, J. P., Arasu, P., Hawdon, J., Martin, J., Dante, M., Wylie, T., Xu, J., Stajich, J. E., Kapulkin, W., Clifton, S. W., Waterston, R. H. & Wilson, R. K., Apr 26 2005, In: BMC genomics. 6, 58.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    45 Scopus citations
  • 2004

    Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans

    Mitreva, M., McCarter, J. P., Martin, J., Dante, M., Wylie, T., Chiapelli, B., Pape, D., Clifton, S. W., Nutman, T. B. & Waterston, R. H., Feb 2004, In: Genome research. 14, 2, p. 209-220 12 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    81 Scopus citations
  • Gene discovery in the adenophorean nematode Trichinella spiralis: An analysis of transcription from three life cycle stages

    Mitreva, M., Jasmer, D. P., Appleton, J., Martin, J., Dante, M., Wylie, T., Clifton, S. W., Waterston, R. H. & McCarter, J. P., Oct 2004, In: Molecular and Biochemical Parasitology. 137, 2, p. 277-291 15 p.

    Research output: Contribution to journalArticlepeer-review

    54 Scopus citations
  • Nematode.net: A tool for navigating sequences from parasitic and free-living nematodes

    Wylie, T., Martin, J. C., Dante, M., Mitreva, M. D., Clifton, S. W., Chinwalla, A., Waterston, R. H., Wilson, R. K. & McCarter, J. P., Jan 1 2004, In: Nucleic acids research. 32, DATABASE ISS., p. D423-D426

    Research output: Contribution to journalArticlepeer-review

    76 Scopus citations
  • 2003

    Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.

    McCarter, J. P., Mitreva, M. D., Martin, J., Dante, M., Wylie, T., Rao, U., Pape, D., Bowers, Y., Theising, B., Murphy, C. V., Kloek, A. P., Chiapelli, B. J., Clifton, S. W., Bird, D. M. & Waterston, R. H., 2003, In: Genome biology. 4, 4, p. R26

    Research output: Contribution to journalArticlepeer-review

    135 Scopus citations
  • Gene discovery in the Apicomplexa as revealed by EST sequencing and assembly of a comparative gene database

    Li, L., Brunk, B. P., Kissinger, J. C., Pape, D., Tang, K., Cole, R. H., Martin, J., Wylie, T., Dante, M., Fogarty, S. J., Howe, D. K., Liberator, P., Diaz, C., Anderson, J., White, M., Jerome, M. E., Johnson, E. A., Radke, J. A., Stoeckert, C. J. & Waterston, R. H. & 3 others, Clifton, S. W., Roos, D. S. & Sibley, L. D., Mar 1 2003, In: Genome research. 13, 3, p. 443-454 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    132 Scopus citations
  • 2002

    A compilation of soybean ESTs: Generation and analysis

    Shoemaker, R., Keim, P., Vodkin, L., Retzel, E., Clifton, S. W., Waterston, R., Smoller, D., Coryell, V., Khanna, A., Erpelding, J., Gai, X., Brendel, V., Raph-Schmidt, C., Shoop, E. G., Vielweber, C. J., Schmatz, M., Pape, D., Bowers, Y., Theising, B. & Martin, J. & 3 others, Dante, M., Wylie, T. & Granger, C., 2002, In: Genome. 45, 2, p. 329-338 10 p.

    Research output: Contribution to journalArticlepeer-review

    111 Scopus citations
  • 2001

    A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: A resource for DNA microarrays and expression profiling

    Akopyants, N. S., Clifton, S. W., Martin, J., Pape, D., Wylie, T., Li, L., Kissinger, J. C., Roos, D. S. & Beverley, S. M., Apr 6 2001, In: Molecular and Biochemical Parasitology. 113, 2, p. 337-340 4 p.

    Research output: Contribution to journalArticlepeer-review

    39 Scopus citations
  • 1999

    An encyclopedia of mouse genes

    Marra, M., Hillier, L. D., Kucaba, T., Allen, M., Barstead, R., Beck, C., Blistain, A., Bonaldo, M., Bowers, Y., Bowles, L., Cardenas, M., Chamberlain, A., Chappell, J., Clifton, S., Favello, A., Geisel, S., Gibbons, M., Harvey, N., Hill, F. & Jackson, Y. & 22 others, Kohn, S., Lennon, G., Mardis, E., Martin, J., Mila, L. A., McCann, R., Morales, R., Pape, D., Person, B., Prange, C., Ritter, E., Soares, M., Schurk, R., Shin, T., Steptoe, M., Swaller, T., Theising, B., Underwood, K., Wylie, T., Yount, T., Wilson, R. & Waterston, R., Feb 1999, In: Nature Genetics. 21, 2, p. 191-194 4 p.

    Research output: Contribution to journalArticlepeer-review

    104 Scopus citations