唐继军——天津大学计算机学院特聘教授

 

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简介

 

 

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唐继军博士，天津大学计算机学院特聘教授，博士生导师，天津市“**计划”入选者。1994年获得天津大学海船系船舶工程学士，1996年获得天津大学海洋 工程硕士，2004年获得美国新墨西哥大学计算机科学博士学位。从2004年起任职美国南卡罗莱纳大学工程和计算学院计算机系至终身教授。主要研究领域为 生物信息，计算生物学，可视化和虚拟现实，研究方向为算法设计分析，高性能计算，数据库构建等。主要通过算法，人工智能以及数学和统计方法，利用全基因组 数据高效和精确分析基因组进化和系统发育，建立和显示基因组三维空间模型，采集和挖掘生态和气候变化数据，以及构建相关生物信息学计算平台。研究项目多次 获得美国NSF，NIH，NEH和其他机构的支持，迄今在国际会议和期刊上发表文章60余篇，他引次数600余次。培养博士和硕士研究生十余人，多数在美 国知名高校，研究所和公司任职。将致力于创建一流的计算生物学研究团队，保持具有国际学术前沿竞争力的研究能力，提高天津大学在生命科学研究方向的国际知 名度。

教育经历

1994	B.S. Naval Architecture, Tianjin University
1996	M.S. Offshore Engineering, Tianjin University
2002	M.S. Computer Science, University of New Mexico
2004	Ph.D. Computer Science, University of New Mexico

工作经历

2004-2009	Assistant Professor, University of South Carolina
2009-	Associate Professor, University of South Carolina
2013-	天津大学计算机学院特聘教授，博士生导师

 

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其他信息

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科学组织成员

Sigma Xi, ACM, ISCB, IEEE
杂志审稿

Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, BMC Genomics, Journal of Computational Biology, IEEE/ACM Transaction on Bioinformatics and Computational Biology, International Journal on Data Mining and Bioinformatics, IEEE Transactions on Parallel and Distributed Systems, Systematic Biology, Genes, Genomics, Evolutionary Genomics, IEEE Transaction on Information Theory
会议组委会

IEEE International Conference on Granular Computing (GrC), International Workshop on Algorithms in Bioinformatics (WABI), IEEE Conference on Bioinformatics and Bioengineering (BIBE), International Conf. on Biomedical Engineering and Informatics (BMEI), ACM Conference on Bioinformatics (ACM-BCB), Intl. Symposium on Network Enabled Health Informatics, Biomedicine and Bioinfo.
荣誉

1999: Excellent in Graduate Research, Sigma Xi UNM Chapter
2000: International Excellence Award, U. New Mexico
2004: Outstanding Graduate Student, Computer Science, U. New Mexico
2009: Research Progress Award, Coll. of Eng. & Comp, Univ. of South Carolina

 

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论文

 

