Charles Du

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Charles Du

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20032023

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  • 2023

    Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

    Jia, J., Zhao, G., Li, D., Wang, K., Kong, C., Deng, P., Yan, X., Zhang, X., Lu, Z., Xu, S., Jiao, Y., Chong, K., Liu, X., Cui, D., Li, G., Zhang, Y., Du, C., Wu, L., Li, T. & Yan, D. & 8 others, Zhan, K., Chen, F., Wang, Z., Zhang, L., Kong, X., Ru, Z., Wang, D. & Gao, L., 4 Dec 2023, In: Molecular Plant. 16, 12, p. 1893-1910 18 p.

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

    Open Access
    5 Scopus citations
  • 2022

    Student Attitudes Contribute to the Effectiveness of a Genomics CURE

    Lopatto, D., Rosenwald, A. G., Burgess, R. C., Key, C. S., Van Stry, M., Wawersik, M., DiAngelo, J. R., Hark, A. T., Skerritt, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G. & Croonquist, P. & 78 others, Du, C., Dubowsky, S., Eisler, H., Escobar, M. A., Foulk, M., Giarla, T., Glaser, R. L., Goodman, A. L., Gosser, Y., Haberman, A., Hauser, C., Hays, S., Howell, C. E., Jemc, J., Jones, C. J., Kadlec, L., Kagey, J. D., Keller, K. L., Kennell, J., Kleinschmit, A. J., Kleinschmit, M., Kokan, N. P., Kopp, O. R., Laakso, M. M., Leatherman, J., Long, L. J., Manier, M., Martinez-Cruzado, J. C., Matos, L. F., McClellan, A. J., McNeil, G., Merkhofer, E., Mingo, V., Mistry, H., Mitchell, E., Mortimer, N. T., Myka, J. L., Nagengast, A., Overvoorde, P., Paetkau, D., Paliulis, L., Parrish, S., Peters, S. T., Preuss, M. L., Price, J. V., Pullen, N. A., Reinke, C., Revie, D., Robic, S., Roecklein-Canfield, J. A., Rubin, M. R., Sadikot, T., Sanford, J. S., Santisteban, M., Saville, K., Schroeder, S., Shaffer, C. D., Sharif, K. A., Sklensky, D. E., Small, C., Smith, S., Spokony, R., Sreenivasan, A., Stamm, J., Sterne-Marr, R., Teeter, K. C., Thackeray, J., Thompson, J. S., Velazquez-Ulloa, N., Wolfe, C., Youngblom, J., Yowler, B., Zhou, L., Brennan, J., Buhler, J., Leung, W., Elgin, S. C. R. & Reed, L. K., Aug 2022, In: Journal of Microbiology and Biology Education. 23, 2

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

    Open Access
    6 Scopus citations
  • 2021

    Identification of ZmNF-YC2 and its regulatory network for maize flowering time

    Su, H., Chen, Z., Dong, Y., Ku, L., Abou-Elwafa, S. F., Ren, Z., Cao, Y., Dou, D., Liu, Z., Liu, H., Tian, L., Zhang, D., Zeng, H., Han, S., Zhu, F., Du, C. & Chen, Y., 4 Dec 2021, In: Journal of Experimental Botany. 72, 22, p. 7792-7807 16 p.

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

    21 Scopus citations

  • Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines

    Tian, L., Ku, L., Yuan, Z., Wang, C., Su, H., Wang, S., Song, X., Dou, D., Ren, Z., Lai, J., Liu, T., Chen, Y., Liu, T. & Du, C., 4 May 2021, In: Journal of Experimental Botany. 72, 10, p. 3582-3596 15 p.

