1. 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.
  2. 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.
  3. 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.
  4. Chen, T., He, H. and Church, G.M. (1999) Modeling Gene Expression with Differential Equations. Pacific Symposium on Biocomputing (PSB99), Page 29-40, 1999.
  5. 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.
  6. Chen, T. and Skiena, S. (2000) A Case Study in Genome-Level Fragment Assembly. Bioinformatics 2000 16:494-500.
  7. Wyrick, J. J., Aparicio, J. G., Chen, T., Barnett, J. D., Jennings, E. G., Young, R. A., Bell, S. P., and Aparicio, O. (2001) M. 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.
  8. Chen, T., Filkov, V. and Skiena, S. (2001) Identifying gene regulartory networks from experimental data. Journal of Parallel Computing, 27(1-2), page 141-162, 2001.
  9. 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.
  10. 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.
  11. Chen, T. (2001) Gene-Finding via Tandem Mass Spectrometry. The ACM-SIGACT Fifth Annual International Conference on Computational Molecular Biology (RECOMB01), Page 85-92, 2001.
  12. 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.
  13. Deng, M., Metah, S., Sun, F., and Chen, T. (2002) Inferring Domain-Domain Interactions from Protein-Protein Interactions. Genome Research 12:1540-8, 2002.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. Borchers, C., Chen, T. and Neamati, N. (2003) Book Chapter: Application of Proteomics in Biological Sciences. Molecular Carcinogenesis. Editor: Joseph R. Landolph's and David Warshawsky. CRC Press, 2003.
  21. Chen, T. and Waterman, M. (2003) Book Chapter: Dynamic Programming. Nature Encyclopedia of Human Genome, Nature Publishing, 2003.
  22. 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.
  23. 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.
  24. 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.
  25. Lu, B. and Chen, T. (2004) Algorithms for de novo peptide sequencing via tandem mass spectrometry. Drug Discovery Today: BioSilico 2: 85-90, 2004.
  26. 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.
  27. Huang YT, Zhang K, Chen T and Chao KM. (2005)  Approximation algorithms for the selection of robust tag SNPs. BMC Bioinformatics, 2005, 6:263
  28. Su S, Kuo CC and Chen T. (2005) Inference of Missing SNPs and Haplotype Block Partitioning. Bioinformatics, 2005 May 1;21(9):2001-7.
  29. 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.
  30. BW Lu, BA Soreghan, SN Thomas, T Chen, & AJ Yang. (2005) Proteomics data management and visualization. Book chapter.
  31. 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.
  32. 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.
  33. 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.
  34. 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. (* corresponding authors)
  35. 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.   
  36. 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.
  37. 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.
  38. Jiang R, Yang H, Sun F and Chen T. (2006) Searching for interpretable rules for disease mutations: A simulated annealing bump hunting strategy. BMC Bioinformatics. 2006 Sep 19;7(1):417.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  1. 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.
  2. Peña-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.
  1. 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.
  2. 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.
  3. 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.
  4. 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, Num 4, p347-370.
  5. Chen Y and Chen T (2009) An Integer Programming Approach for the Selection of Tag SNPs using Multi-allelic LD. Communications in Information and Systems. Vol. 9, No. 3, pp. 253-268, 2009.
  6. 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.
  7. 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.
  8. 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.  July 27, 2011, doi: 10.1093/bioinformatics/btr441.
  9. Xia C, Chen T, Furhman J, 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.
  10. Cho S, Kuo CC, and Chen T (2011) MetaSEQ: De Novo Sequence Assembly of Short Regions in Metagenomics. IEEE 2nd International Workshop on Genomic Signal Processing. GSP 2011.
  11. 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. doi:10.1089/cmb.2011.0027.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. Hao X and Chen T* (2012) OTU Analysis Using Metagenomic Shotgun Sequencing Data. PLoS ONE. 7(11): e49785. doi:10.1371/journal.pone.0049785.
  18. 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.
  19. 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.
  20. 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.
  21. 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, doi:10.1093/bioinformatics/btt512.
  22. Wang Y*, Liu L, Chen T, Sun F* (2014) Comparison of metatranscriptomic samples based on k-tuple frequencies.  PLoS ONE.  9(1):e8348. DOI: 10.1371/journal.pone.0084348.
  23. Liang M, Li Z, Chen T, and Zeng J* (2014) Integrative Data Analysis of Multi-platform Cancer Data with a Multimodal Deep Learning Approach. IEEE/ACM Transaction on Computational Biology and Bioinformatics. Vol. PP Issue 99, DOI 10.1109/TCBB.2014.2377729.
  24. Zhu C, Jiang R* and Chen T* (2014) Constructing a Boolean implication network for the study of interactions between OTUs and environmental factors. Quantitative Biology. Vol 2, Issue 4, pp 127-141, DOI 10.1007/s40484-014-0037-3
  25. Ning K and Chen T (2014) Biomedical Big Data: Current Status and Future Perspective. Chinese Science Bulletin.
  26. Zheng H, Xu L, Wang Z, Li L, Zhang J, Zhang Q, Chen T*, Lin J*, and Chen F* (2015) Subgingival microbiome in patients with healthy and ailing dental implants. Scientific Reports 5:10948, DOI:10.1038/srep10948.
