- 张韬
- 电子邮件：zhangtao@cib.ac.cn
- 职 称：研究员
- 学 历：博士
- 通讯地址：四川省成都市天府新区群贤南街23号
- 邮 编：610213
个人简历
张韬，研究员，博导，主要研究方向为利用人工智能大语言模型、基因组学、分子生物学多学科交叉分析及实验方法进行重要调控元件进行预测、鉴定及深度挖掘，对植物基因组编辑体系进行系统优化等工作;先后承担国家自然科学基金、国家转基因重大专项等课题；在Molecular Plant,Nature Plants,Nature Communications,Genome Biology,PNAS,Plant Cell,Nucleic Acids Research等期刊发表SCI论文60余篇，H-Index 36；先后入选神农英才计划神农青年英才、江苏特聘教授、江苏省“双创计划”双创团队领军人才等人才计划
研究方向
围绕植物基因组语言建模与智能预测，基于“深度学习+基因组大数据”方法，创新性构建了DNA大语言模型体系，采用表征学习框架将DNA序列转化为高维语义向量，进而预测染色质开发性、组蛋白修饰、转录因子结合等数功能特征，突破传统基因组功能位点预测依赖复杂人工规则设计的瓶颈。
对植物开放染色质位点进行全基因组作图，利用生物信息学结合表观遗传学方法建立了植物基因组调控元件的高通量预测体系,解析了调控元件与表观遗传学标记、染色质构象之间的关系，为植物功能基因组学研究提供了重要的数据支持。在近期的研究中采用不依赖基因组参考序列的方法，成功在落叶松中挖掘了一系列落叶松高效调控元件，并运用于落叶松转基因及基因编辑体系中。
以水稻等模式为模型，基于“全基因组测序+大数据+人工智能”分析策略，对CRISPR-Cas9、CRISPR-Cas12a及单碱基编辑器等进行编辑体系的效率优化、准确性提升及拓展编辑系统的适用范围，整合人工智能、大数据、基因编辑方法对作物进行定向改良育种。在近期的研究中通过对开放染色质、转录因子结合基序、序列保守性、组蛋白修饰以及基因型表型关联性等关键特征的提取，运用机器学习方法对水稻启动子关键区域进行评估，并利用基因编辑方法对关键区域进行编辑获得了数量性状连续性变化的遗传材料。
利用基因组分析方法，创立植物Oligo-FISH靶向性荧光原位杂交实验体系，该体系被成功运用于于水稻、玉米、土豆、杨树、小麦等动植物的细胞遗传研究中。在近期的就中该方法成功运用于甘蔗、鸡的基因组拼装完整性评估中，为基因组学、细胞遗传学的研究引入了新的研究方法。
社会任职
中国生物信息学学会（筹）农林信息学专业委员会秘书长
江苏省生物信息学学会理事
承担科研项目情况
国家自然科学基金面上项目、国家转基因重大专项等
代表论著
1.Liu GQ,Chen L,Wu YC,Han YS,Bao Y, Zhang T*. PDLLMs: A group of tailored DNA large language models for analyzing plant genomes. Molecular Plant 2025,18(2):175-178
2.Yang QQ,Zhu WJ,Tang X,Wu YC,Liu GQ,Zhao DS,Liu QQ*,Zhang Y*,Zhang T*.Improving rice grain shape through upstream open reading frame editing-mediated translation regulation. Plant Physiology 2025,197(1):kiae557
3.Han YS†,Liu GQ†,Wu YC,Bao Y,Zhang Y*,Zhang T*. CrisprStitch: Fast evaluation of the efficiency of CRISPR editing systems. Plant Communications 2024,5(3):100783
4.Fan TT†,Cheng YH†,Wu YC†,Liu SS†,Tang Xu†,He Y,Liao SY,Zheng XL,Zhang T*,Qi YP*,Zhang Y*.High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants. Nature Communications 2024,15:5103
5.Chen L,Liu GQ,Zhang T*. Integrating machine learning and genome editing for crop improvement. aBIOTECH2024,5:262-277
6.Zhou JP†,Liu GQ†,Zhao YX,Zhang R,Tang X,Li L,Jia XY,Guo YC,Han YS,Bao Y,He Y,Han QQ,Yang H,Zheng XL,Qi YP*,Zhang T*, Zhang Y*. An efficient CRISPR–Cas12a promoter editing system for crop improvement. Nature Plants 2023,9:588-604
7.Wu YC†,Ren QR†,Zhong ZH†,Liu GQ†,Han YS,Bao Y,Liu L,Xiang SY,Liu S,Tang X,Zhou JP,Zheng XL,Sretenovic S,Zhang T*, Qi YP*,Zhang Y*. Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice. Plant Biotechnology Journal 2022,20(9):1670-1682