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

    5 Scopus citations
  • 2020

    facilitating growth through frustration: Using genomics research in a course-based undergraduate research experience

    Lopatto, D., Rosenwald, A. G., DiAngelo, J. R., Hark, A. T., Skerritt, M., Wawersik, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bazinet, C., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., Burgess, R. C., Croonquist, P. & Du, C. & 83 others, Dubowsky, S., Eisler, H., Escobar, M. A., Foulk, M., Furbee, E., Giarla, T., Glaser, R. L., Goodman, A. L., Gosser, Y., Haberman, A., Hauser, C., Hays, S., Howell, C. E., Jemc, J., Logan Johnson, M., Jones, C. J., Kadlec, L., Kagey, J. D., Keller, K. L., Kennell, J., Catherine Silver Key, S., Kleinschmit, A. J., Kleinschmit, M., Kokan, N. P., Kopp, O. R., Laakso, M. M., Leatherman, J., Long, L. J., Manier, M., Martinez-Cruzado, J. C., Matos, L. F., McClellan, A. J., McNeil, G., Merkhofer, E., Mingo, V., Mistry, H., Mitchell, E., Mortimer, N. T., Mukhopadhyay, D., Myka, J. L., Nagengast, A., Overvoorde, P., Paetkau, D., Paliulis, L., Parrish, S., Preuss, M. L., Price, J. V., Pullen, N. A., Reinke, C., Revie, D., Robic, S., Roecklein-Canfield, J. A., Rubin, M. R., Sadikot, T., Sanford, J. S., Santisteban, M., Saville, K., Schroeder, S., Shaffer, C. D., Sharif, K. A., Sklensky, D. E., Small, C., Smith, M., Smith, S., Spokony, R., Sreenivasan, A., Stamm, J., Sterne-Marr, R., Teeter, K. C., Thackeray, J., Thompson, J. S., Peters, S. T., van Stry, M., Velazquez-Ulloa, N., Wolfe, C., Youngblom, J., Yowler, B., Zhou, L., Brennan, J., Buhler, J., Leung, W., Reed, L. K. & Elgin, S. C. R., Feb 2020, In: Journal of Microbiology and Biology Education. 21, 1

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

    Open Access
    17 Scopus citations

  • Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize

    Li, C., Xiang, X., Huang, Y., Zhou, Y., An, D., Dong, J., Zhao, C., Liu, H., Li, Y., Wang, Q., Du, C., Messing, J., Larkins, B. A., Wu, Y. & Wang, W., 1 Dec 2020, In: Nature Communications. 11, 1, 17.

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

    Open Access
    47 Scopus citations
  • 2019

    Adaptation of photosynthesis to water deficit in the reproductive phase of a maize (Zea mays L.) inbred line

    Zheng, H. F., Xin, L. F., Guo, J. M., Mao, J., Han, X. P., Jia, L., Zheng, B. Y., Du, C. G., Elmore, R. W., Yang, Q. H. & Shao, R. X., 2019, In: Photosynthetica. 57, 2, p. 399-408 10 p.

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

    Open Access
    6 Scopus citations

  • Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions

    Dooner, H. K., Wang, Q., Huang, J. T., Li, Y., He, L., Xiong, W. & Du, C., 28 May 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 166, 22, p. 10734-10743 10 p.

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

    Open Access
    17 Scopus citations

  • The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

    Li, M., Yang, S., Xu, W., Pu, Z., Feng, J., Wang, Z., Zhang, C., Peng, M., Du, C., Lin, F., Wei, C., Qiao, S., Zou, H., Zhang, L., Li, Y., Yang, H., Liao, A., Song, W., Zhang, Z. & Li, J. & 5 others, Wang, K., Zhang, Y., Lin, H., Zhang, J. & Tan, W., 1 Apr 2019, In: BMC Plant Biology. 19, 1, 119.

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

    Open Access
    34 Scopus citations
  • 2018

    Salicylic acid-induced photosynthetic adaptability of Zea mays L. to polyethylene glycol-simulated water deficit is associated with nitric oxide signaling

    Shao, R. X., Xin, L. F., Guo, J. M., Zheng, H. F., Mao, J., Han, X. P., Jia, L., Jia, S. J., Du, C. G., Song, R., Yang, Q. H. & Elmore, R. W., 1 Dec 2018, In: Photosynthetica. 56, 4, p. 1370-1377 8 p.

