Jianwei Zhang

Research Assistant Professor - School of Plant Sciences
520-626-9590

Research Lab/Affiliation

Dr. Rod Wing

Educational Background

  • 2013.3 – : Research Assistant Professor
  • 2011.5 – : Leader of Bioinformatics Group
  • Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Tucson, Arizona
  • 2010.11 – 2013.2: Assistant Research Scientist
  • Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Tucson, Arizona
  • 2006.9 – 2010.10: Research Associate
  • Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Tucson, Arizona
  • 2001.9- 2006.6: Master-Doctoral research phase, Bioinformatics in Biochemistry & Molecular Biology
  • Research adviser: Prof. Shiping Wang
  • College of Life Science and Technology
  • Huazhong Agricultural University, Wuhan, China
  • 1997.9-2001.6: Bachelor of science, Biotechnology
  • College of Life Science and Technology
  • Huazhong Agricultural University, Wuhan, China
  • Editorial Board Member:
  • − Academic Editor, PLoS ONE (2011-present)
  • − Associate Editor, BMC Genomics (2017-present)
  • − Associate Editor, BMC Bioinformatics (2017-present)

Research Interests

Bioinformatics
Genomics

Selected Publications

Research articles
1.      Song J-M, Lei Y, Shu C-C, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J# and Chen L-L# (#corresponding authors). Rice Information GateWay (RIGW): A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Mol. Plant, 2017, in press. DOI: 10.1016/j.molp.2017.10.003
2.      Wu W, Liu X, Wang M, Meyer R, Luo X, Ndjiondjop M-N, Tan L, Zhang J, Wu J, Cai H-W, Sun C, Wang X, Wing R and Zhu Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 2017, 3:17064. DOI: 10.1038/nplants.2017.64
3.      Lee C-R, Wang B, Mojica J, Mandáková T, Prasad K, Goicoechea J, Perera N, Hellsten U, Hundley H, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins J, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz E, Wing R, Lysak M, Schmutz J, Rokhsar D and Mitchell-Olds T. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution, 2017, 1:0119. DOI: 10.1038/s41559-017-0119
4.      Thakare D, Zhang J, Wing R, Cotty P and Schmidt M. Aflatoxin-free transgenic maize using host-induced gene silencing. Science Advances, 2017, 3:e1602382. DOI: 10.1126/sciadv.1602382
5.      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, McGuire P E, Dvorak J, Luo, M-C, Liu Z, Gu Y Q and Sun Q. Sequencing and comparative analysis of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genomes. Journal of Genetics and Genomics, 2017, 44(1):51-61. DOI: 10.1016/j.jgg.2016.09.005
6.      Zhang J*, Chen L* (*co-first authors), Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao W, Xing F, Lee S, Talag J, Song J, Du B, Xie W, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado B, Danowitz A, Wing R and Zhang Q. Building two indica rice reference genomes with PacBio long read and Illumina paired-end sequencing data. Sci. Data, 2016, 3:160076. DOI: 10.1038/sdata.2016.76
7.      Zhang J*, Chen L*, Xing F* (*co-first authors), Kudrna D, Yao W, Copetti D, Mu T, Li W, Song J, Xie W, Lee S, Talag J, Shao L, An Y, Zhang C, Ouyang Y, Sun S, Jiao W, Lv F, Du B, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou Z, Hurtado B, Danowitz A, Wing R and Zhang Q. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc. Natl. Acad. Sci. USA, 2016, 113(35):E5163-E5171. DOI: 10.1073/pnas.1611012113
8.      Zhang J#, Kudrna D, Mu T, Li W, Copetti D, Yu Y, Goicoechea J, Lei Y and Wing R# (#corresponding authors). Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 2016, 32(20):3058-3064. DOI: 10.1093/bioinformatics/btw370
9.      Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing R and Fan C. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biol., 2016, 17:92. DOI: 10.1186/s13059-016-0954-8
10.   Copetti D, Zhang J, Baidouri M, Gao D, Wang J, Barghini E, Cossu R, Angelova A, Maldonado C, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Oliveira A, Han B, Henry R, Hsing Y, Kurata N, Wang W, Jackson S, Panaud O and Wing R. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 2015, 16:538. DOI: 10.1186/s12864-015-1762-3
11.   Xie K, Zhang J and Yang Y. Genome-wide Prediction of Highly Specific Guide RNA Spacers for the CRISPR-Cas9 Mediated Genome Editing in Model Plants and Major Crops. Mol. Plant, 2014, 7(5):923-926. DOI: 10.1093/mp/ssu009
12.   Wang X, Kudrna D, Pan Y, Wang H, Liu L, Lin H, Zhang J, Song X, Goicoechea JL, Wing R, Zhang Q and Luo M. Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping. Genetics, 2014, 196:937-949. DOI: 10.1534/genetics.113.159970