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期刊

•Gao, N., Yang, N. and Tang, J., “Ancestral Genome Inference using a Genetic Algorithm Approach,” PLoS one 8(5): e62156, 2013.
•Luo, H., Arndt, W., Zhang, Y., Shi, J., Alekseyev, M., Tang, J., Hughes, A. and Friedman, R., "Phylogenetic Analysis of Genome Rearrangements among Five Mammalian Orders," Molecular Phylogenetics and Evolution, 65 (3): 871-882, 2012.
•Hu, L., Zhang, M., Zhang, Y. and Tang, J., "Label-guided Graph Exploration with Adjustable Ration of Labels," International Journal of Foundations of Computer Science 23 (04), 903-929, 2012.
•Zhang, Y., Hu, F. and Tang, J., "A Mixture Framework for Inferring Ancestral Gene Orders," APBC 2012, in BMC Bioinformatics, 13(Suppl 1):S7, 2012.
•Sakib, M., Tang, J., Zheng, W. and Huang, C., "Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files," PLoS ONE, 6(12):e28251, 2011.
•Zhang, M., Zhang, Y., Tang, J. and Bai, X.," Multi-pattern Matching with Wildcards," Journal of Software 6(12): 2391-2398, 2011.
• Luo, H., Tang, J., Friedman, R. and Hughes, A., "Ongoing purifying selection on the intergenic spacers in the group A streptococcus," Infection, Genetics and Evolution, 11, 343-348, 2011.
•Kang, S., Tang, J., Schaeffer, S. and Bader, A., "Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time," PLoS One, 6(8): e22483, 2011.
•Luo, H., Friedman, R., Tang, J. and Hughes, A., "Genome Reduction by Deletion of Paralogs in the Marine Cyanobacterium Prochlorococcus," Mol Biol Evol, 28 (10), 2751-2760, 2011.
•Asbury, T., Mitman, M., Tang, J. and Zheng, W., “Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome,” BMC Bioinformatics, 11, 444, 2010.
•Shi, J., Zhang, Y., Luo, H. and Tang, J., “Using Jackknife to Assess the Quality of Gene Order Phylogenies,” BMC Bioinformatics, 11 (168), 2010.
•Luo, H. Shi, J., Arndt, W., Tang, J. and Friedman, R., “Gene Order Phylogeny of the Genus Prochlorococcus,” PLoS ONE 3(12): e3837, 2009.
•Luo, H., Sun, Z., Arndt, W., Shi, J., Friedman, R. and Tang, J., "Gene Order Phylogeny and the Evolution of Methanogens," PLoS ONE 4(6):e6069.
• Yue, F., Shi, J., and Tang, J., "Simultaneous phylogeny reconstruction and multiple sequence alignment", Proc. 7th Asia-Pacific Conf on Bioinformatics, in BMC Bioinformatics, 10 (suppl1):s11, 2009
•Swenson, K.M., Dong, Y., Tang, J., and Moret, B.M.E, "Maximum independent sets of commuting and noninterfering inversions," Proc. 7th Asia-Pacific Bioinformatics Conf. (APBC 2009), in BMC Bioinformatics 2009, 10(Suppl 1):S6.
•Yue, F. and Tang, J., “A Space-Efficient Algorithm for Three Sequence Alignment and Ancestor Inference,” International Journal of Data Mining and Bioinformatics, 3 (2), 192-204 (2009).
•Yue, F., Zhang, M. and Tang, J., “Phylogenetic Reconstruction from Transposition,” BMC Genomics, 2008, 9 (Suppl 2):S15.
•Yue, F., Cui, L., dePamphilis, C. Moret, B., and Tang, J., “Gene rearrangement analysis from chloroplast genomes with inverted repeat,” BMC Genomics, 2008, 9 (Suppl 1):S25.
•Arndt, W. and Tang, J., “Improving Reversal Median Computation using Commuting Reversals and Cycle Information,” Journal of Computational Biology, 15 (8) 1079-1092, 2008.
•Cui, L., Leebens-Mack, J., Wang, L., Tang, J., Rymarquis, L., Stern, D., and dePamphilis, C., “Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach,” BMC Evolutionary Biology, 6:13, 2006.
•Tang, J., and Moret, B., “Scaling up accurate phylogenetic reconstruction from gene-order data,” Proc. 11th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2003), in Bioinformatics 19 (Suppl. 1) (2003), i305-i312.
•Moret, B., Tang, J., Wang, L., and Warnow, T., “Steps toward accurate reconstruction of phylogenies from gene-order data,” J. Comput. Syst. Sci. 65, 3 (2002), 508-525.

 

