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Yanda Li, Professor

Member of CAS

Dept of Automation

Tsinghua University

Beijing 100084, China

Tel: +86-10-6279-4295

Fax: +86-10-6278-6911

Email: daulyd@tsinghua.edu.cn

 

Last Update: 2012.2.17

 

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Yanda Li's Lab

 

 

 

Research Scopes

      ncRNAs (non-coding RNAs)

    In higher eukaryotic organisms, the protein-coding gene regions only account for very small part of the whole genome. What are the "hidden" functions of other regions? Few non-coding genes which can be transcribed into ncRNAs are identified before the burst of hundreds of miRNAs. After lin-4 and let-7 are discovered in C. elegans, the tiny ~22nt molecules attract extensive attentions. These molecules are important posttranscriptional regulators by repressing or degrading mRNAs by base-pairing to their 3'-UTRs or coding regions. Recent studies show that miRNAs can maintain or change the expression profiles of cell lineage. Many cancer tissues show low-expressions of miRNAs. Computational methods can greatly forward our understanding miRNAs and other ncRNAs. We mainly use secondary structures, comparative genomics and expression data (ESTs, microarray, CAGE) to identify ncRNAs and to explore their functions.

      Alternative Splicing

    The sequencing of human genome shows a surprisingly small number of genes, which raises great interests in the origin of organism complexity. The problem can partly be explained by the post-transcriptional process termed alternative splicing, which can produce many mRNA isoforms from a single gene. Alternative splicing is prevalent in higher eukaryotes and plays important regulatory and functional roles in these organisms. Moreover, alternative splicing has extensive relation with human diseases. It is reported that mis-regulation of alternative splicing is involved in 15% of human genetic diseases and may also promote tumorigenesis. In our lab, we mainly exploit computational methods to study alternative splicing. Computational methods have provided us great insights into almost all aspects of alternative splicing including its regulation, function and evolution and we believe it is indispensable in the post-genome era.

      Complex Diseases

     The research in human disease genomics has begun to deal with the difficult complex diseases. Because the multigenic disorders are caused by the effects of multiple genes, and the dynamic regulation in the gene network is very complicated, the research in complex diseases needs big improvements in population and marker selection, mathematic models, and statistical methods, etc. We made a great effort in development of new statistic methods to detect the susceptibility loci of complex diseases with epistatic interactions. In this area, we made deep and wide research in schizophrenia by cooperation with Peking Union Medical College. We developed two multi-locus association methods which have some advantages over the current popular methods in detecting susceptibility loci with complex and weak epistatic interactions. Besides, in the schizophrenia research, we found the joint effects of two genes significantly associated with schizophrenia in dopaminergic pathway. We will make further research in detection of susceptibility genes of the complex diseases and their etiopathogenesis. Our future research will focus on the problems in genomewide association study, population stratification, genotype error and missing data, etc.

Graduate Students

Yu Liu, Ting Wang, Honglei Liu, Zhen Zhao, Zijian Ding

Graduated Students (From 2007)

2010: Wanwan Tang

2009: Pufeng Du, Tao Peng, Jin Gu, Jing Zhang

2008: Tao He, Xiaowo Wang, Jianning Bi

2007: Huiyu Xia, Xiangqing Sun

Selected Publications (From 2006)

Year 2011

Xin Yao, Han Hao, Yanda Li, Shao Li. Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. BMC System Biology 2011, 5:79.

Year 2010

Jin Gu, Yang Chen, Shao Li, Yanda Li. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC System Biology 2010, 4:47.

Li Tang, Zhen Chen, Hao Yin, Jun Li, Yanda Li. CORS: A cooperative overlay routing service to enhance interactive multimedia communications. JOURNAL OF VISUAL COMMUNICATION AND IMAGE REPRESENTATION 2010, 21(2):107-119.

Year 2009

Wanwan Tang, Xuebing Wu, Rui Jiang, Yanda Li. Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy. PLoS Genet 2009, 5(5):e1000464.

Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution human core-promoter prediction with CoreBoost_HM, Genome Research 2009, 19(2):266-75.

Pufeng Du, Shengjiao Cao and Yanda Li. SubChlo: Predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm. Journal of Theoretical Biology 2009, 261(2):330-335.

