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19992022

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  • 2013

    Ancient eudicot hexaploidy meets ancestral eurosid gene order

    Zheng, C., Chen, E., Albert, V. A., Lyons, E. & Sankoff, D., 2013, In: BMC genomics. 14, S3.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    10 Scopus citations
  • Ancient eudicot hexaploidy meets ancestral eurosid gene order.

    Zheng, C., Chen, E., Albert, V. A., Lyons, E. & Sankoff, D., 2013, In: BMC genomics. 14 Suppl 7

    Research output: Contribution to journalArticlepeer-review

    10 Scopus citations
  • Architecture and evolution of a minute plant genome

    Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G., Pérez-Torres, C. A., Carretero-Paulet, L., Chang, T. H., Lan, T., Welch, A. J., Juárez, M. J. A., Simpson, J., Fernández-Cortés, A., Arteaga-Vázquez, M., Góngora-Castillo, E., Acevedo-Hernández, G., Schuster, S. C., Himmelbauer, H., Minoche, A. E., Xu, S., Lynch, M., Oropeza-Aburto, A., & 9 othersCervantes-Pérez, S. A., De Jesús Ortega-Estrada, M., Cervantes-Luevano, J. I., Michael, T. P., Mockler, T., Bryant, D., Herrera-Estrella, A., Albert, V. A. & Herrera-Estrella, L., 2013, In: Nature. 498, 7452, p. 94-98 5 p.

    Research output: Contribution to journalArticlepeer-review

    219 Scopus citations
  • From data to function: Functional modeling of poultry genomics data

    McCarthy, F. M. & Lyons, E., Aug 2013, In: Poultry science. 92, 9, p. 2519-2529 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

    Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J., Bowers, J. E., Tang, H., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y., & 51 othersDer, J. P., Zeng, F., Han, J., Min, X. J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M. J., Xiong, W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., William Schopf, J., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. & Shen-Miller, J., May 10 2013, In: Genome biology. 14, 5, R41.

    Research output: Contribution to journalArticlepeer-review

    253 Scopus citations
  • The Amborella genome and the evolution of flowering plants

    DePamphilis, C. W., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Ammiraju, J. S. S., Barbazuk, W. B., Chamala, S., Chanderbali, A. S., Determann, R., Hong, M., Ralph, P., Talag, J., Tomsho, L., Walts, B., Wanke, S., Wing, R. A., Chang, T. H., Lan, T., Soltis, D. E., & 57 othersArikit, S., Axtell, M. J., Ayyampalayam, S., Burnette, J. M., De Paoli, E., Farrell, N. P., Harkess, A., Jiao, Y., Leebens-Mack, J., Liu, K., Mei, W., Meyers, B. C., Shahid, S., Wafula, E., Wessler, S. R., Zhai, J., Zhang, X., Albert, V. A., Carretero-Paulet, L., Lyons, E., Tang, H., Zheng, C., Altman, N. S., Chen, F., Chen, J. Q., Chiang, V., Der, J. P., Fogliani, B., Guo, C., Harholt, J., Job, C., Job, D., Kim, S., Kong, H., Li, G., Li, N., Liu, J., Park, J., Qi, X., Rajjou, L., Burtet-Sarramegna, V., Sederoff, R., Sun, Y. H., Ulvskov, P., Villegente, M., Xue, J. Y., Yeh, T. F., Yu, X., Acosta, J. J., Bruenn, R. A., De Kochko, A., Herrera-Estrella, L. R., Ibarra-Laclette, E., Kirst, M., Pissis, S. P., Poncet, V. & Soltis, P. S., 2013, In: Science. 342, 6165, 1241089.

    Research output: Contribution to journalArticlepeer-review

    551 Scopus citations
  • The dynamics of functional classes of plant genes in rediploidized ancient polyploids.

    Chen, E. C. H., Buen Abad Najar, C., Zheng, C., Brandts, A., Lyons, E., Tang, H., Carretero-Paulet, L., Albert, V. A. & Sankoff, D., 2013, In: BMC bioinformatics. 14 Suppl 15, p. S19 S19.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    11 Scopus citations
  • Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family

    Hofberger, J. A., Lyons, E., Edger, P. P., Chris Pires, J. & Eric Schranz, M., Nov 2013, In: Genome biology and evolution. 5, 11, p. 2155-2173 19 p.

    Research output: Contribution to journalArticlepeer-review

    67 Scopus citations
  • 2012

    Genome-wide analysis of syntenic gene deletion in the grasses

    Schnable, J. C., Freeling, M. & Lyons, E., Jan 1 2012, In: Genome biology and evolution. 4, 3, p. 265-277 13 p.