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

    Open Access
    25 Scopus citations

  • The maize w22 genome provides a foundation for functional genomics and transposon biology

    Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Kelly Dawe, R., Davenport, R., Dooner, H. K., Du, L. H. & Du, C. & 34 others, Easterling, K. A., Gault, C., Guan, J. C., Hunter, C. T., Jander, G., Jiao, Y., Koch, K. E., Kol, G., Köllner, T. G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D. R., Noshay, J. M., Portwood, J. L., Ronen, G., Settles, A. M., Shem-Tov, D., Shi, J., Soifer, I., Stein, J. C., Stitzer, M. C., Suzuki, M., Vera, D. L., Vollbrecht, E., Vrebalov, J. T., Ware, D., Wei, S., Wimalanathan, K., Woodhouse, M. R., Xiong, W. & Brutnell, T. P., 1 Sep 2018, In: Nature Genetics. 50, 9, p. 1282-1288 7 p.

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

    Open Access
    142 Scopus citations
  • 2017

    Highly interwoven communities of a gene regulatory network unveil topologically important genes for maize seed development

    Xiong, W., Wang, C., Zhang, X., Yang, Q., Shao, R., Lai, J. & Du, C., Dec 2017, In: Plant Journal. 92, 6, p. 1143-1156 14 p.

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

    Open Access
    21 Scopus citations

  • Integrated regulatory network reveals the early salt tolerance mechanism of Populus euphratica

    Chen, J., Zhang, J., Hu, J., Xiong, W., Du, C. & Lu, M., 1 Dec 2017, In: Scientific Reports. 7, 1, 6769.

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

    Open Access
    20 Scopus citations

  • iTRAQ-based proteomics analysis and network integration for kernel tissue development in maize

    Zhang, L., Dong, Y., Wang, Q., Du, C., Xiong, W., Li, X., Zhu, S. & Li, Y., Sep 2017, In: International Journal of Molecular Sciences. 18, 9, 1840.

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

    Open Access
    13 Scopus citations
  • 2016

    Rolling-circle amplification of centromeric Helitrons in plant genomes

    Xiong, W., Dooner, H. K. & Du, C., 1 Dec 2016, In: Plant Journal. 88, 6, p. 1038-1045 8 p.

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

    Open Access
    18 Scopus citations
  • 2015

    Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution

    Participating Students and Faculty of the Genomics Education Partnership, 2015, In: G3: Genes, Genomes, Genetics. 5, 5, p. 719-740 22 p.

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

    Open Access
    71 Scopus citations

  • Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn

    Dong, Y., Wang, Q., Zhang, L., Du, C., Xiong, W., Chen, X., Deng, F., Ma, Z., Qiao, D., Hu, C., Ren, Y. & Li, Y., 1 Nov 2015, In: PLoS ONE. 10, 11, e0143181.

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

    Open Access
    9 Scopus citations
  • 2014

    A central support system can facilitate implementation and sustainability of a classroom-based undergraduate research experience (CURE) in genomics