8.Wu YC†,He Y†,Sretenovic S,Liu SS,Cheng YH,Han YS,Liu GQ,Bao Y,Fang Q,Zheng XL,Zhou JP,Qi YP*,Zhang Y*,Zhang T*. CRISPR-BETS: A base editing design tool for generating stop codons. Plant Biotechnology Journal 2022,20(3):499-510
9.Xue C†,Liu GQ†,Sun S,Liu XY,Guo R,Cheng ZK,Yu HX,Gu MH,Liu K,Zhou Y*,Zhang T*,Gong ZY*. De Novo Centromere Formation in Pericentromeric Region of Rice Chromosome 8. The Plant Journal 2022,111(3):859-871
10.Zhang T†*, Liu GQ†,Zhao HN,Braz G.T,Jiang JM*. Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization. Plant Biotechnology Journal 2021,19(10):1967-1978
11.Zhao HN†,Zhang WL†*,Zhang T†,Lin Y,Hu YD,Fang C,Jiang JM*. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biology 2020,21:24
12.Liu GQ,Zhang Y*,Zhang T*. Computational approaches for effective CRISPR guide RNA design and evaluation. Computational and Structural Biotechnology Journal 2020,18:35-44
13.Xue C†,Liu GQ†,Sun S,Liu XY,Guo R,Cheng ZK,Yu HX,Gu MH,Liu K,Zhou Y*,Zhang T*,Gong ZY*. De Novo Centromere Formation in Pericentromeric Region of Rice Chromosome 8. The Plant Journal 2022,111(3):859-871
14.Albert P.S†,Zhang T†, Semrau K,Rouillard JM,Kao YH,Wang CJ,Danilova T.V,Jiang JM,and Birchler J*. Whole-chromosome paints in maize reveal rearrangements,nuclear domains,and chromosomal relationships. Proceedings of the National Academy of Sciences of the United States of America 2019,16(5):1679-1685
15.Tang X†,Liu GQ†,Zhou JP†,Ren QR,You Q,Tian L,Xin XH,Zhong ZH,Liu BL,Zheng XL,Zhang DW,Malzahn A,Gong ZY,Qi YP*,Zhang,T*,and Zhang Y*. (2018). A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1(Cas12a) nucleases in rice. Genome Biology 2018,19:84
16.Zhang T,Marand A,Jiang JM*. PlantDHS: A Database for DNase I Hypertensive Sites in Plants. Nucleic Acids Research 2016,44(D1):D1148-D1153.
17.Zhang T†,Zhang WL†,and Jiang JM*. Genome-wide nucleosome occupancy and positioning and their impact on gene expression and evolution in plants. Plant Physiology 2015,168(4):1406-1416.
18.Zhu B†,Zhang WL†,Zhang T†,Liu B,Jiang JM*. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signature. The Plant Cell 2015,27(9):2415-2426.
19.Zhang T†,Talbert PB†,Zhang WL†,Wu YF,Yang ZJ,Henikoff JG,Henikoff S,Jiang JM. The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proceedings of the National Academy of Sciences of the United States of America 2013,110(50):E4875–E4883.
20.Zhang WL†,Zhang T†,Wu YF†,Jiang JM. Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis. The Plant Cell 2012,24(7):2719-2731.
