Ting Chen, Ph.D

Professor of Biology, Computer Science and Mathematics

University of Southern California


Address: 1050 Childs Way, RRI 408H, Los Angeles, CA 90089-2910 USA

Email : tingchen at usc dot edu,

Phone: 213-740-2415



Research Interest: Within the fields of computational biology and bioinformatics, Professor Chen seeks to apply computer algorithms and mathematical methods to answer questions in biology and medicine, specifically in studies of human genetics, proteomics, and genomics. His research includes (1) large-scale sequence analysis for the next generation sequencing data, (2) analysis of genetic variations of the human genome for their relationships to human diseases, (3) studies of functions and dynamic of large-scale biochemical networks inside the cell, and (4) identification of proteins through analyzing mass spectrometry data.


Short Bio: Professor Chen is currently a professor of biological sciences, computer science, and mathematics at USC.  Before joining USC in 2000, he had been a lecturer of genetics at Harvard University, working as a research fellow in George M. Church’s Laboratory.  He obtained his Ph.D. degree in computer science from SUNY Stony Brook in 1997, and B.E. degree in computer science and technology from Tsinghua University in 1993.

He is a Sloan Research Fellow (2004),  His Google Scholar Profile (Accuracy: 90%)  His Complete Resume/CV/Publications.

Software Tools for Next Generation Sequencing (NGS) Data

·         PerM (http://code.google.com/p/perm/): a read-mapping software based on periodic spaced seeds for both Illumina and SOLiD sequencing data. (paper)

·         Clippers (http://code.google.com/p/clippers/): a sister gap-mapping program of PerM, allowing one gap plus multiple substitutions, with applications for finding novel splice junctions and structural variations.

·         ComB (http://code.google.com/p/ComB): a Bayesian model for SNP-calling for both Illumina and SOLiD sequencing data, which iteratively maps reads to the genome, calls SNPs, and updates the genome sequences. (paper)

·         WeaV (http://code.google.com/p/weav-assembler/): a de novo assembly program for both genome and RNA.

·         CROP (http://code.google.com/p/crop-tingchenlab/): an un-supervised Bayesian clustering tool for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTUs). (paper)

·         RseqFlow (http://genomics.isi.edu/rnaseq): an RNA-seq data analysis workflow, which uses Pegasus Workflow Management System to manage workflow execution. RseqFlow can be installed as Virtual Machine.

·         FadE (http://code.google.com/p/fade/ ): a Bayesian method for DNA methylation detection.

·         PyroHMMsn (https://code.google.com/p/pyrohmmsnp/): A method which combines accurate error model and realignment strategy to call SNPs for Ion Torrent and 454 sequencing data. 

·         PyroHMMvar(https://code.google.com/p/pyrohmmvar/): A method extending PyroHMMsnp with weighted alignment graph to call short indels and SNPs for Ion Torrent and 454 sequencing data.


Other software tools

·         SInBaD(http://tingchenlab.cmb.usc.edu/sinbad/): a database for human functional variant prediction in promoter, coding, and intron regions.

·         MSRV(http://tingchenlab.cmb.usc.edu/msrv/): a sequence-based prioritization of non-synonymous single nucleotide polymorphisms for disease.

·         PepHMM(http://tingchenlab.cmb.usc.edu/PepHMM/): an HMM model for tandem mass spectral protein database search.

·         MSNovo (http://tingchenlab.cmb.usc.edu/msnovo/): a de novo peptide sequencing program for tandem mass spectrometry.

·         EMDDI(http://tingchenlab.cmb.usc.edu/emddi/): Inference of domain-domain interactions from protein-protein interactions.

·         KLR(http://tingchenlab.cmb.usc.edu/klr/): A kernel based logistic regression model for integrated protein function prediction.

·         REL(http://tingchenlab.cmb.usc.edu/rel/): assessment of reliability of protein-protein interaction data sets.




The fear of the Lord is the beginning of wisdom, and the knowledge of the Holy One is understanding. (Proverbs 9:10)