• 4049 Citations
  • 21 h-Index
20032019

Research output per year

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Research Output

  • 4049 Citations
  • 21 h-Index
  • 40 Article
  • 4 Comment/debate
  • 3 Letter
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Article
2019

Rapid evolution of protein diversity by de novo origination in Oryza

Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A. R., Yu, Y., Hou, G., Zi, J., Zhou, R., Wen, B., Zhang, J. ., Chougule, K., Wang, M., Copetti, D., Peng, Z., Zhang, C., Zhang, Y., Ouyang, Y., Wing, R. A. & 2 others, Liu, S. & Long, M., Apr 1 2019, In : Nature Ecology and Evolution. 3, 4, p. 679-690 12 p.

Research output: Contribution to journalArticle

Open Access
14 Scopus citations
2018

ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-selected pink bollworm

Mathew, L. G., Ponnuraj, J., Mallappa, B., Chowdary, L. R., Zhang, J., Tay, W. T., Walsh, T. K., Gordon, K. H. J., Heckel, D. G., Downes, S., Carrière, Y., Li, X., Tabashnik, B. E. & Fabrick, J. A., Dec 1 2018, In : Scientific reports. 8, 1, 13531.

Research output: Contribution to journalArticle

17 Scopus citations

CRISPR-PLANT v2: an online resource for highly specific guide RNA spacers based on improved off-target analysis

Minkenberg, B., Zhang, J. ., Xie, K. & Yang, Y., Jan 1 2018, (Accepted/In press) In : Plant Biotechnology Journal.

Research output: Contribution to journalArticle

4 Scopus citations

Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Ndjiondjop, M. N., Semagn, K., Zhang, J. ., Gouda, A. C., Kpeki, S. B., Goungoulou, A., Wambugu, P., Dramé, K. N., Bimpong, I. K. & Zhao, D., Nov 1 2018, In : Molecular Breeding. 38, 11, 131.

Research output: Contribution to journalArticle

4 Scopus citations

Genetic control of seed shattering during African rice domestication

Lv, S., Wu, W., Wang, M., Meyer, R. S., Ndjiondjop, M. N., Tan, L., Zhou, H., Zhang, J. ., Fu, Y., Cai, H., Sun, C., Wing, R. A. & Zhu, Z., Jun 1 2018, In : Nature Plants. 4, 6, p. 331-337 7 p.

Research output: Contribution to journalArticle

18 Scopus citations

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D. A., Zhang, J. ., Londono, C. E. M., Song, X. & 45 others, Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J. S. S., Talag, J., Danowitz, A., Rivera, L. F., Gschwend, A. R., Noutsos, C., Wu, C. C., Kao, S. M., Zeng, J. W., Wei, F. J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M. C., Lasserre, E., Cooke, R., Rosa Farias, D. D., Da Maia, L. C., Dos Santos, R. S., Nyberg, K. G., McNally, K. L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K. K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y. I. C., Kurata, N., De Oliveira, A. C., Panaud, O., Jackson, S. A., Machado, C. A., Sanderson, M., Long, M., Ware, D. & Wing, R. A., Feb 1 2018, In : Nature Genetics. 50, 2, p. 285-296 12 p.

Research output: Contribution to journalArticle

90 Scopus citations

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., Mansueto, L., Copetti, D., Sanciangco, M., Palis, K. C., Xu, J., Sun, C., Fu, B., Zhang, H., Gao, Y., Zhao, X. & 51 others, Shen, F., Cui, X., Yu, H., Li, Z., Chen, M., Detras, J., Zhou, Y., Zhang, X., Zhao, Y., Kudrna, D. A., Wang, C., Li, R., Jia, B., Lu, J., He, X., Dong, Z., Xu, J., Li, Y., Wang, M., Shi, J., Li, J., Zhang, D., Lee, S., Hu, W., Poliakov, A., Dubchak, I., Ulat, V. J., Borja, F. N., Mendoza, J. R., Ali, J., Gao, Q., Niu, Y., Yue, Z., Naredo, M. E. B., Talag, J., Wang, X., Li, J., Fang, X., Yin, Y., Glaszmann, J. C., Zhang, J. ., Li, J., Hamilton, R. S., Wing, R. A., Ruan, J., Zhang, G., Wei, C., Alexandrov, N., McNally, K. L., Li, Z. & Leung, H., May 3 2018, In : Nature. 557, 7703, p. 43-49 7 p.

Research output: Contribution to journalArticle

176 Scopus citations
2017

Aflatoxin-free transgenic maize using host-induced gene silencing

Thakare, D., Zhang, J. ., Wing, R. A., Cotty, P. J. & Schmidt, M., Mar 1 2017, In : Science advances. 3, 3, e1602382.

