Ting Chen
Department of Biological Sciences

University of Southern California
Los Angeles, CA 90089-2910 USA


Research Interests

 

Education

 

Academic Experience

 

Awards and Grants

 

Publications (74 total)

Next Generation Sequencing

  1. Zeng F, Jiang R and Chen T (2013)  PyroHMMvar: an accurate and sensitive SNP and short indel caller for Ion Torrent and 454 Sequencing Data. Bioinformatics. In revision.
  2. Zeng F, Jiang R and Chen T (2013) PyroHMMSNP: a SNP caller for Ion Torrent and 454 Sequencing Data. Nucleic Acid Research. 1-13, doi:10.1093/nar/gkt372.
  3. Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Chen T, Zhang X and Li S (2012) Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome.  Scientific Report. 2:936. doi: 10.1038/srep00936. Epub 2012 Dec 6.
  4. Hao X and Chen T (2012) OTU Analysis Using Metagenomic Shotgun Sequencing Data. PLoS ONE. 7(11): e49785. doi:10.1371/journal.pone.0049785.
  5. Souaiaia T, Zhang Z and Chen T (2012)  FadE: Whole Genome Methylation Analysis for Multiple Sequencing Platforms. Nucleic Acid Research, September 2012, doi:10.1093/nar/gks830.
  6. Lehmann K and Chen T (2012)  Exploring functional variant discovery in non-coding regions with SInBaD. Nucleic Acid Research, August 31, 2012 doi:10.1093/nar/gks800.

7.      Wan L, Yan X, Chen T and Sun F (2012) Modeling RNA degradation for RNA-Seq with applications. Biostatistics, 2012; doi: 10.1093/biostatistics/kxs001.

8.      Mehta G, Deelman E, Knowles J, Chen T, et al. (2012) Enabling Data and Compute Intensive Workflows in Bioinformatics. Lecture Notes in Computer Science, 2012, Volume 7156, EURO-PAR 2011: PARALLEL PROCESSING WORKSHOPS, Pages 23-32. DOI:10.1007/978-3-642-29740-3_4. 

9.      Chang Q, Luan Y, Chen T, Fuhrman J and Sun F (2011) Computational methods for the analysis of tag sequences in metagenomics studies. Frontiers in Bioscience, S4, 1333-1343, June 1.

10.  Wang Y, Mehta G, Mayani R, Clark A, Lu J, Chen Y, Knowles J, Deelman E and Chen T (2011) RseqFlow: Workflows for RNA-seq data analysis. Bioinformatics. 27(18): 2598-2600.

11.  Xia C, Chen T, Furhman, and Sun F (2011) Accurate Genome Relative Abundance Estimation for Shotgun Metagenomics by Accommodating Read Assignment Ambiguities. PLOS One. 6(12), e27992. doi:10.1371/journal.pone.0027992.

12.  Cho S, Kuo CC, and Chen T (2011) MetaSEQ: De Novo Sequence Assembly of Short Regions in Metagenomics. IEEE International Workshop on Genomic Signal Processing. GSP 2011.

13.  Souaiaia T, Frazer Z and Chen T (2011) ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms. Journal of Computational Biology. 18(6): 795-807.

14.  Hao X, Jiang R, and Chen T (2011) Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics. 2011 Mar 1;27(5):611-8. Epub 2011 Jan 13.

15.  Chen Y, Souaiaia T, and Chen T (2009) PerM: Efficient Mapping of Short Sequencing Reads with Periodic Full Sensitive Spaced Seeds. Bioinformatics. 25(19):2514-21.

SNPs and Haplotypes

16.  Chen Y and Chen T (2010) An Integer Programming Approach for the Selection of Tag SNPs using Multi-allelic LD. Communications in Information and Systems.

17.  Jiang R, Yang H, Kuo J CC, Sun F and Chen T.(2007) Sequence-based prioritization of nonsynonymous single nucleotide polymorphisms for the study of disease mutations. American Journal of Human Genetics. 2007 Aug;81(2):346-60.

18.  Su, S, Kuo J CC, Chen T.(2007) Signal Processing Techniques for SNP (Single Nucleotide Polymorphism) Data Analysis. IEEE Signal Processing Magzine: Special Issue on Signal Processing Methods in Genomics and Proteomics. 2007.

19.  Jiang R, Yang H, Sun F and Chen T.(2005) Searching for interpretable rules for disease mutations: A simulated annealing bump hunting strategy. BMC Bioinformatics. 2006 Sep 19;7(1):417.

20.  Huang YT, Chao KM, and Chen T.(2005) An approximation algorithm for haplotype inference by maximum parsimony. Journal of Computational Biology, Dec 2005;12(10):1261-74.

21.  Huang YT, Zhang K, Chen T and Chao KM.(2005) Approximation algorithms for the selection of robust tag SNPs. BMC Bioinformatics, 2005, 6:263.

