LIFENG CHEN

Department of BioMedical Informatics &

Center for Computaional Biology and Bioinformatics

Irving Cancer Research Center, 8th Floor

1130 St. Nicholas Avenue

New York , NY 10032

Phone: (212)-851-4672

E-mail: lifeng.chen@dbmi.columbia.edu

 

Mr. Lifeng Chen is a fifth year PhD student in the Department of Biomedical Informatics at Columbia University in the City of New York . He obtained a B.S. in Genetics from Fudan University in China followed by a Masters' degree in Biological Science from the University of Maryland , Baltimore County .

  His research interests include:

1. Reconstruction of metabolic networks using combined genomic context-based information such as phylogenetic profile, protein fusion events, gene co-expression, gene neighborhood, gene clustering and traditional homology-based methods.

2. Prediction of responsible sequences for orphan metabolic activities - biochemically known reactions without any representative sequences - based on combined homology and genomic context-based correlations.

3. Making the predictions in 2) available to the scientific community (the beta verison of the informatic resource is available at: ADOMETA - adoption of orphan metabolic activities website) and actively validate the computational predictions using experimental methods via collaboration with wet-lab biologists.

4. Evolution and diversification of sequences and structure of metaboic enzymes in Archaea, Bacteria, and Eucarya.

5. Detecting transcriptional domains in metabolic enzymes or gene moonlighting.

6. Naming ambiguities of gene/protein names and their effect in de-orphaning orphan activities.

7. Utilizing Natural Language Processing (NLP) to extract biomedical knowledge from the online literature.

 

Publications :

Tobias Fuhrer#, Lifeng Chen#, Uwe Sauer, Dennis Vitkup. Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli.THE JOURNAL OF BACTERIOLOGY. 2007 (Accepted).
# These authors contributed equally to this work.

Lifeng Chen and Dennis Vitkup. Distribution of orphan metabolic activities. TRENDS IN BIOTECHNOLOGY. 2007 Aug;25(8):343-8.

Tulipano PK, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. JOUNAL OF BAIMEDICAL INFORMATICS. 2007 Jun;40(3):270-81.

Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., Church, G. M. Identifying metabolic enzymes with multiple types of association evidence. BMC BIOINFORMATICS. 2006: 7:177.

Lifeng Chen, Dennis Viktup. Predicting Genes for Orphan Metabolic Activities using Phylogenetic Profiles. GENOME BIOLOGY. 2006: 7:R17.

Lifeng Chen, Hongfang Liu and Carol Friedman. Gene Name Ambiguity of Eukaryotic Nomenclatures. BIOINFORMATICS. 2005: 15;21(2):248-56.

Stahl G, Salem SN, Chen L, Zhao B, Farabaugh PJ.Translational Accuracy during Exponential, Postdiauxic, and Stationary Growth Phases in Saccharomyces cerevisiae. EUKAROT CELL. 2004 3:331-338.

Lifeng Chen, Carol Friedman. Extracting Phenotypic Information from the Literature via Natural Language Processing. MEDINFO 2004: 758-62

Olivia Tuason, Lifeng Chen, Hongfang Liu, Judy Blake, Carol Friedman. Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity. PAC. SYMP. BIOCOMPUT. 2004: 238-49.

Ke Y, Su B, Song X, Lu D, Chen L, Li H, Qi C, Marzuki S, Deka R, Underhill P, Xiao C, Shriver M, Lell J, Wallace D, Wells RS, Seielstad M, Oefner P, Zhu D, Jin J, Huang W, Chakraborty R, Chen Z, Jin L. African Origin of Modern Humans in East Asia: A tale of 12,000 Y chromosomes. SCIENCE. 2001. 292(5519): 1151-3

KE Yuehai, SU Bing, LI Hongyu, CHEN Lifeng, QI Chunjian, GUO Xinjun, HUANG Wei, JIN Jianzhong, LU Daru, JIN Li. Y-chromosome evidence for no independent origin of modern human in China. CHINESE SCIENCE BULLETIN. 2001; 46-11: 935-37

(In Chinese) Ke Y, Su B, Li H, Chen L, Qi C, Guo X, Huang W, Jin J, Lu D, Jin L. Y-chromosome evidence for African origin of modern humans in China. SCIENCE CHINA . 2001; 46-5: 411-414

 

Presentations :

  MedInfo 2004 Conference. Extracting Phenotypes from the online literature. San Fransisco. September 10th, 2004

Pacific Symposium for Biocomputing. Acquisition of lexical Knowledge using Biological Nomenclatures. The Big Island , Hawaii , January 10th, 2004

 

Abstracts :

BioLink 2004 Conference. Eukaryotic Nomenclature Ambiguities for 21 organisms. Boston , May 6th, 2004

CAT 2004 Technology Forum. Gene Name Ambiguities of Eukaryotic Organisms. New York , Oct 12th, 2004

 

Professional Affiliations :

International Society for Computational Biologists (ISCB)

American Medical Informatics Association (AMIA)

New York Academy of Sciences (NYAS)