Research output: Contribution to journalArticle

35 Scopus citations

A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication

Wu, W., Liu, X., Wang, M., Meyer, R. S., Luo, X., Ndjiondjop, M. N., Tan, L., Zhang, J. ., Wu, J., Cai, H., Sun, C., Wang, X., Wing, R. A. & Zhu, Z., May 8 2017, In : Nature Plants. 3, 17064.

Research output: Contribution to journalArticle

53 Scopus citations

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes

Xie, J., Huo, N., Zhou, S., Wang, Y., Guo, G., Deal, K. R., Ouyang, S., Liang, Y., Wang, Z., Xiao, L., Zhu, T., Hu, T., Tiwari, V., Zhang, J. ., Li, H., Ni, Z., Yao, Y., Peng, H., Zhang, S., Anderson, O. D. & 6 others, McGuire, P. E., Dvorak, J., Luo, M. C., Liu, Z., Gu, Y. Q. & Sun, Q., Jan 20 2017, In : Journal of Genetics and Genomics. 44, 1, p. 51-61 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Young inversion with multiple linked QTLs under selection in a hybrid zone

Lee, C. R., Wang, B., Mojica, J. P., Mandáková, T., Prasad, K. V. S. K., Goicoechea, J. L., Perera, N., Hellsten, U., Hundley, H. N., Johnson, J., Grimwood, J., Barry, K., Fairclough, T., Jenkins, J. W., Yu, Y., Kudrna, D., Zhang, J., Talag, J., Golser, W., Ghattas, K. & 6 others, Schranz, M. E., Wing, R., Lysak, M. A., Schmutz, J., Rokhsar, D. S. & Mitchell-Olds, T., Apr 3 2017, In : Nature Ecology and Evolution. 1, 5, 0119.

Research output: Contribution to journalArticle

31 Scopus citations
2016

Data Descriptor: Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data

Zhang, J. ., Chen, L. L., Sun, S., Kudrna, D. A., Copetti, D., Li, W., Mu, T., Jiao, W. B., Xing, F., Lee, S., Talag, J., Song, J. M., Du, B., Xie, W., Luo, M., Maldonado, C. E., Goicoechea, J. L., Xiong, L., Wu, C., Xing, Y. & 10 others, Zhou, D. X., Yu, S., Zhao, Y., Wang, G., Yu, Y., Luo, Y., Hurtado, B. E. P., Danowitz, A., Wing, R. A. & Zhang, Q., Sep 13 2016, In : Scientific data. 3, 160076.

Research output: Contribution to journalArticle

12 Scopus citations

DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements

Wang, J., Yu, Y., Tao, F., Zhang, J., Copetti, D., Kudrna, D., Talag, J., Lee, S., Wing, R. A. & Fan, C., May 6 2016, In : Genome biology. 17, 1, 92.

Research output: Contribution to journalArticle

11 Scopus citations

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Zhang, J., Chen, L. L., Xing, F., Kudrna, D. A., Yao, W., Copetti, D., Mu, T., Li, W., Song, J. M., Xie, W., Lee, S., Talag, J., Shao, L., An, Y., Zhang, C. L., Ouyang, Y., Sun, S., Jiao, W. B., Lv, F., Du, B. & 17 others, Luo, M., Maldonado, C. E., Goicoechea, J. L., Xiong, L., Wu, C., Xing, Y., Zhou, D. X., Yu, S., Zhao, Y., Wang, G., Yu, Y., Luo, Y., Zhou, Z. W., Hurtado, B. E. P., Danowitz, A., Wing, R. A. & Zhang, Q., Aug 30 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 35, p. E5163-E5171

Research output: Contribution to journalArticle

73 Scopus citations

Genome puzzle master (GPM): An integrated pipeline for building and editing pseudomolecules from fragmented sequences

Zhang, J., Kudrna, D., Mu, T., Li, W., Copetti, D., Yu, Y., Goicoechea, J. L., Lei, Y. & Wing, R. A., Oct 15 2016, In : Bioinformatics. 32, 20, p. 3058-3064 7 p.

Research output: Contribution to journalArticle

7 Scopus citations
2015

RiTE database: A resource database for genus-wide rice genomics and evolutionary biology

Copetti, D., Zhang, J., El Baidouri, M., Gao, D., Wang, J., Barghini, E., Cossu, R. M., Angelova, A., Maldonado L., C. E., Roffler, S., Ohyanagi, H., Wicker, T., Fan, C., Zuccolo, A., Chen, M., Costa de Oliveira, A., Han, B., Henry, R., Hsing, Y. I., Kurata, N. & 4 others, Wang, W., Jackson, S. A., Panaud, O. & Wing, R. A., Jul 22 2015, In : BMC genomics. 16, 1, 538.