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会议（经审稿录用）

•Hu, F., Zhou, J., Zhou, L. and Tang, J., “Probabilistic Reconstruction of Ancestral Genomes with Gene Insertions and Deletions,” 12th Asia Pacific Bioinformatics Conference (APBC), accepted, 2014.
•Yin, Z., Tang, J., Schaeffer, S. and Bader, D., "Streaming Breakpoint Graph Analytics for Accelerating and Parallelizing the Computation of DCJ Median of Three Genomes," Proceedings of the International Conference on Computational Science (ICCS): 561-570, 2013.
•Gao, N., Hu, F. and Tang, J., "A Genetic Algorithm for the Reversal Median Problem," 5th International Conference on Bioinformatics and Computational Biology (BICoB), 2013.
•Hu, F., Zhou, L. and Tang, J., “Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models,” 9th International Symposium on Bioinformatics Research and Applications (ISBRA), 17-21, 2013.
•Lin,Y., Hu, F., Tang, J. and Moret, B., "Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes," Pacific Symposium on Biocomputing 18:285-296, 2013.
•Shepherd, J., Doe, R., Arnold, M., Zhu, Y. and Tang, J., "A different approach to teaching Chinese through Serious Games," Foundation of Digital Games, 304-306, 2011.
•Hu, F., Gao, N. and Tang, J., "Maximum Likelihood Phylogenetic Reconstruction Using Gene Order Encodings", the eighth Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 117-122, 2011.
•Shi, J., Arndt, W. and Tang, J., "Isolating - A New Resampling Method for Gene Order Data," the eighth Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 135-140, 2011.
•Arndt, W. and Tang, J., "Emulating Insertion and Deletion Events in Genome Rearrangement Analysis," 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'11), 105-108.
•Shepherd, J., Doe, R., Arnold, M., Cheek, N., Zhu, Y. and Tang, J., "Lost in the Middle Kingdom: a second language acquisition video game," ACM Southeast Regional Conference 2011: 290-294, 2011.
•Zhang, T., Shepherd, J., Tang, J. and Dougal, R.A., "A Gaming Environment Approach to Analysis of Energy Storage for Electric/Hybrid Vehicle," 2011 International Conference on Clean Electrical Power, 400-406, 2011.
•Shi, J., Dougal, R. Langland, B., Tang, J. and Zhang, Y., "New Basic Linear Algebra Methods for Simulation on GPUs," Grand Challenges in Modeling and Simulation (GCMS), 258-265, 2011.
•Zhang, Y., Dougal, R., Leonard, R., and Tang, J., "Optimally applying latency insertion method in large system models," Grand Challenges in Modeling and Simulation (GCMS), 271-276, 2011.
•Zhang, T., Dougal, R., Shepherd, J. and Tang, J., "The Simulation Tool for Mission-Optimized System Design," Grand Challenges in Modeling and Simulation, 348-355, 2011.
•Zhang, M., Zhang, Y. and Tang, J., "Matching a set of patterns with wildcards," Third International Symposium on Parallel Architectures, Algorithms and Programming (PAAP'10).
•Zhang, Y., Hu, F. and Tang, J., “Phylogenetic Reconstruction with Gene Rearrangements and Gene Losses,” IEEE International Conference on Bioinformatics and Biomedicine, (BIBM 2010).
•Shepherd, J., Dougal, R. and Tang, J., “The Simulation and Data Visualization Potential of Microsoft's XNA,” Grand Challenges in Modeling Simulation, 306-310, 2010.
•Shepherd, J., Tang, J. and O’Kane, J., "Path-Finding with Motion Constraints in Real Time Strategies," 2nd Annual International Conference on Computer Games and Allied Technology (CGAT 2009), 83-90.
•Shi, J. and Tang, J., “An Experimental Evaluation of Corrected Inversion and DCJ Distance Metric through Simulation,” 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), 2010.
•Zhang, M., Arndt, W. and Tang, J., “An Exact Median Solver for the DCJ Distance,” Proc. 2009 Pacific Symposium on Biocomputing (PSB), 138-149, 2009.