Pufeng Du, Liyan Jia and Yanda Li. CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics 2009, 10:135.

Jin Gu, Shao Li, Yang Chen, Yanda Li. Integrative computational identifications of the signaling pathway network related to TNF-alpha stimulus in vascular endothelial cells. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS'09) 2009, 422-427.

Pufeng Du and Yanda Li. Computational analysis of RNA editing: seeking tiny discrepancies between transcriptome and genome. Frontiers of Electrical and Electronic Engineering in China 2009, 4(3): 251?58.

Pufeng Du, Yang Chen and Yanda Li. Computational evidence of A-to-I RNA editing in nucleus transcriptome of Arabidopsis thaliana. Frontiers of Electrical and Electronic Engineering in China 2009, 4(4):349-361.

Tao Peng, Pufeng Du and Yanda Li. PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions. Bioinformation 2009, 3(8): 349-351.

Year 2008

Pufeng Du and Yanda Li. Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information. Journal of Theoretical Biology 2008, 253:579-586.

Tao Peng, Chenghai Xue, Jianning Bi, Xiaowo Wang, Xuegong Zhang, Yanda Li. Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics 2008, 9:191.

Jianning Bi, Tao Peng, Yanda Li. Evidence for association of multi-exon skipping events with tumors. Front Electr Electron Eng China 2008, 3(3):260-266.

Xiaowo Wang, Jin Gu, Michael Zhang, Yanda Li. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics 2008, 24(2):165-171. [Software] [Abstract]

Xiaowo Wang , Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of miRNAs in vertebrates, Sci China Ser C-Life Sci, 51(6):552-9 2008

汪小我,张学工,李衍达,脊椎动物中微小RNA进化模式研究, 中国科学C辑:生命科学,2008, 38(4):348-355

Zhang J, Ma T, Li YD, Li S. dbNEI2.0: building multilayer network for drug-NEI-disease. Bioinformatics,2008,24:2409-2411.

Year 2007

Xiaowo Wang, Jin Gu, Michael Zhang, Yanda Li. Identification of Drosophila microRNA cis-regulatory elements by phylogenetic footprinting. in Genome Informatics 2007: CSHL, NY, United States (Poster).

Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li. Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics 2007, 8:432. [Software] [Abstract]

Pufeng Du, Tao He, Yanda Li. Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features. Biochem Biophys Res Commun 2007, 358(1):336-341. [Abstract]

Shao Li, Zhongqi Zhang, Lijiang Wu, Xuegong Zhang, Yanda Li, Wang Y. Understanding ZHENG in Traditional Chinese Medicine in the context of neuro-endocrine-immune network. IEE Systems Biology 2007, 1(1):51-60. [Abstract]

Xiaowo Wang, Yanda Li. The active evolution of microRNAs. in NSF Sponsored International Conference on Bioinformatics. 2007: Hang Zhou, China (Oral).

Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li. Neighbor number, valley seeking and clustering. Pattern Recognition Letters 2007, 28:173-180.

Tao He, Pufeng Du, Yanda Li. dbRES: a web-oriented database for annotated RNA Editing Sites. Nucleic Acids Res 2007, 35(Database issue):D141-4.

Year 2006

Pufeng Du, Yanda Li. Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioiformatics 2006, 7:518.

Huiyu Xia, Jianning Bi, Yanda Li. Identification of alternative 5'/3' splice sites based on the mechanism of splice site competition. Nucleic Acids Res 2006, 34(21):6305-6313.

Jin Gu, Tao He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xuegong Zhang, Yanda Li. Primary Transcripts and Expressions of Mammal Intergenic MicroRNAs Detected by Mapping ESTs to Their Flanking Sequences. Mamm Genome 2006, 17(10):1033-1041.

  Before Year 2005 (Selected Publications)

Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li. MicroRNA Identification Based On Sequence and Structure Alignment. Bioinformatics 2005, 21:3610-3614.

Fang Wen, Fei Li, Huiyu Xia, Xin Lu, Xuegong Zhang, Yanda Li. The impact of very short alternative splicing on protein structures and functions in the human genome. Trends in Genet 2004, 20(5): 232-236.

Ying Huang, Yanda Li. Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics 2004, 20: 21-28.

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   Bioinformatics Division, TNLIST and Department of Automation