    Lopatto, D., Hauser, C., Jones, C. J., Paetkau, D., Chandrasekaran, V., Dunbar, D., MacKinnon, C., Stamm, J., Alvarez, C., Barnard, D., Bedard, J. E. J., Bednarski, A. E., Bhalla, S., Braverman, J. M., Burg, M., Chung, H. M., DeJong, R. J., DiAngelo, J. R., Du, C. & Eckdahl, T. T. & 53 others, Emerson, J., Frary, A., Frohlich, D., Goodman, A. L., Gosser, Y., Govind, S., Haberman, A., Hark, A. T., Hoogewerf, A., Johnson, D., Kadlec, L., Kaehler, M., Key, S. C. S., Kokan, N. P., Kopp, O. R., Kuleck, G. A., Lopilato, J., Martinez-Cruzado, J. C., McNeil, G., Mel, S., Nagengast, A., Overvoorde, P. J., Parrish, S., Preuss, M. L., Reed, L. D., Regisford, E. G., Revie, D., Robic, S., Roecklien-Canfield, J. A., Rosenwald, A. G., Rubin, M. R., Saville, K., Schroeder, S., Sharif, K. A., Shaw, M., Skuse, G., Smith, C. D., Smith, M., Smith, S. T., Spana, E. P., Spratt, M., Sreenivasan, A., Thompson, J. S., Wawersik, M., Wolyniak, M. J., Youngblom, J., Zhou, L., Buhler, J., Mardis, E., Leung, W., Shaffer, C. D., Threlfall, J. & Elgin, S. C. R., 21 Dec 2014, In: CBE Life Sciences Education. 13, 4, p. 711-723 13 p.

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

    Open Access
    60 Scopus citations

  • A course-based research experience: How benefits change with increased investment in instructional time

    Shaffer, C. D., Alvarez, C. J., Bednarski, A. E., Dunbar, D., Goodman, A. L., Reinke, C., Rosenwald, A. G., Wolyniak, M. J., Bailey, C., Barnard, D., Bazinet, C., Beach, D. L., Bedard, J. E. J., Bhalla, S., Braverman, J., Burg, M., Chandrasekaran, V., Chung, H. M., Clase, K. & DeJong, R. J. & 64 others, DiAngelo, J. R., Du, C., Eckdahl, T. T., Eisler, H., Emerson, J. A., Frary, A., Frohlich, D., Gosser, Y., Govind, S., Haberman, A., Hark, A. T., Hauser, C., Hoogewerf, A., Hoopes, L. L. M., Howell, C. E., Johnson, D., Jones, C. J., Kadlec, L., Kaehler, M., Catherine Silver Key, S., Kleinschmit, A., Kokan, N. P., Kopp, O., Kuleck, G., Leatherman, J., Lopilato, J., MacKinnon, C., Martinez-Cruzado, J. C., McNeil, G., Mel, S., Mistry, H., Nagengast, A., Overvoorde, P., Paetkau, D. W., Parrish, S., Peterson, C. N., Preuss, M., Reed, L. K., Revie, D., Robic, S., Roecklein-Canfield, J., Rubin, M. R., Saville, K., Schroeder, S., Sharif, K., Shaw, M., Skuse, G., Smith, C. D., Smith, M. A., Smith, S. T., Spana, E., Spratt, M., Sreenivasan, A., Stamm, J., Szauter, P., Thompson, J. S., Wawersik, M., Youngblom, J., Zhou, L., Mardis, E. R., Buhler, J., Leung, W., Lopatto, D. & Elgin, S. C. R., 3 Mar 2014, In: CBE Life Sciences Education. 13, 1, p. 111-130 20 p.

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

    Open Access
    136 Scopus citations

  • HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

    Xiong, W., He, L., Lai, J., Dooner, H. K. & Du, C., 15 Jul 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 28, p. 10263-10268 6 p.

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

    Open Access
    168 Scopus citations
  • 2013

    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 others, Der, 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., 10 May 2013, In: Genome Biology. 14, 5, R41.

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

    Open Access
    312 Scopus citations

  • InsertionMapper: A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data

    Xiong, W., He, L., Li, Y., Dooner, H. K. & Du, C., 4 Oct 2013, In: BMC Genomics. 14, 1, 679.

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

    Open Access
    4 Scopus citations
  • 2011

    The complete Ac/Ds transposon family of maize

    Du, C., Hoffman, A., He, L., Caronna, J. & Dooner, H. K., 1 Dec 2011, In: BMC Genomics. 12, 588.