Research output: Contribution to journalArticle

28 Scopus citations
2014

Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping

Wang, X., Kudrna, D. A., Pan, Y., Wang, H., Liu, L., Lin, H., Zhang, J., Song, X., Goicoechea, J. L., Wing, R. A., Zhang, Q. & Luo, M., Apr 2014, In : Genetics. 196, 4, p. 937-949 13 p.

Research output: Contribution to journalArticle

7 Scopus citations
2012

Cloning and characterization of paleoAP3-like MADS-box gene in London plane tree

Li, Z., Liu, G., Zhang, J., Lu, S., Yi, S. & Bao, M., Sep 1 2012, In : Biologia Plantarum. 56, 3, p. 585-589 5 p.

Research output: Contribution to journalArticle

7 Scopus citations

OsLIS-L1 encoding a lissencephaly type-1-like protein with WD40 repeats is required for plant height and male gametophyte formation in rice

Gao, X., Chen, Z., Zhang, J., Li, X., Chen, G., Li, X. & Wu, C., Apr 1 2012, In : Planta. 235, 4, p. 713-727 15 p.

Research output: Contribution to journalArticle

21 Scopus citations
2011

Conservation and purifying selection of transcribed genes located in a rice centromere

Fan, C., Walling, J. G., Zhang, J., Hirsch, C. D., Jiang, J. & Wing, R. A., Aug 1 2011, In : Plant Cell. 23, 8, p. 2821-2830 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

The FLOWERING LOCUS T orthologous gene of Platanus acerifolia is expressed as alternatively spliced forms with distinct spatial and temporal patterns

Zhang, J., Liu, G., Guo, C., He, Y., Li, Z., Ning, G., Shi, X. & Bao, M., Sep 1 2011, In : Plant Biology. 13, 5, p. 809-820 12 p.

Research output: Contribution to journalArticle

12 Scopus citations
2010

Cloning of porcine chemerin, ChemR23 and GPR1 and their involvement in regulation of lipogenesis

Huang, J., Zhang, J., Lei, T., Chen, X., Zhang, Y., Zhou, L., Yu, A., Chen, Z., Zhou, R. & Yang, Z., Jul 1 2010, In : BMB Reports. 43, 7, p. 491-498 8 p.

Research output: Contribution to journalArticle

19 Scopus citations

Porcine KLF gene family: Structure, mapping, and phylogenetic analysis

Chen, Z., Lei, T., Chen, X., Zhang, J., Yu, A., Long, Q., Long, H., Jin, D., Gan, L. & Yang, Z., Feb 1 2010, In : Genomics. 95, 2, p. 111-119 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

Resistin up-regulates COX-2 expression via TAK1-IKK-NF-κB signaling pathway

Zhang, J., Lei, T., Chen, X., Peng, Y., Long, H., Zhou, L., Huang, J., Chen, Z., Long, Q. & Yang, Z., Feb 1 2010, In : Inflammation. 33, 1, p. 25-33 9 p.

Research output: Contribution to journalArticle

22 Scopus citations
2009

Detailed analysis of a contiguous 22-Mb region of the maize genome

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J. & 35 others, Kim, H. R., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K. & Wing, R. A., Nov 1 2009, In : PLoS genetics. 5, 11, e1000728.

Research output: Contribution to journalArticle

35 Scopus citations

Molecular cloning, chromosomal location and expression pattern of porcine CIDEa and CIDEc

Li, Y. H., Lei, T., Chen, X. D., Xia, T., Peng, Y., Long, Q. Q., Zhang, J., Feng, S. Q., Zhou, L. & Yang, Z. Q., Mar 1 2009, In : Molecular Biology Reports. 36, 3, p. 575-582 8 p.

Research output: Contribution to journalArticle

13 Scopus citations

Single feature polymorphisms between two rice cultivars detected using a median polish method

Xie, W., Chen, Y., Zhou, G., Wang, L., Zhang, C., Zhang, J., Xiao, J., Zhu, T. & Zhang, Q., Jun 1 2009, In : Theoretical and Applied Genetics. 119, 1, p. 151-164 14 p.

Research output: Contribution to journalArticle

13 Scopus citations

The B73 maize genome: Complexity, diversity, and dynamics

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M. & 137 others, Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W., Ying, K., Yeh, C. T., Emrich, S. J., Jia, Y., Kalyanaraman, A., Hsia, A. P., Barbazuk, W. B., Baucom, R. S., Brutnell, T. P., Carpita, N. C., Chaparro, C., Chia, J. M., Deragon, J. M., Estill, J. C., Fu, Y., Jeddeloh, J. A., Han, Y., Lee, H., Li, P., Lisch, D. R., Liu, S., Liu, Z., Nagel, D. H., McCann, M. C., Sanmiguel, P., Myers, A. M., Nettleton, D., Nguyen, J., Penning, B. W., Ponnala, L., Schneider, K. L., Schwartz, D. C., Sharma, A., Soderlund, C., Springer, N. M., Sun, Q., Wang, H., Waterman, M., Westerman, R., Wolfgruber, T. K., Yang, L., Yu, Y., Zhang, L., Zhou, S., Zhu, Q., Bennetzen, J. L., Dawe, R. K., Jiang, J., Jiang, N., Presting, G. G., Wessler, S. R., Aluru, S., Martienssen, R. A., Clifton, S. W., McCombie, W. R., Wing, R. A. & Wilson, R. K., Nov 20 2009, In : Science. 326, 5956, p. 1112-1115 4 p.