13.   Fan C, Walling J, Zhang J, Hirsch C, Jiang J, and Wing R. Conservation and Purifying Selection of Transcribed Genes Located in a Rice Centromere. Plant Cell, 2011, 23(8):2821-2830. DOI: 10.1105/tpc.111.085605
14.   Wei F*, Zhang J* (*co-first authors), Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga B, Wissotski M, Golser W, Rock S, Graves T, Fulton R, Coe E, Schnable P, Schwartz D, Ware D, Clifton S, Wilson R and Wing R. The Physical and Genetic Framework of the Maize B73 Genome. PLoS Genet., 2009, 5(11):e1000715. DOI: 10.1371/journal.pgen.1000715
15.   Wei F, Stein J, Liang C, Zhang J, Fulton R, Baucom R, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh C, Ying K, Nagel D, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves T, Rock S, Adams S, Fulton L, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon J, Miguel P, Jiang N, Wessler S, Green P, Yu Y, Schwartz D, Meyers B, Bennetzen J, Martienssen R, McCombie W, Aluru S, Clifton S, Schnable P, Ware D, Wilson R and Wing R. Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet., 2009, 5(11):e1000728. DOI: 10.1371/journal.pgen.1000728
16.   Schnable P, Ware D, Fulton R, Stein J, Wei F, Pasternak S, Liang C, Zhang J (one of eight major contributors), Fulton L, Graves T, Minx P, Reily A, Courtney L, Kruchowski S, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock S, Belter E, Du F, Kim K, Abbott R, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson S, 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, McMahan L, Van Buren P, Vaughn M, Ying K, Yeh C, Emrich S, Jia Y, Kalyanaraman A, Hsia A, Barbazuk W, Baucom R, Brutnell T, Carpita N, Chaparro C, Chia J, Deragon J, Estill J, Fu Y, Jeddeloh J, Han Y, Lee H, Li P, Lisch D, Liu S, Liu Z, Nagel D, McCann M, SanMiguel P, Myers A, Nettleton D, Nguyen J, Penning B, Ponnala L, Schneider K, Schwartz D, Sharma A, Soderlund C, Springer N, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber T, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen J, Dawe R, Jiang J, Jiang N, Presting G, Wessler S, Aluru S, Martienssen R, Clifton S, McCombie W, Wing R and Wilson R. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science, 2009, 326:1112-1115. DOI: 10.1126/science.1178534
17.   Xie W, Chen Y, Zhou G, Wang L, Zhang C, Zhang J, Xiao J, Zhu T and Zhang Q. Single feature polymorphisms between two rice cultivars detected using a median polish method. Theor. Appl. Genet., 2009, 119:151-164. DOI: 10.1007/s00122-009-1025-2
18.   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 and Wu C. 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. Plant J., 2007, 49:947-959. DOI: 10.1111/j.1365-313X.2006.03001.x
19.   Huang Y, Zhang L, Zhang J, Yuan D, Xu C, Li X, Zhou D, Wang S and Zhang Q. Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol. Biol., 2006, 62:579-591. DOI: 10.1007/s11103-006-9040-z
20.   Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B and Zhang Q. Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol. Biol., 2006, 60:617-631. DOI: 10.1007/s11103-005-5441-7
21.   Liang D, Wu C, Li C, Xu C, Zhang J, Kilian A, Li X, Zhang Q and Xiong L. Establishment of a patterned GAL4-VP16 transactivation system for discovering gene function in rice. Plant J., 2006, 46:1059-1072. DOI: 10.1111/j.1365-313X.2006.02747.x
22.   Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q and Wang S. RMD: a rice mutant database for functional analysis of the rice genome. Nucl. Acids Res., 2006, 34:D745-748. DOI: 10.1093/nar/gkj016
23.   Xie K, Zhang J, Xiang Y, Feng Q, Han B, Chu Z, Wang S, Zhang Q and Xiong L. Isolation and annotation of 10,828 putative full length cDNAs from indica rice. Science in China Ser. C Life Sciences, 2005, 48:445-451. DOI:10.1360/062004-90
24.   Zhang J, Feng Q, Jin C, Qiu D, Zhang L, Xie K, Yuan D, Han B, Zhang Q and Wang S. 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. Plant J., 2005, 42:772-780. DOI: 10.1111/j.1365-313X.2005.02408.x
25.   Chu Z, Ouyang Y, Zhang J, Yang H and Wang S. Genome-wide analysis of defense-responsive genes in bacterial blight resistance of rice mediated by the recessive R gene xa13. Mol. Genet. Genomics, 2004, 271:111-120. DOI: 10.1007/s00438-003-0964-6
26.   Zhang L, Yuan D, Zhang J, Wang S and Zhang Q. A new method for EST clustering. Acta Genetica Sinica, 2003, 30:147-153 (Chinese with English Abstract)

