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/
·
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)