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EducationNational Taiwan University, Taipei, Taiwan, B.S.,1986, Agricultural Chemistry National Taiwan University, Taipei, Taiwan, M.S., 1988, MicrobiologyUniversity of Massachusetts, Amherst, MA, Ph.D. 1995, Microbiology

Research FocusBioinformaticsis a thriving scientific discipline that integrates computer sciencewith applications in molecular biology. During the last decade, thecompletion of genomic sequences from many organisms has provided much valuabledata to be analyzed, organized and stored. Among the genomes that have beenor are currently being sequenced are those of several pathogens associatedwith oral and dental diseases. The Chen lab develops and uses high-throughputcomputational and experimental approaches to unveil information hiddenin certain oral pathogenic genome sequences. The results of our work,to be shared via public and proprietary databases, will lead to betterunderstanding of oral disease mechanisms and, ultimately, to bettercures or disease prevention.

Specificprojects in our lab include the following:Automatic annotation of oral pathogen genome sequencesGenomicsequences, both finished and unfinished, hold a tremendous amount of biologicalinformation that is yet to be discovered. The first phase in the mining and functionaldiscovery process is automatic, computer-assisted annotation. We are developingannotation tools that will help reveal important biological information fromboth finished and unfinished genome sequences. The algorithm would predict thefunctions of genes based on multiple evidences such as Blast, Motif, and structuralinformation. The derived functions would then be mapped to gene ontology treesand metabolic pathways for easy browsing and searching.

Functional prediction of unknown genes based on gene expression profiling dataManygenes derived from genome sequences remain functionally unknown after annotationbased on multiple sequence, motif, and structural homology searches.For example, of a total of 2043 predicted open reading frames in thegenome of the periodontal pathogen Porphyromonas gingivalis, nearly half(1003) have no known function after annotation based on computer-aidedanalysis. This phenomenon is similar in all other organisms whose genomeshave been sequenced. Global gene expression profiling patterns usingDNA microarrays can be used to predict functions of those unknown genes.The rationale is that genes of similar functions tend to be regulatedand expressed in similar ways, thus presenting similar gene expressionpatterns that can be recognized and clustered together with special computationalgorithms. We are gathering microarray gene expression profiles fromP. gingivalis and aim to expand our knowledge of the functions of genesin this organism.

Oral bioinformatic databasesBioinformatic data such as sequences, annotations and microarray gene expressiondata are rich in biological information and should be shared within the scientificcommunity. We are constructing proprietary and public bioinformatic databasesthat will serve information such as genome annotation and gene expression dataas well as useful tools for analyzing the data.

Selected Publications

Chen, T., K. Abbey, W.J. Deng, M.C. Cheng. (2005) The bioinformatics resource for oral pathogens.Nucleic Acids Res. 33(Web Server issue):W734-40.

Dewhirst, F.E., Z. Shen, M.S. Scimeca, L.N. Stokes, T. Boumenna, T. Chen, B.J. Paster, J.G. Fox (2005) Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: implications for phylogenetic inference and systematics. J. Bacteriol. 187:6106-18.

Chen,T., M.J.Duncan. (2004) Gingipain adhesin domains mediate Porphyromonasgingivalis adherence to epithelial cells. Microb. Pathog. 36:205-209.

Chen,T., K. Nishikawa, Y. Hosogi, S. Long, and M. J. Duncan. (2004) Comparativewhole genome analysis of virulent and avirulent strains of Porphyromonasgingivalis. J. Bacteriol. 186:5473-5479.

Tsute Chen, Koji Nakayama, Lynn Belliveau, and Margaret J. Duncan. (2001) Porphyromonasgingivalis gingipains and adhesion to epithelial cells. Infect. Immun. 69:3048-2056.

Renata O. Mattos-Graner, Song Jin, William F. King, Tsute. Chen, Daniel J. Smith,and Margaret J. Duncan. (2001) Cloning of the Streptococcus mutans geneencoding glucan binding protein B and analysis of genetic diversity andprotein production in clinical isolates. Infect. Immum. 69:6931-6941.

Tsute Chen, Hong Dong, Rothsovann Yong, and Margaret J. Duncan.(2000) Pleiotropicpigmentation mutants of Porphyromonas gingivalis. Microb.Pathogen. 28:235-247

Tsute Chen, Lillian Ouko, Thomas Warnick and Susan B. Leschine. (2000)Detection, cloning and sequencing analysis of an indigenous plasmid from cellulolyticclostridial strain MCF1. Plasmid 43:153-158.

Tsute Chen, Rothosovann Yong, Hong Dong, and Margaret J. Duncan. (1999) A general methodfor direct sequencing of transposon mutants by randomly primed PCR. TechnicalTips Online (http://tto.biomednet.com)T01834.

Tsute Chen, Hong Dong, Yixin P. Tang, Mary M. Dallas, Michael H. Malamy, and Margaret J. Duncan. (2000) Identification andcloning of genes from Porphyromonas gingivalis after mutagenesis witha modified Tn4400 transposon from Bacteroides. Infect.Immun. 68: 420-423

Hong Dong, Tsute Chen, Floyd E. Dewhirst, Robert D. Fleischmann, Claire M. Fraser, and Margaret.J. Duncan (1999) Genomic Loci of the Porphyromonas gingivalis InsertionElement IS1126. Infect. Immun. 67:3416-3423.