22.  Su S, Kuo CC and Chen T.(2005) Inference of Missing SNPs and Haplotype Block Partitioning. Bioinformatics, 2005 May 1;21(9):2001-7.

23.  Zhang, K., Qin, Z., Chen, T., Liu, J., Waterman, MS, and Sun, F. (2005) HapBlock: Haplotype Block Partitioning and Tag SNP Selection Software Using a Set of Dynamic Programming Algorithms. Bioinformatics, 2005 Jan 1;21(1):131-4.

24.  Zhang, K., Qin, Z., Liu, J., Chen, T., Waterman, MS, and Sun, F.(2004) Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies. Genome Res. 2004 May;14(5): 908-16.

25.  Zhang, K., Sun, F., Waterman, MS and Chen, T.(2003) Dynamic programming algorithms for partitioning sequence variation in human chromosomes. HERMIS 4:15-26, 2003.

26.  Zhang, K., Sun, F., Waterman, MS, Chen, T. (2003) Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. American Journal of Human Genetics, 73:63-73, 2003.

27.  Zhang, K., Deng, M., Chen, T., Waterman, M., and Sun, F.(2002) A dynamic programming approach for haplotype partitioning. The Proceeding of National Academy of Sciences (PNAS), 99(11): 7335-9, May 28 2002.

Protein Interactions and Gene Expression

  1. Ma X, Chen T, Sun F (2013)  Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Briefings in Bioinformatics; doi:10.1093/bib/bbt041.

29.  Jiang R, Chen T, Sun FZ (2009) Bayesian models and Gibbs sampling strategies for local graph alignment and network motif identification in stochastic biological networks. Communications in Systems and Information. Vol 9, No 4, pp 347-370.

30.  Wang L, Sun F and Chen T. (2008) Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy. Genome Biology. 9:R174, 2008.

31.  Pena-Castillo L. et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 2008; 9 Suppl 1:S2.

32.  Jiang R, Tu Z, Chen T and Sun F. (2006) Network Motif Identification in Stochastic Networks. The Proceeding of National Academy of Sciences (PNAS). 2006. vol 103 no 2 page 9404-9.

33.  Lee H, Deng M, Sun F and Chen T. (2006) Inferring domain-domain interactions from multiple biological data sources. BMC Bioinformatics. 2006 May 25;7(1):269.

34.  Tu Z, Wang L, Arbeitman M, Chen T and Sun F. (2006)  An Integrative Approach for Causal Gene Identification and Gene Regulatory Pathway Inference. Bioinformatics (ISMB 2006). Jul 15;22(14):e489-96.

35.  Tu Z, Wang L, Xu M, Zhou J, Chen T and Sun F. (2006)  Further understanding human disease genes by comparing with housekeeping genes and other genes. 2006, BMC Genomics. 2006 Feb 21;7:31.

36.  Lee H, Tu Z, Deng M, Sun F and Chen T. (2006) Diffusion kernel based logistic regression models for protein function prediction. OMICS: Integrative Biology. 2006 Spring;10(1):40-55.

37.  Lee H, Sun F and Chen T. (2005) Assessment of the Reliability of Protein-Protein Interactions Using Protein Localization and Gene Expression Data. BIOINFO 2005.

38.  Deng, M., Chen, T. and Sun, F. (2004)  An Integrative Analysis of Protein Function Prediction. Journal of Computational Biology, 2004;11(2-3): 463-75.

39.  Deng, M., Tu, Z., Sun, F., and Chen, T. (2004)  Mapping Gene Ontology to Proteins Based on Protein-protein Interaction Data. Bioinformatics, Apr 12;20(6):895-902, 2004.

40.  Deng, M., Zhang, K., Mehta, S., Chen, T. and Sun, F. (2003) Prediction of protein function using protein-protein interaction data.  Journal of Computational Biology, 10(6): 947-960, 2003.

41.  Deng, M., Sun, F. and Chen, T. (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing. Page 140-51, 2003.

42.  Deng, M., Metah, S., Sun, F., and Chen, T. (2002) Inferring Domain-Domain Interactions from Protein-Protein Interactions. Genome Research 12:1540-8, 2002.

43.  Chen, T., Filkov, V. and Skiena, S. (2001) Identifying gene regulatory networks from experimental data. Journal of Parallel Computing, 27(1-2), page 141-162, 2001.

44.  Chen, T., He, H. and Church, G.M. (1999) Modeling Gene Expression with Differential Equations. Pacific Symposium on Biocomputing (PSB99), Page 29-40, 1999.

Mass Spectrometry

45.  Mo L, Wan Y, Yang A and Chen T (2010) MSPEP: A spectral alignment algorithm for the detection of post translational modifications. RECOMB Satellite Conference on Computational Proteomics 2010.