•Zhang, Y., Dougal, R., Langland, B., Shi, J. and Tang, J., “Method for partitioning large system models when using latency insertion method to speed network solution,” Conference on Grand Challenges in Modeling and Simulation, 2009.
•Guo, Y., Ye, F. and Tang, J., "Phylogenetic Reconstruction with Disk-Covering and Bayesian Approaches," Proc. 8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2008).
•Zhang, M., Arndt, W. and Tang, J., "A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem," Proc. 8th Int'l Workshop on Algorithms in Bioinformatics (WABI 2008), in Lecture Notes in Bioinformatics 5251, 14-24.
•Yue, F. and Tang, J., “A New Approach for Tree Alignment Based on Local Re-Optimization,” 2008 International Conference on BioMedical Engineering and Informatics (BMEI 2008), 34-38.
•Swenson, K., Arndt, W., Tang, J. and Moret, B., “Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes,” Sixth Asia Pacific Bioinformatics Conference (APBC 2008), in Advances in Bioinformatics and Computational Biology, Vol. 6, 241–250, Imperial Press (2008).
•Shepherd, J., Shi, J., Zhang, T., Tang, J., and Dougal, R., "Application of multiplayer computer gaming paradigm to engineering Design Tools", 2008 Summer Simulation Multi-conference, Grand Challenges in Modeling and Simulation, Edinburgh, Scotland.
•Yue, F. and Tang, J., “A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference with Affine Gap Costs,” IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), 143–150.
•Bakos, J., Elenis, P., and Tang, J., “FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data,” Proc. 7th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2007), 888–895.
•Yue, F., Zhang, M. and Tang, J., “A Heuristic for Phylogenetic Reconstruction Using Transposition,” Proc. 7th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2007), 802–808.
•Arndt, W. and Tang, J., “Improving Inversion Median Computation using Commuting Reversals and Cycle Information,” Fifth Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2007), in Lecture Notes in Computer Science 4751, 30-44.
•Ye, F., Guo, Y., Lawson, A. and Tang, J. “Improving Tree Search in Phylogenetic Reconstruction from Genome Rearrangement Data,” 6th Workshop on Experimental Algorithms, in Lecture Notes in Computer Science 4525, 352-364.
•Dalal, P., Munsell, B.C., Wang, S., Tang, J., Oliver, K., Ninomiya, H., Zhou, X. and Fujita, H., “A Fast 3D Correspondence Method for Statistical Shape Modeling,” IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2007).
•Zhang, M. and Tang, J., “Succinct Text Indexes on Large Alphabet,” Third Annual Conference on Theory and Applications of Models of Computation (TAMC 2006), 528–537.
•Tang, J. and Wang, L., “Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony,” Proc. 5th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2005), 137–144.
•Liu, T., Tang, J., and Moret, B., “Quartet methods for phylogeny reconstruction from gene orders,” Proc. 11th Int'l Computing and Combinatorics Conference (COCOON 2005), 63–73.
•Tang, J., and Moret, B., “Linear programming for phylogenetic reconstruction based on gene rearrangements,” Proc. 16th Symp. on Combinatorial Pattern Matching, (CPM 2005), 406–416.
•Tang, J., Moret, B.M.E., Cui, L., and dePamphilis, C., “Phylogenetic reconstruction from arbitrary gene-order data,” Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2004), 592-599.
•Tang, J., and Moret, B., “Phylogenetic reconstruction from gene rearrangement data with unequal gene contents,” Proc. 8th Workshop on Algorithms and Data Structures (WADS 2003), in Lecture Notes in Computer Science 2748, 37–46.
•Moret, B., Siepel, A., Tang, J., and Liu, T., “Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data,” Proc. 2nd Int'l Workshop on Algorithms in Bioinformatics (WABI 2002), in Lecture Notes in Computer Science 2452, 521–536.

