Liping Wei, Ph.D.

Professor, Director
Center for Bioinformatics
Life Science College
Peking University

Associate Director
National Laboratory of Protein Engineering and Plant Genetic Engineering

Contact

E-mail:
Tel: +86 10 6275 5206

Address

Room 606
New Life Science Building
Peking University
Beijing, P. R. China,
100871

Degrees, Qualifications:

• Ph.D. in Medical Information Sciences (now called Biomedical Informatics), Stanford University, 1994-2000
• M.S. in Applied Mathematics, Brown University, 1993-1994
• Undergraduate in Radio Electronics (now called Electrical Engineering and Information Systems), University of Science and Technology of China 1989-1993

Previous Experience

• 2002-2004 Consulting Assistant Professor, Department of Medicine, Stanford University, Stanford, CA, USA
• 2001-2003 Chief Scientific Officer, Nexus Genomics, Inc., Mountain View, CA, USA
• 2001-2003 Adjunct Chief Scientist in Computational Biology, Hangzhou Genomics Institute, Hangzhao, China
• 2000-2001 Informatics Research Scientist, Exelixis, Inc., South San Francisco, CA, USA

Courses Taught

• Methods in Bioinformatics

Research Interests

• Antisense regulation of transcription and translation
• Expression regulation of and by noncoding RNAs
• Functional effects of SNPs in coding and noncoding regions
• Identification and evolution studies of protein pathway networks

Research Description

There are three dimensions in our research. (1) At the molecular level, we are interested in studying the expression, evolution, and function of natural antisense and noncoding RNAs. (2) At the disease level, we are interested in constructing the metabolic, signal transduction, and regulatory network underlying neurobiological diseases such as addiction. (3) At the technology level, we develop and provide new bioinformatic databases and algorithms for the study of expression regulation and molecular networks.

Recent data have shown that the human genome is widely transcribed and most transcripts involve noncoding RNAs. Some genomic loci may be transcribed from both strands in opposite directions, resulting in cis-natural antisense transcript pairs. Some transcripts may be transcribed from different genomic loci, but are still complementary in sequence, forming trans-natural antisense transcript pairs. Natural antisense play important regulatory roles in several levels including transcription, splicing, and translation. We have used bioinformatic approach to identify thousands of natural antisense pairs in 10 species. We are studying their expression profiles, conservation across different species, origin of the overlaps, and possible regulatory functions. Our focus is noncoding RNAs, many of which are involved in antisense regulation.

Advances of high-throughput technologies have generated tremendous amount of genetic, transcriptomic, and proteomic data related to neurobiological diseases such as addiction. We are interested in constructing the metabolic, signal transduction, and regulatory networks underlying neurobiological diseases by the integration and systematic analysis of multiple sources of data. We are particularly interested in putting noncoding RNAs in the regulatory networks underlying neurobiological diseases. Borrowing from control theories, we search for interlinked feedback loops and other critical modules that may be related to characteristics of addiction and other neurobiological diseases such as bi-stability and tolerance.

In our research we take the approach of first and primarily using bioinformatic analysis to find statistical patterns and promising candidates followed by experimental validation. Our lab combines “dry” lab computing and “wet” lab experiments. We have developed a number of bioinformatic databases and web servers for studying expression regulation and metabolic and regulatory networks. All tools were made freely available on the web and most of them have millions of hits annually.