    Research output: Contribution to journalArticlepeer-review

    105 Scopus citations
  • Long identical multispecies elements in plant and animal genomes

    Reneker, J., Lyons, E., Conant, G. C., Pires, J. C., Freeling, M., Shyu, C. R. & Korkin, D., May 8 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 19, p. E1183-E1191

    Research output: Contribution to journalArticlepeer-review

    Open Access
    35 Scopus citations
  • The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

    D'hont, A., Denoeud, F., Aury, J. M., Baurens, F. C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., Alberti, A., & 44 othersBernard, M., Correa, M., Ayyampalayam, S., Mckain, M. R., Leebens-Mack, J., Burgess, D., Freeling, M., Mbéguié-A-Mbéguié, D., Chabannes, M., Wicker, T., Panaud, O., Barbosa, J., Hribova, E., Heslop-Harrison, P., Habas, R., Rivallan, R., Francois, P., Poiron, C., Kilian, A., Burthia, D., Jenny, C., Bakry, F., Brown, S., Guignon, V., Kema, G., Dita, M., Waalwijk, C., Joseph, S., Dievart, A., Jaillon, O., Leclercq, J., Argout, X., Lyons, E., Almeida, A., Jeridi, M., Dolezel, J., Roux, N., Risterucci, A. M., Weissenbach, J., Ruiz, M., Glaszmann, J. C., Quétier, F., Yahiaoui, N. & Wincker, P., Aug 9 2012, In: Nature. 488, 7410, p. 213-217 5 p.

    Research output: Contribution to journalArticlepeer-review

    752 Scopus citations
  • Unleashing the genome of Brassica rapa

    Tang, H. & Lyons, E., Jul 31 2012, In: Frontiers in Plant Science. 3, JUL, 172.

    Research output: Contribution to journalArticlepeer-review

    36 Scopus citations
  • 2011

    Screening synteny blocks in pairwise genome comparisons through integer programming

    Tang, H., Lyons, E., Pedersen, B., Schnable, J. C., Paterson, A. H. & Freeling, M., Apr 18 2011, In: BMC bioinformatics. 12, 102.

    Research output: Contribution to journalArticlepeer-review

    84 Scopus citations
  • The iPlant collaborative: Cyberinfrastructure for plant biology

    Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U. K. K., & 45 othersGonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B. S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S. M., Cranston, K. A., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L. & Stanzione, D., Jul 25 2011, In: Frontiers in Plant Science. 2, JUL, 34.

    Research output: Contribution to journalArticlepeer-review

    320 Scopus citations
  • The selaginella genome identifies genetic changes associated with the evolution of vascular plants

    Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., DePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Correa, L. G. G., Dacre, M., & 83 othersDeBarry, J., Dreyer, I., Elias, M., Engstrom, E. M., Estelle, M., Feng, L., Finet, C., Floyd, S. K., Frommer, W. B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K. G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T. P., Mikami, K., Miyazaki, S., Morinaga, S. I., TakashiMurata, Mueller-Roeber, B., Nelson, D. R., Obara, M., Oguri, Y., Olmstead, R. G., Onodera, N., Petersen, B. L., Pils, B., Prigge, M., Rensing, S. A., Riaño-Pachón, D. M., Roberts, A. W., Sato, Y., Scheller, H. V., Schulz, B., Schulz, C., Shakirov, E. V., Shibagaki, N., Shinohara, N., Shippen, D. E., Sørensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theißen, G., Ulvskov, P., Wakazuki, S., Weng, J. K., Willats, W. W. G. T., Wipf, D., Wolf, P. G., Yang, L., Zimmer, A. D., Zhu, Q., Mitros, T., Hellsten, U., Loqué, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D. & Grigoriev, I. V., May 20 2011, In: Science. 332, 6032, p. 960-963 4 p.

    Research output: Contribution to journalArticlepeer-review

    614 Scopus citations
  • Using genomic sequencing for classical genetics in E. coli K12

    Lyons, E., Freeling, M., Kustu, S. & Inwood, W., 2011, In: PloS one. 6, 2, e16717.

    Research output: Contribution to journalArticlepeer-review

    37 Scopus citations
  • 2010

    Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs

    Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S. & Freeling, M., Jun 2010, In: PLoS biology. 8, 6

    Research output: Contribution to journalArticlepeer-review

    192 Scopus citations
  • The evolution of a high copy gene array in arabidopsis

    Kane, J., Freeling, M. & Lyons, E., Jun 2010, In: Journal of Molecular Evolution. 70, 6, p. 531-544 14 p.

