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19992022

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  • Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived

    Hao, Y., Washburn, J. D., Rosenthal, J., Nielsen, B., Lyons, E., Edger, P. P., Pires, J. C. & Conant, G. C., Mar 1 2018, In: Genome biology and evolution. 10, 3, p. 999-1011 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    8 Scopus citations
  • Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

    Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R. K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S. K., Wang, H., Jiang, Y., Couderc, M., Katta, M. A. V. S. K., & 45 othersPaudel, D. R., Mungra, K. D., Chen, W., Harris-Shultz, K. R., Garg, V., Desai, N., Doddamani, D., Kane, N. A., Conner, J. A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O. P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H. D., Cubry, P., Rhoné, B., Gueye, M. C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R. S., Singh, B., Yadav, R. S., Lyons, E., Datta, S. K., Tom Hash, C., Devos, K. M., Buckler, E., Bennetzen, J. L., Paterson, A. H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T., Weckwerth, W., Reif, J. C., Liu, X., Vigouroux, Y. & Xu, X., Oct 1 2017, In: Nature biotechnology. 35, 10, p. 969-976 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    191 Scopus citations
  • Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

    Henkhaus, N., Bartlett, M., Gang, D., Grumet, R., Jordon-Thaden, I., Lorence, A., Lyons, E., Miller, S., Murray, S., Nelson, A., Specht, C., Tyler, B., Wentworth, T., Ackerly, D., Baltensperger, D., Benfey, P., Birchler, J., Chellamma, S., Crowder, R., Donoghue, M., & 24 othersDundore-Arias, J. P., Fletcher, J., Fraser, V., Gillespie, K., Guralnick, L., Haswell, E., Hunter, M., Kaeppler, S., Kepinski, S., Li, F. W., Mackenzie, S., McDade, L., Min, Y., Nemhauser, J., Pearson, B., Petracek, P., Rogers, K., Sakai, A., Sickler, D., Taylor, C., Wayne, L., Wendroth, O., Zapata, F. & Stern, D., Aug 1 2020, In: Plant Direct. 4, 8, e00252.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    16 Scopus citations
  • Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

    Emery, M., Willis, M. M. S., Hao, Y., Barry, K., Oakgrove, K., Peng, Y., Schmutz, J., Lyons, E., Pires, J. C., Edger, P. P. & Conant, G. C., Mar 2018, In: PLoS genetics. 14, 3, e1007267.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    31 Scopus citations
  • Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data

    Peri, S., Roberts, S., Kreko, I. R., McHan, L. B., Naron, A., Ram, A., Murphy, R. L., Lyons, E., Gregory, B. D., Devisetty, U. K. & Nelson, A. D. L., Jan 24 2020, In: Frontiers in Genetics. 10, 1361.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    8 Scopus citations
  • 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
  • Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

    Vanburen, R., Bryant, D., Edger, P. P., Tang, H., Burgess, D., Challabathula, D., Spittle, K., Hall, R., Gu, J., Lyons, E., Freeling, M., Bartels, D., Ten Hallers, B., Hastie, A., Michael, T. P. & Mockler, T. C., Nov 26 2015, In: Nature. 527, 7579, p. 508-511 4 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    190 Scopus citations
  • SynFind: Compiling syntenic regions across any set of genomes on demand

    Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C. & Lyons, E., Dec 2015, In: Genome biology and evolution. 7, 12, p. 3286-3298 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    41 Scopus citations
  • SynMap2 and SynMap3D: Web-based whole-genome synteny browsers

    Haug-Baltzell, A., Stephens, S. A., Davey, S., Scheidegger, C. E. & Lyons, E., Jul 15 2017, In: Bioinformatics. 33, 14, p. 2197-2198 2 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    64 Scopus citations
  • Tail wags the dog? Functional gene classes driving genome-wide GC content in Plasmodium spp