Publications

• Jiong-Tang Li, Yong Zhang, Lei Kong, Qing-Rong Liu and Liping Wei, Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, July 24, 2008, doi:10.1093/nar/gkn470 [Full text]
• Wei L, Yu J., Bioinformatics in china: a personal perspective., Plos Computational Biology, 2008 Apr 25;4(4):e1000020 [Full Text]
• Li CY, Mao X, Wei L, Genes and (Common) Pathways Underlying Drug Addiction, Plos Computational Biology, [PubMed]
• Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei and Ge Gao, CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine, Nucleic Acids, Research 2007 35(Web Server issue):W345-W349; doi:10.1093/nar/gkm391, [PubMed] [Full Text]
• Ye ZQ, Zhao SQ, Gao G, Liu XQ, Langlois RE, Lu H, Wei L. Finding New Structural and Sequence Attributes to Predict Possible Disease-Association of Single Amino Acid Polymorphism (SAP). Bioinformatics 2007 23(12):1444-1450; doi:10.1093/bioinformatics/btm119; [Abstract] [Full Text]
• Li CY, Yu Q, Ye ZQ, Sun Y, He Q, Li XM, Zhang W, Luo J, Gu X, Zheng X, Wei L. A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir. Cell Research (2007) 17: 357–362. doi: 10.1038/cr.2007.27; (Cover story) [Abstract]
• Zhang Y, Li J, Kong L, Gao G, Liu QR, Wei L. NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res. 2007, Jan;35: D156-61 [Abstract] [Full Text]
• Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, Zhou Z, Wei L. SynDB: A Synapse protein DataBase based on Synapse Ontology, Nucleic Acids Res. 2007, Jan;35:D737-41 [Abstract] [Full Text]
• Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 2006 Jul 18;34(12):3465-75. [Abstract] [Full Text]
• Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J. DATF: a database of Arabidopsis transcription factors. Bioinformatics 21(10): 2568-9 [Abstract]
• Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res 32: W204-7 [Abstract]
• Zhou Y, Huang GM, Wei L. UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation. Bioinformatics 18(9): 1268-9 [Abstract]
• Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu LJ, Gu H. A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot 57(6): 1263-73 [Abstract]
• Wu J, Mao X, Cai T, Luo J, Wei L. KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 34: W720-4 [Abstract]
• Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. DRTF: a database of rice transcription factors. Bioinformatics 22(10): 1286-7 [Abstract]
• Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Res 34: W551-4 [Abstract]
• Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 34(12): 3465-75 [Abstract]
• Cai Z, Mao X, Li S, Wei L. Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics 7(1): 374 [Abstract] [Full Text]
• Lu XC, Gong HQ, Huang ML, Bai SL, He YB, Mao X, Geng Z, Li SG, Wei L, Yuwen JS, Xu ZH, Bai SN. Molecular analysis of early rice stamen development using organ-specific gene expression profiling. Plant Mol Biol 61(6): 845-61 [Abstract]
• Cheng HP, Wei S, Wei LP, Verkhratsky A. Calcium signaling in physiology and pathophysiology. Acta Pharmacol Sin 27(7): 767-72 [Abstract] [Full Text]
• Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18(3): 651-64 [Abstract] [Full Text]
• Zhou M, Xu H, Wei X, Ye Z, Wei L, Gong W, Wang Y, Zhu Z. Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol 140(1): 184-95 [Abstract] [Full Text]
• Wu X, Walker MG, Luo J, Wei L. GBA server: EST-based digital gene expression profiling. Nucleic Acids Res 33: W673-6 [Abstract] [Full Text]
• Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19): 3787-3793 [Abstract] [Full Text]
• Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 14(3): 451-8 [Abstract]
• Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L. Database and analyses of known alternatively spliced genes in plants. Genomics 82(6): 584-95 [Abstract]
• Wei L, Altman RB. Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function. J Bioinform Comput Biol 1(1): 119-38 [Abstract]
• Wei L, Liu Y, Dubchak I, Shon J, Park J. Comparative genomics approaches to study organism similarities and differences. J Biomed Inform 35(2): 142-50 [Abstract]
• Waugh A, Williams GA, Wei L, Altman RB. Using meta computing tools to facilitate large-scale analyses of biological databases. Pac Symp BiocomputPac Symp Biocomput: 360-71 [Abstract]
• Bagley SC, Wei L, Cheng C, Altman RB. Characterizing oriented protein structural sites using biochemical properties. Proc Int Conf Intell Syst Mol Biol 3: 12-20 [Abstract]
• Wei L, Altman RB, Chang JT. Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac Symp BiocomputPac Symp Biocomput: 465-76 [Abstract]
• Wei L, Altman RB. Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac Symp BiocomputPac Symp Biocomput: 497-508 [Abstract]
• Wei L, Huang ES, Altman RB. Are predicted structures good enough to preserve functional sites?. Structure 7(6): 643-50 [Abstract]