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Todd Wylie

Associate Professor of Pediatrics

 https://orcid.org/0000-0001-8834-8404
    • 43929
      Citations
    19992024

    Research activity per year

    Search results

    • 2010

      Next-generation sequencing identifies the natural killer cell microRNA transcriptome

      Fehniger, T. A., Wylie, T., Germino, E., Leong, J. W., Magrini, V. J., Koul, S., Keppel, C. R., Schneider, S. E., Koboldt, D. C., Sullivan, R. P., Heinz, M. E., Crosby, S. D., Nagarajan, R., Ramsingh, G., Link, D. C., Ley, T. J. & Mardis, E. R., Nov 2010, In: Genome research. 20, 11, p. 1590-1604 15 p.

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

      Open Access
      124 Scopus citations
    • 2009

      Nematode.net update 2008: Improvements enabling more efficient data mining and comparative nematode genomics

      Martin, J., Abubucker, S., Wylie, T., Yin, Y., Wang, Z. & Mitreva, M., 2009, In: Nucleic acids research. 37, SUPPL. 1, p. D571-D578

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

      Open Access
      31 Scopus citations

    • 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 journal › Article › peer-review

      Open Access
      1944 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 journal › Article › peer-review

      Open Access
      1030 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 journal › Article › peer-review

      Open Access
      1070 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 journal › Article › peer-review

      Open Access
      559 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 journal › Comment/debate

      Open Access
      11 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 journal › Article › peer-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 journal › Article › peer-review

      346 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 journal › Review article › peer-review

      1121 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 journal › Article › peer-review

      Open Access
      58 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 journal › Article › peer-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 journal › Review article › peer-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 journal › Article › peer-review

      55 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 journal › Article › peer-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 journal › Article › peer-review

      139 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 journal › Article › peer-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 journal › Article › peer-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 journal › Article › peer-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 journal › Article › peer-review

      104 Scopus citations