  27. Zu SP, Chen T, and Shao L (2015) Global Optimizationbased Inference of Chemogenomic Features from Drug-Target Interactions. Bioinformatics. 2015 Aug 1; 31(15):2523-9. doi: 10.1093/bioinformatics/btv181.
  28. Wu M, Wu J, Chen T and Jiang R* (2015) Prioritization of nonsynonymous single nucleotide variants for exome sequencing studies via integrative learning on multiple genomic data. Scientific Reports 2015 Oct 13;5:14955. doi: 10.1038/srep14955.
  29. Wang Y, Lei X, Wang X, Wang Z, Song N, Zeng F, and Chen T(2015). Effect of k-tuple length on sample-comparison with high-throughput sequencing data. Biochemical and Biophysical Research Communications.
  30. Li R, Chen T* and Li S* (2015) Network-based method to infer the contributions of proteins to the etiology of drug side effects.  Quantitative Biology. Sept 2015, Vol 3, Iss 3, pp 124-134.
  31. Ren W, Xun Z, Wang Z, Zhang Q, Liu X, Zheng H, Zhang Q, Zhang Y, Zhang L, Wu C, Zheng S, Qin N, Ehrlich S, Li Y, He X, Chen T*, Xu T*, Chen F* (2016).  Tongue coating and the salivary microbial communities vary in children with halitosis original research.  Scientific Reports 2016. 5:10948, DOI: 10.1038/srep10948.
  32. Lu Y, Chen T, Fuhrman J, Sun F* (2016) COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read Linkage. Bioinformatics. 2016 Jun 2. pii: btw290.
  33. Chen H, Smith A* and Chen T* (2016) WALT: fast and accurate read mapping for bisulfite sequencing. Bioinformatics. doi:10.1093/bioinformatics/btw490.
  34. Jiang L, Chen N* and Chen T* (2016) DACE: A Scalable DP-means algorithm for clustering extremely large sequence data. Bioinformatics. doi:10.1093/bioinformatics/btw722.
  35. Wu M, Chen T and Jiang R* (2016) Global inference of disease-causing single nucleotide variants from exome sequencing data. BMC Bioinformatics 2016 17(Suppl 17):468 DOI: 10.1186/s12859-016-1325-x.
  36. Xu M, Chen N, Chen T* and Jiang R* (2016) DeepEnhancer: Predicting Enhancers by Convolutional Neural Networks. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 637-644, 2016, doi:10.1109/BIBM.2016.7822593.
  37. Wu J, Wu M, Chen T, Jiang R* (2016) Whole genome sequencing and its applications in medical genetics, Quantitative Biology, 4(2): 115-128, 2016
  38. Zhang X*, Liu S, Cui H, Chen T (2017) Reading the underlying information from massive metagenomic sequencing data, Proceedings of the IEEE, 2017.03.01, 105(3),459~473.
  39. Yang Y, Chen N*, Chen T* (2017). mLDM: a new hierarchical Bayesian statistical model for sparse microbial association discovery. RECOMB 2016. Cell Systems. Volume 4, Issue 1, p129–137.e5, 25 January 2017.
  40. Zeng F*, Wang Y, Zhou J and Chen T* (2017) Large-scale 16S gene assembly using metagenomics shotgun sequences. Bioinformatics. 10.1093/bioinformatics/btx018.
  41. Min X, Zeng W, Chen N, Chen T* and Jiang R* (2017) Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer Embedding, ISMB 2017, Bioinformatics, 10.1093/bioinformatics/btx234.
  42. Liu Z, Lou H, Wang H, Xie K, Aparicio O, Zhang M, Jiang R* and Chen T* (2017) Reconstructing Cell Cycle Pseudo Time-Series via Single-cell Transcriptome Data. Nature Communications. In press.
  43. Wu J, Wu M, Chen T*, Jiang R* (2017) Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data. Scientific Reports  10.1038/s41598-017-01834-w (SREP-16-50930)
  44. Ahlgren NA, Chen Y, Needham DM, Parada AF, Sachdeva R, Trinh V, Chen T, Fuhrman JA (2017) Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification, and multiple restriction systems. Environmental Microbiology. In press.
  45. Wu M, Lin Z, Ma S, Chen T, Jiang R, Wong W (2017) Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks. International Conference on Systems Biology 2017, Journal of Molecular Cell Biology. Accepted.
  46. Wu M, Zeng, W, Liu W, Zhang Y, Chen T*, Jiang R (2017) Integrating embedding of multiple gene networks to prioritize complex disease-associated genes. IEEE BIBM 2017.
  47. Feng Y, Min X, Chen N, Xie X, Wang H, Chen T* (2017) Patient Outcome Prediction via Convolutional Neural Networks based on Multi-Granularity Medical Concept Embedding. IEEE BIBM 2017.
  48. Chen N, Zhu J, Chen J and Chen T (2017) Dropout Training for SVMs with Data Augmentation. Frontiers in Computer Science. DOI:1007/s11704-018-7314-7.
  49. Wu M, Zeng W, Liu W, Lv H*, Chen T*, Jiang R* (2018) Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning. Method. Accepted.
  50. Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun F (2018) Identifying Group-Specific Sequences for Microbial Communities using Long k-mer Sequence Signatures. Frontier in Microbiology. Accepted.