Invited presentations
1.      Zhang J, Chen L, Xing F, Kudrna D, Yao W, Copetti D, Mu T, Li W, Song J, Xie W, Lee S, Talag J, Shao L, An Y, Zhang C, Ouyang Y, Sun S, Jiao W, Lv F, Du B, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou Z, Hurtado B, Danowitz A, Wing R and Zhang Q. A Case Study from ReSeq to RefSeq-Two High-Quality Reference Genome Sequences for indica Rice. Plant and Animal Genome, January 2017, San Diego, California, USA
2.      Zhang J, Kudrna D, Copetti D, Yu Y, Lee S, Talag J, Maldonado C, Padilla B, Wing R and Zhang Q. Two New indica Platinum Standard Reference Genomes. Plant and Animal Genome ASIA 2015, July 12 - 15, 2015, Singapore
3.      Zhang J, Kudrna D, Yu Y, Copetti D, Lee S, Talag J, Maldonado C, Mu T, Li W, Danowitz A and Wing R. Platinum standard reference genome sequencing: We can do it! The 12th International Symposium on Rice Functional Genomics, November 2014, Tucson, Arizona, USA

Posters
1.      Zhang J, Chen L, Xing F, Kudrna D, Yao W, Copetti D, Mu T, Li W, Song J, Xie W, Lee S, Talag J, Shao L, An Y, Zhang C, Ouyang Y, Sun S, Jiao W, Lv F, Du B, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou Z, Hurtado B, Danowitz A, Wing R and Zhang Q. Reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63 reveal their extensive sequence divergence. The 14th International Symposium on Rice Functional Genomics, September 2016, Le Corum, Montpellier, France
2.      Zhang J, Yu Y, Lee S, Goicoechea JL, Baynast K, Kudrna D, Wissotski M, Wing R. Genome Puzzle Master (GPM) - an Integrated Platform for Assembling. Plant and Animal Genome, January 2012, San Diego, California, USA
3.      Zhang J, Wei F, Maize Genome Sequencing Consortium and Wing R. An AGP Pipeline for Maize Genome Sequencing Project. Genomics of Energy & Environment – Fourth Annual DOE Joint Genome Institute User Meeting, March 2009, Walnut Creek, California, USA
4.      Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q and Wang S. RMD: a rice mutant database for rice functional genomics. Plant Genomics in China VI, August 2005, Kunming, China
5.      Zhang J, Feng Q, Jin C, Qiu D, Zhang L, Xie K, Yuan D, Han B, Zhang Q, Wang S. Large Scale Analysis of Expressed Sequence Tags from Indica Rice. The 4th International Crop Science Congress, September 2004, Brisbane, Australia
6.      Zhang J, Feng Q, Jin C, Qiu D, Zhang L, Xie K, Yuan D, Han B, Zhang Q, Wang S. Analysis of large-scale ESTs from indica rice and their relationships with important QTLs. Plant Genomics in China V, August 2004, Wuhan, China