Zhang’s lab combines the method of computational system biology with the latest experimental technique to study the structure and function of genome, and gene regulatory network in the condition of disease (tumor) and development. There are three major research areas in our group:
    The micro-evolution of the gene regulatory network (GRN). We are focusing on how the topology and network dynamics change by the mutation in the process of tumorigenesis, the formation and development of tumor heterogeneity and tumor metastasis and how the changes affect the evolution of tumor in vivo further . We anticipate to develop a new computational method to identify the genetic or epigenetic viarations which play important roles in this process from the point of view of the dynamic and evolution of the GRN.
    The remote reaction of gene regulatory elements. We are interested in these questions: a) how to predict a specific target gene of a specific regulatory element in this complex interaction network; b) how to predict the spatiotemporal expressive pattern by the feature of GRN; c) how to understand the spatial structure formation of chromatin fibers in nuclei and its relationship with the GRN functions.
    The noncoding RNA (ncRNA) in the GRN of remote reaction. We pay special attention to ncRNAs associated with enhancer and their formation, regulation and evolutionary pattern. We expect to develop a new computational method to predict the long noncoding RNA expression associated with specific enhancer and its target gene

2002 – 2006  Ph.D.  Computational Biology. 
With Prof. Runsheng Chen. IBP, CAS.

   

2006 – 2011 Postdoc. Systems Biology.
With: Prof. Jianzhi (George) Zhang, UMICH, USA.
Prof. Michael Q. Zhang. CSHL, USA.

Bioinformatics and Computational Biology,  30 class hours, audience: graduate students;
Evolutionary Biology,  4 class hours, audience: graduate students.

   

（1） Computational inference of physical spatial organization of eukaryotic genomes, Quantitative Biology, 2016
（2） ESCRT-0 complex modulates Rbf mutant cell survival by regulating Rhomboid endosomal trafficking and EGFR signaling, J Cell Sci, 2016
（3） 3CDB: A manually curated database of Chromosome Conformation Capture Data, Database, 2016
（4） Functional diversity of CTCFs is encoded in their binding motifs, BMC Genomics, 2015
（5） The evolution of heterogeneities altered by mutational robustness, gene expression noise and bottlenecks in gene regulatory networks, PLos One, 2014
（6） Computational identification of active enhancers in model organisms , Genomics, Proteomics and Bioinformatics, 2013
（7） Bivalent-like chromatin markers are predictive for transcription start site distribution in human, PLoS ONE, 2012
（8） Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study, BMC Bioinformatics, 2012,
（9） Histone modification profiles are predictive for both protein coding and microRNA genes tissue cell-type specific expression, BMC Bioinfomatics, 2011
（10） positive selection for elevated gene expression noise in yeast, molecular systems biology, 2009
（11） a big world inside small-world networks, PLoS ONE, 2009
（12） accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation, nucleic acids research, 2008
（13） dynamic changes in subgraph preference profiles of crucial transcription factors, PLoS computational biology, 2006

（1） 863 project "A bioinformatics platform of systematical identification and analysis for long noncoding RNAs", presider, national, 2014-01--2016-12
（2） 973 project " A study on the transcriptome and the proteome of  tumorigenesis", participant, national, 2014-01--2018-12
（3）"Hundred people plan" preferential support , presider, CAS, 2013-01--2015-12
（4） A study on the coupling between transcription and splicing based on the integration of multiple "-omics" data, ministry, 2013-01--2016-12

（1） An efficient and assumption free method to approximate protein level distribution，The 2nd national conference of computional biology and bioinfoematics , 2015-04, Bingxiang Xu 
（2） Mutational robustness and gene expression noise in GRN alter the evolution of phenotypic heterogeneity in tumor therapies，Society for Molecular Biology & Evolution Annual Meeting 2014 , 2014-06, Zhihua Zhang 
（3） The evolution of heterogeneities altered by mutational robustness, gene expression noise and bottlenecks in gene regulatory networks，Huazhong System Biology Forum, 2014-04, Zhihua Zhang

（1） 863 project "A bioinformatics platform of systematical identification and analysis for long noncoding RNAs", coorperated with  Tsinghua University; Institute of Computing Technology, CAS; Peking University; Institute of Zoology, CAS;  Institute of  Biophysics, CAS; The Second Military Medical University.
（2） 973 project " A study on the transcriptome and the proteome of tumorigenesis" , cooperated with Institute of Cancer, Chinese Academy of Medical Sciences.

已指导学生

张轶群  硕士研究生  071021-生物信息学  

俞丽佳  硕士研究生  071021-生物信息学  

云霄霄  硕士研究生  0710J3-生物信息学  

夏莉莉  硕士研究生  0710J3-生物信息学  

唐碧霞  博士研究生  0710J3-生物信息学  

张辉  博士研究生  0710J3-生物信息学  

刘聪  博士研究生  0710J3-生物信息学  

李小丽  博士研究生  0710J3-生物信息学  

徐炳祥  博士研究生  0710J3-生物信息学  

李笑  硕士研究生  0710J3-生物信息学  

安子扬  硕士研究生  085238-生物工程  

现指导学生

张潇  博士研究生  0710J3-生物信息学  

高晓萌  硕士研究生  0710Z1-基因组学  

王丹阳  博士研究生  0710J3-生物信息学  

李子健  硕士研究生  0710J3-生物信息学