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

    Open Access
    22 Scopus citations
  • 2010

    The genomics education partnership: Successful integration of research into laboratory classes at a diverse group of undergraduate institutions

    Shaffer, C. D., Alvarez, C., Bailey, C., Barnard, D., Bhalla, S., Chandrasekaran, C., Chandrasekaran, V., Chung, H. M., Dorer, D. R., Du, C., Eckdahl, T. T., Poet, J. L., Frohlich, D., Goodman, A. L., Gosser, Y., Hauser, C., Hoopes, L. L. M., Johnson, D., Jones, C. J. & Kaehler, M. & 33 others, Kokan, N., Kopp, O. R., Kuleck, G. A., McNeil, G., Moss, R., Myka, J. L., Nagengast, A., Morris, R., Overvoorde, P. J., Shoop, E., Parrish, S., Reed, K., Regisford, E. G., Revie, D., Rosenwald, A. G., Saville, K., Schroeder, S., Shaw, M., Skuse, G., Smith, C., Smith, M., Spana, E. P., Spratt, M., Stamm, J., Thompson, J. S., Wawersik, M., Wilson, B. A., Youngblom, J., Leung, W., Buhler, J., Mardis, E. R., Lopatto, D. & Elgin, S. C. R., 2010, In: CBE Life Sciences Education. 9, 1, p. 55-69 15 p.

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

    Open Access
    159 Scopus citations
  • 2009

    The polychromatic Helitron landscape of the maize genome

    Du, C., Fefelova, N., Caronna, J., He, L. & Dooner, H. K., 24 Nov 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 47, p. 19916-19921 6 p.

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

    Open Access
    89 Scopus citations
  • 2008

    Computational prediction and molecular confirmation of Helitron transposons in the maize genome

    Du, C., Caronna, J., He, L. & Dooner, H. K., 28 Jan 2008, In: BMC Genomics. 9, 51.

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

    Open Access
    46 Scopus citations

  • Undergraduate research: Genomics education partnership

    Lopatto, D., Alvarez, C., Barnard, D., Chandrasekaran, C., Chung, H. M., Du, C., Eckdahl, T., Goodman, A. L., Hauser, C., Jones, C. J., Kopp, O. R., Kuleck, G. A., McNeil, G., Morris, R., Myka, J. L., Nagengast, A., Overvoorde, P. J., Poet, J. L., Reed, K. & Regisford, G. & 18 others, Revie, D., Rosenwald, A., Saville, K., Shaw, M., Skuse, G. R., Smith, C., Smith, M., Spratt, M., Stamm, J., Thompson, J. S., Wilson, B. A., Witkowski, C., Youngblom, J., Leung, W., Shaffer, C. D., Buhler, J., Mardis, E. & Elgin, S. C. R., 31 Oct 2008, In: Science. 322, 5902, p. 684-685 2 p.

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

    Open Access
    139 Scopus citations
  • 2006

    Retrotranspositions in orthologous regions of closely related grass species

    Du, C., Swigoňová, Z. & Messing, J., 16 Aug 2006, In: BMC Evolutionary Biology. 6, 62.

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

    Open Access
    35 Scopus citations

  • Uneven chromosome contraction and expansion in the maize genome

    Bruggmann, R., Bharti, A. K., Gundlach, H., Lai, J., Young, S., Pontaroli, A. C., Wei, F., Haberer, G., Fuks, G., Du, C., Raymond, C., Estep, M. C., Liu, R., Bennetzen, J. L., Chan, A. P., Rabinowicz, P. D., Quackenbush, J., Barbazuk, W. B., Wing, R. A. & Birren, B. & 4 others, Nusbaum, C., Rounsley, S., Mayer, K. F. X. & Messing, J., 2006, In: Genome Research. 16, 10, p. 1241-1251 11 p.

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

    Open Access
    102 Scopus citations
  • 2004

    Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.)

    He, L., Du, C., Covaleda, L., Xu, Z., Robinson, A. F., Yu, J. Z., Kohel, R. J. & Zhang, H. B., Nov 2004, In: Molecular Plant-Microbe Interactions. 17, 11, p. 1234-1241 8 p.

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

    60 Scopus citations