Research output: Contribution to journalArticle

2385 Scopus citations

The physical and genetic framework of the maize B73 genome

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D., Clifton, S. W., Wilson, R. K. & Wing, R. A., Nov 1 2009, In : PLoS genetics. 5, 11, e1000715.

Research output: Contribution to journalArticle

77 Scopus citations
2007

Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library

Zhang, J., Guo, D., Chang, Y., You, C., Li, X., Dai, X., Weng, Q., Zhang, J., Chen, G., Li, X., Liu, H., Han, B., Zhang, Q. & Wu, C., Mar 1 2007, In : Plant Journal. 49, 5, p. 947-959 13 p.

Research output: Contribution to journalArticle

85 Scopus citations
2006

Establishment of a patterned GAL4-VP16 transactivation system for discovering gene function in rice

Liang, D., Wu, C., Li, C., Xu, C., Zhang, J., Kilian, A., Li, X., Zhang, Q. & Xiong, L., Jun 1 2006, In : Plant Journal. 46, 6, p. 1059-1072 14 p.

Research output: Contribution to journalArticle

29 Scopus citations

Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray

Lian, X., Wang, S., Zhang, J., Feng, Q., Zhang, L., Fan, D., Li, X., Yuan, D., Han, B. & Zhang, Q., Mar 1 2006, In : Plant Molecular Biology. 60, 5, p. 617-631 15 p.

Research output: Contribution to journalArticle

126 Scopus citations

Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs

Huang, Y., Zhang, L., Zhang, J., Yuan, D., Xu, C., Li, X., Zhou, D., Wang, S. & Zhang, Q., Nov 1 2006, In : Plant Molecular Biology. 62, 4-5, p. 579-591 13 p.

Research output: Contribution to journalArticle

85 Scopus citations

Identification of novel stress-responsive transcription factor genes in rice by cDNA array analysis

Wu, C. Q., Hu, H. H., Zeng, Y., Liang, D. C., Xie, K. B., Zhang, J. W., Chu, Z. H. & Xiong, L. Z., Oct 1 2006, In : Journal of Integrative Plant Biology. 48, 10, p. 1216-1224 9 p.

Research output: Contribution to journalArticle

7 Scopus citations

Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice

Zhang, J., Li, X., Jiang, G., Xu, Y. & He, Y., Dec 1 2006, In : Plant Breeding. 125, 6, p. 600-605 6 p.

Research output: Contribution to journalArticle

71 Scopus citations

RMD: a rice mutant database for functional analysis of the rice genome.

Zhang, J., Li, C., Wu, C., Xiong, L., Chen, G., Zhang, Q. & Wang, S., Jan 1 2006, In : Nucleic acids research. 34, Database issue, p. D745-748

Research output: Contribution to journalArticle

Open Access
149 Scopus citations
2005

Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63

Zhang, J., Feng, Q., Jin, C., Qiu, D., Zhang, L., Xie, K., Yuan, D., Han, B., Zhang, Q. & Wang, S., Jun 1 2005, In : Plant Journal. 42, 5, p. 772-780 9 p.

Research output: Contribution to journalArticle

37 Scopus citations

Isolation and annotation of 10828 putative full length cDNAs from indica rice

Xie, K., Zhang, J., Xiang, Y., Feng, Q., Han, B., Chu, Z., Wang, S., Zhang, Q. & Xiong, L., Dec 1 2005, In : Science in China, Series C: Life Sciences. 48, 5, p. 445-451 7 p.

Research output: Contribution to journalArticle

16 Scopus citations
2004

Genome-wide analysis of defense-responsive genes in bacterial blight resistance of rice mediated by the recessive R gene xa13

Chu, Z., Ouyang, Y., Zhang, J., Yang, H. & Wang, S., Feb 1 2004, In : Molecular Genetics and Genomics. 271, 1, p. 111-120 10 p.

Research output: Contribution to journalArticle

45 Scopus citations
2003

A new method for EST clustering

Zhang, L. D., Yuan, D. J., Zhang, J. W., Wang, S. P. & Zhang, Q. F., Feb 1 2003, In : Acta Genetica Sinica. 30, 2, p. 147-153 7 p.

Research output: Contribution to journalArticle

8 Scopus citations