    Research output: Contribution to journalArticlepeer-review

    9 Scopus citations
  • 2009

    The Sorghum bicolor genome and the diversification of grasses

    Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., Grigoriev, I. V., & 25 othersLyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Mehboob-Ur-Rahman, Ware, D., Westhoff, P., Mayer, K. F. X., Messing, J. & Rokhsar, D. S., Jan 29 2009, In: Nature. 457, 7229, p. 551-556 6 p.

    Research output: Contribution to journalArticlepeer-review

    2122 Scopus citations
  • 2008

    Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids

    Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D. & Freeling, M., Dec 2008, In: Plant physiology. 148, 4, p. 1772-1781 10 p.

    Research output: Contribution to journalArticlepeer-review

    276 Scopus citations
  • How to usefully compare homologous plant genes and chromosomes as DNA sequences

    Lyons, E. & Freeling, M., Feb 2008, In: Plant Journal. 53, 4, p. 661-673 13 p.

    Research output: Contribution to journalArticlepeer-review

    307 Scopus citations
  • Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

    Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R. & Lisch, D., Dec 2008, In: Genome Research. 18, 12, p. 1924-1937 14 p.

    Research output: Contribution to journalArticlepeer-review

    131 Scopus citations
  • The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

    Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., & 65 othersTong, E., Tang, H., Lyons, E., Paull, R. E., Michael, T. P., Wall, K., Rice, D. W., Albert, H., Wang, M. L., Zhu, Y. J., Schatz, M., Nagarajan, N., Acob, R. A., Guan, P., Blas, A., Wai, C. M., Ackerman, C. M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J. K., Shakirov, E. V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J. E., Gschwend, A. R., Delcher, A. L., Singh, R., Suzuki, J. Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M. J., Feltus, F. A., Porter, B., Li, Y., Burroughs, A. M., Luo, M. C., Liu, L., Christopher, D. A., Mount, S. M., Moore, P. H., Sugimura, T., Jiang, J., Schuler, M. A., Friedman, V., Mitchell-Olds, T., Shippen, D. E., Depamphilis, C. W., Palmer, J. D., Freeling, M., Paterson, A. H., Gonsalves, D., Wang, L. & Alam, M., Apr 24 2008, In: Nature. 452, 7190, p. 991-996 6 p.

    Research output: Contribution to journalArticlepeer-review

    781 Scopus citations
  • 2007

    Arabidopsis intragenomic conserved noncoding sequence

    Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B. & Freeling, M., Feb 27 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 9, p. 3348-3353 6 p.

    Research output: Contribution to journalArticlepeer-review

    45 Scopus citations
  • G-boxes, bigfoot genes, and environmental response: Characterization of intragenomic conserved noncoding sequences in Arabidopsis

    Freeling, M., Rapaka, L., Lyons, E., Pedersen, B. & Thomas, B. C., May 2007, In: Plant Cell. 19, 5, p. 1441-1457 17 p.

    Research output: Contribution to journalArticlepeer-review

    38 Scopus citations
  • 2005

    Differential inhibition of inducible T cell cytokine secretion by potent iron chelators

    Leung, S., Holbrook, A., King, B., Lu, H. T., Evans, V., Miyamoto, N., Mallari, C., Harvey, S., Davey, D., Ho, E., Li, W. W., Parkinson, J., Horuk, R., Jaroch, S., Berger, M., Skuballa, W., West, C., Pulk, R., Phillips, G., Bryant, J., & 9 othersSubramanyam, B., Schaefer, C., Salamon, H., Lyons, E., Schilling, D., Seidel, H., Kraetzschmar, J., Snider, M. & Perez, D., Mar 2005, In: Journal of Biomolecular Screening. 10, 2, p. 157-167 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    21 Scopus citations
  • 2003

    Culture-independent molecular analysis of microbial constituents of the healthy human outer ear

    Frank, D. N., Spiegelman, G. B., Davis, W., Wagner, E., Lyons, E. & Pace, N. R., Jan 1 2003, In: Journal of clinical microbiology. 41, 1, p. 295-303 9 p.

    Research output: Contribution to journalArticlepeer-review

    84 Scopus citations
  • 1999

    Multiple nucleocapsid packaging of Autographa californica nucleopolyhedrovirus accelerates the onset of systemic infection in Trichoplusia ni

    Washburn, J. O., Lyons, E. H., Haas-Stapleton, E. J. & Volkman, L. E., 1999, In: Journal of virology. 73, 1, p. 411-416 6 p.

    Research output: Contribution to journalArticlepeer-review

    52 Scopus citations