46.  Wan Y, Cripps D, Thomas S, Campbell P, Ambulos N, Chen T, Yang A. (2008) PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. J Proteome Res. 2008 Jul;7(7):2803-11. Epub 2008 Jun 13.

47.  Mo L, Dutta D, Wan Y and Chen T (2007) MSNovo: A new dynamic programming algorithm for de novo peptide sequencing. Analytical Chemistry 2007 Jul 1;79(13):4870-8.

48.  Dutta D. and Chen T (2007) Speeding up Tandem Mass Spectrometry Database Search: Metric Embeddings and Fast Near Neighbor Search. Bioinformatics 2007; Mar 1;23(5):612-8.

49.  Wan Y and Chen T (2006) PepHMM: A hidden Markov model based scoring function for tandem mass spectrometry. Analytical Chemistry. 2006 Jan 15;78(2):432-7.

50.  BA Soreghan, BW Lu, SN Thomas, K Duff, EA Rakhmatulin, T Nikolskaya, T Chen, & AJ. Yang (2005) Redox proteomic analysis of a PS1+APP mouse model of Alzheimer’s disease. The Journal of Alzheimer’s Disease. 2005 Dec;8(3):227-41.

51.  Lu, B. and Chen, T (2004) Algorithms for de novo peptide sequencing via tandem mass spectrometry. Drug Discovery Today: BioSilico 2: 85-90, 2004.

52.  Lu, B. and Chen, T (2003) A Suffix Tree Approach to the Interpretation of Tandem Mass Spectra: Applications to Peptides of Nonspecific Digestion and Post-translational Modifications. Bioinformatics Suppl. 2 (ECCB), Page 113-121, 2003.

53.  Lu, B. and Chen, T (2003) A Suboptimal Algorithm for De novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology, 10(1):1-12, 2003.

54.  Chen, T., Jaffe, J. and Church, G.M. (2001) Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry, Journal of Computational Biology, 8(6):571-583, 2001.

55.  Chen, T., Kao, M.Y., Tepel, M., Rush, J., and Church, G.M.(2001) A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology, 8(3): 325-337, 2001.

56.  Chen, T. Gene-Finding via Tandem Mass Spectrometry.(2001) The ACM-SIGACT Fifth Annual International Conference on Computational Molecular Biology (RECOMB01), Page 85-92, 2001.

Chemical Informatics and Drug Screening

57.  Guha R, Dutta D, Wild DJ, Chen T(2007) Counting Clusters Using R-NN Curves. J Chem Inf Model. 2007 Jul-Aug;47(4):1308-18. Epub 2007 Jun 30.

58.  Dutta D, Guha R, Wild D and Chen T(2007) Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models. ACS J. Chem. Inf. Model. 2007. May-Jun;47(3):989-97.

59.  Guha R, Dutta D, Jurs P. and Chen T(2006) R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method.  ACS J. Chem. Inf. Model. 2006.  Jul-Aug;46(4):1713-22. 

60.  Dutta D, Guha R, Jurs P. and Chen T(2006) Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions. ACS J. Chem. Inf. Model., 2006. Jul-Aug;46(4):1836-47.

61.  Dutta D, Guha R, Jurs P. and Chen T(2006) Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing. ACS J. Chem. Inf. Model., 2006. Jan-Feb;46(1):321-33.

Books and Book Chapters

62.  Sun FZ, Chen T, Deng MH, Lee HJ, Tu ZD (2006) Data integration for the study of protein interactions. In Rudy Guerra and David Allison: Meta-analysis and Combining Information in Genetics, Chapman and Hall.

63.  Huang, Y.-T., Zhang, K., Chen, T., and Chao, K. -M. (2006) “Approximation Algorithms for the Selection of Robust Tag SNPs,” a chapter of the book “Handbook of Approximation Algorithms and Metaheuristics," edited by Teofilo F. Gonzalez (University of California, Santa Barbara), to be published by Chapman & Hall/CRC Press, USA.

64.  BW Lu, BA Soreghan, SN Thomas, T Chen, & AJ Yang. (2005) Proteomics data management and visualization. Book chapter.

65.  Borchers, C., Chen, T. and Neamati, N. Book Chapter: Application of Proteomics in Biological Sciences. Molecular Carcinogenesis. Editor: Joseph R. Landolph's and David Warshawsky. CRC Press, 2003.

66.  Chen, T. and Waterman, M. Book Chapter: Dynamic Programming. Nature Encyclopedia of Human Genome, Nature Publishing, 2003. 