    Castillo, A. I., Nelson, A. D. L. & Lyons, E., Feb 1 2019, In: Genome biology and evolution. 11, 2, p. 497-507 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    5 Scopus citations
  • Ten simple rules to ruin a collaborative environment

    Lawrence-Dill, C. J., Allscheid, R. L., Boaitey, A., Bauman, T., Buckler, E. S., Clarke, J. L., Cullis, C., Dekkers, J., Dorius, C. J., Dorius, S. F., Ertl, D., Homann, M., Hu, G., Losch, M., Lyons, E., Murdoch, B., Navabi, Z. K., Punnuri, S., Rafiq, F., Reecy, J. M., & 8 othersSchnable, P. S., Scott, N. M., Sheehan, M., Sirault, X., Staton, M., Tuggle, C. K., Van Eenennaam, A. & Voas, R., Apr 2022, In: PLoS computational biology. 18, 4 April, e1009957.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 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

    565 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

    761 Scopus citations
  • The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible

    Hao, Y., Mabry, M. E., Edger, P. P., Freeling, M., Zheng, C., Jin, L., VanBuren, R., Colle, M., An, H., Abrahams, R. S., Washburn, J. D., Qi, X., Barry, K., Daum, C., Shu, S., Schmutz, J., Sankoff, D., Barker, M. S., Lyons, E., Pires, J. C., & 1 othersConant, G. C., 2021, In: Genome Research. 31, 5, p. 799-810 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    4 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

    783 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
  • 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
  • The genome of black raspberry (Rubus occidentalis)

    VanBuren, R., Bryant, D., Bushakra, J. M., Vining, K. J., Edger, P. P., Rowley, E. R., Priest, H. D., Michael, T. P., Lyons, E., Filichkin, S. A., Dossett, M., Finn, C. E., Bassil, N. V. & Mockler, T. C., Sep 1 2016, In: Plant Journal. 87, 6, p. 535-547 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    73 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

    322 Scopus citations
  • The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

    Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D. & Antin, P., Jan 11 2016, In: PLoS biology. 14, 1, e1002342.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    193 Scopus citations
  • The pineapple genome and the evolution of CAM photosynthesis

    Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., & 50 othersYim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A. C., Cushman, J. C., Paull, R. E. & Yu, Q., Dec 1 2015, In: Nature Genetics. 47, 12, p. 1435-1442 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    316 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

    620 Scopus citations
  • 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

    2138 Scopus citations
  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

    Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St John, J. A., Capella-Gutiérrez, S., Castoe, T. A., Kern, C., Fujita, M. K., Opazo, J. C., Jurka, J., Kojima, K. K., Caballero, J., Hubley, R. M., Smit, A. F., Platt, R. N., Lavoie, C. A., & 35 othersRamakodi, M. P., Finger, J. W., Suh, A., Isberg, S. R., Miles, L., Chong, A. Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S. C., Edwards, S. V., Lyons, E., Williams, C., Breen, M., Howard, J. T., Gresham, C. R., Peterson, D. G., Schmitz, J., Pollock, D. D., Haussler, D., Triplett, E. W., Zhang, G., Irie, N., Jarvis, E. D., Brochu, C. A., Schmidt, C. J., McCarthy, F. M., Faircloth, B. C., Hoffmann, F. G., Glenn, T. C., Gabaldón, T., Paten, B. & Ray, D. A., 2014, In: Science. 346, 6215, 1254449.

    Research output: Contribution to journalArticlepeer-review

    220 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
  • 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
  • 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

    69 Scopus citations
  • Wild tobacco genomes reveal the evolution of nicotine biosynthesis

    Xu, S., Brockmöller, T., Navarro-Quezada, A., Kuhl, H., Gase, K., Ling, Z., Zhou, W., Kreitzer, C., Stanke, M., Tang, H., Lyons, E., Pandey, P., Pandey, S. P., Timmermann, B., Gaquerel, E. & Baldwin, I. T., Jun 6 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 23, p. 6133-6138 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    89 Scopus citations