Other Works

67.  Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. (2008) Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. PLoS ONE. 2008;3(11):e3645. Epub 2008 Nov 10

68.  Smith E, Meyerrose TE, Kohler T, Namdar-Attar M, Bab N, Lahat O, Noh T, Li J, Karaman MW, Hacia JG, Chen T, Nolta JA, Muller R, Bab I, Frenkel B.(2005) Leaky ribosomal scanning in mammalian genomes: Physiological consequences of histone H4 alternative translation. Nucleic Acid Research. 2005 Mar 1;33(4):1298-308.

69.  Wyrick, J. J., Aparicio, J. G., Chen, T., Barnett, J. D., Jennings, E. G., Young, R. A., Bell, S. P., and Aparicio, O. M.(2001) Genome-Wide Location Analysis of ORC and MCM Proteins: High Resolution Mapping of Replication Origins Reveals Novel Origin Classes in Saccharomyces cerevisiae. Science, 2357-2360, Dec 14, 2001.

70.  Chen, T. and Skiena, S.(2000) A Case Study in Genome-Level Fragment Assembly. Bioinformatics 2000 16:494-500.

71.  Chen, T. and Kao, M.Y. (1999) On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees. The 7th Annual European Symposium on Algorithms (ESA’99), Page 248-256, 1999. LNCS, Lecture Notes in Computer Science, Springer-Verlag.

72.  Chen, T. and Zhang, M.Q.(1998) Pombe: A Fission Yeast gene-finding and exon-intron structure prediction system. Yeast, Vol. 14: 701-710, 1998.

73.  Chen, T. and Skiena, S.(1997) Trie-based data structures for fragment assembly. The Eighth Symposium on Combinatorial Pattern Matching (CPM97), page 206-223, 1997.

74.  Chen, T. and Skiena, S.(1996) Sorting with fixed-length reversals. Journal of Discrete Applied Mathematics, Special Volume on Computational Molecular Biology, page 269-296, vol.71, December 5 1996.

 

Grant Review and Paper Review

·         Review for Journals: Nature Biotechnology, Genome Research, PNAS, Genome Biology, Nucleic Acid Research, Genetics, Proteomics, Bioinformatics, Journal of Proteomic Research, Analytical Chemistry, BMC Bioinformatics, Journal of Computational Biology, IEEE Transaction of Computational Biology and Bioinformatics, Journal of Bioinformatics and Computational Biology, Pacific Symposium of Biocomputing, Discrete Applied Mathematics, RECOMB, ISMB, APBC

Software Development

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

·         Clippers (http://code.google.com/p/clippers/): a sister gap-mapping program of PerM, which is designed to map 75-bp or longer Illumina reads with one gap plus multiple substitutions. Clippers has been used to find novel spliced junctions and junctions of 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. ComB has been used to analyze allele specific gene expression, and RNA-editing sites.

·         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 supervised Bayesian clustering tool for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).

·         RseqFlow (http://genomics.iss.edu/rnaseq): an RNA-seq data analysis workflow, which uses Pegasus Workflow Management System to develop and manage workflow execution. RseqFlow has been applied to analyze the RNA-seq data sets generated from the NIHM funded human brain transcriptome atlas project.

·         Fade (http://code.google.com/p/fade): a DNA methylation calling program.

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

·         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.

 

Research Activities

University Committee Services

o   USC High Performance Computing Committee, 2007-present.

o   Graduate Student Advisor, PhD program in Computational Biology and Bioinformatics, 2006-present.

o   USC College Biology Undergraduate Curriculum Committee, 2007-2008, 2011-present

o   USC Clinical Translational Science Institute (CTSI): Computational Biology Advisory Committee, 2007-present.

o   USC College Faculty Council, 2005-2006.

o   Faculty Recruit Committee, 2006-present.

Advised Postdocs and Graduate Students (22)

o   Current PhD students (5)

Misagh Bagheria,

Zohreh Irannia,

Haifeng Chen,

Henry Dong,

Feng Zeng

 

o   Former Postdocs (5)

Ying Wang (Associate Professor, Department of Automation, Xiamen University)

Rui Jiang (Associate Professor, Department of Automation, Tsinghua University)

Minghua Deng (Professor, Department of Mathematics, Peking University)

Debo Dutta (Senior Scientist, Cisco)

Lei Zhuge (Countrywide)

 

o   Former Graduated PhD students (12)

Hyun-Ju Lee (Assistiant Professor, Department of Computer Science, Gwangju Inst. Of Tech, Korea),

Hua Yang (Deputy Director, China Banking Regulatory Commission)

Bingwen Lu (Pfizer),

Shipra Metah,

Yunhu Wan (Consultant, National Cancer Institute),

Shih-Chieh Su (Analytic Scientist, Fair Isaac Co),

Lijuan Mo (CEO, Archiwood)

Yangho Chen (Microsoft)

Tade Souaiaia (USC)

Kjong Lehmman (Sloan Kettering Cancer Center),

Sungje Cho (Amazon),

Xiaolin Hao (Bethesda)

TEACHING