书章节

•Moret, B.M.E., Lin, Y., and Tang, J., "Rearrangements in phylogenetic inference: Compare, model, or encode?" in Models and Algorithms for Genome Evolution, vol. 19 of Computational Biology series, Chauve, C., et al., eds, Springer Verlag (2013), 147-172.
•Moret, B.M.E., Tang, J., and Warnow. T., "Reconstructing phylogenies from gene-content and gene-order data," in Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford Univ. Press (2005), 321-352.

 

书主编

Benjamin J. Raphael, Jijun Tang (Eds.): Algorithms in Bioinformatics – Proceedings for the 12th International Workshop, WABI 2012. Lecture Notes in Computer Science 7534, Springer 2012, ISBN 978-3-642-33121-3.

 

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完成的研究项目

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NSF OCI 0904179 (09/01/2009-08/31/2013)
Collaborative Research: Understanding Whole-genome Evolution through Petascale Simulation. 
  
National Endowment of Humanities HT-50046-11 (10/01/2011-12/31/2012)
High Performance Computing Collaboratory.

Office of Naval Research N00014-07-1-0686 (06/01/2007-05/31/2011)
Infusion of a Gaming Paradigm into Computer-Aided Engineering Design Tools. 
  
NSF CNS 0708391 (06/01/2007-05/31/2011)
CRI: CRD Acquisition of a High-Performance Shared-Memory Computer for Biological and Medical Research in South Carolina. Total amount is $470,000. 
  
NIH R01 GM078991 Administrative Supplement (09/01/2009-05/31/2010)
Phylogenetic Analysis with Complex Genome Rearrangement Events. 
  
NIH R01 GM078991 (06/01/2006-05/31/2010)
Phylogenetic Analysis with Complex Genome Rearrangement Events. 
  
Univ. of South Carolina Internal Grant (06/01/2009-09/30/2010)
Algorithm Development to Reconstruct Ancestral Genomes. 
  
Subcontract to NSF CIPRES project (NSF EF 03-31654) (10/01/2005-09/30/2006)
Phylogenetic Multiple Sequence Alignment 
  
Summer Support from National Evolutionary Synthesis Center (Funded by NSF) (Summer 2005)
Algorithm development for gene-order phylogeny

 

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教学和指导学生

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开课

CSCE 552 Computer Game Design (seven times)
CSCE 146 Algorithm Design II (once)
CSCE 206 Scientific Computing (once)
CSCE 245 Object Oriented Programming (five times)
CSCE 500 Perl Programming for Biologist (once)
CSCE 555 Algorithms in Bioinformatics (four  times),
CSCE 850 Advanced Algorithm (once).
  

已毕业博士生

Fei Hu
Topic: Phylogeny and Ancestral Genome Reconstruction from Gene Order using Maximum Likelihood and Binary Encoding
Started in Fall 2009, Graduated in Fall 2013
Will start in Amazon 
  
Yiwei Zhang
Topic: Graph based optimization for scientific computing
Started in Fall 2008, graduated in Aug 2012
Now in Microsoft 
  
Jian Shi
Topic: Improving Simulation Performance with GPUs
Started in Spring 2008, graduated in Aug 2011
Now in Unitrends 
  
William Arndt
Topic: Phylogenetic reconstruction with gene order and content information
Started in Fall 2006, graduated in Aug 2011
Now Research Scientist in Howard Hughes Medical Institute (HHMI) 
  
Haiwei Luo
Co-advised, Advisor Dr. Bob Friedman (Bio)
Topic: Evolutionary analysis of large-scale genomic changes
Graduated in May 2010.
Now Post-doc in University of Georgia 
  
Yan Guo (Pursuing Ph.D.)
Topic: Phylogenetic Reconstruction with Bayesian Approach
Started in Summer 2005, graduated in May 2009
Now Assistant Professor in Department of Cancer Biology, Vanderbilt University and Technical Director for Bioinformatics Vanderbilt Center for Quantitative Sciences. 
  
Feng Yue
Topic: Simultaneously Phylogenetic Reconstruction and Multiple Sequence Alignment
Started in Spring 2005, graduated in May 2008
Recipient of Outstanding Graduate Student, CSCE, 2008
Now tenure track Assistant Professor in Penn State University 
  
Fei Ye
Co-advised, Advisor Dr. John Drane (Biostatistics)
Topic: Statistic Approaches for High Throughput Bioinformatics Data
Graduated in Summer 2007
Now Assistant Professor in Vanderbilt University
  

已毕业硕士生

Thorben Primke
Topic: New Heuristics for Genome Median Problems
Started in Fall 2006, graduated in May 2008
Now software engineer in Facebook. 
  
Jeremiah Shepherd (Pursuing Master Degree)
Topic: Massive Multiplayer Game Technologies to Improve Engineering Simulation
Started in Summer 2007, graduated in 2009
Now continue to pursue Ph.D. in my lab
  

指导的本科生

Safiya Moran (Summer 2007), Patrick Clements and Jeremy Pesner (Summer 2008), David He (Spring 2008), Nadine Luedicke (2011), Edward Kim (2012), Morgan Honaker (2012), Kevin Wang (2013), Robert Bailey (2013), Logan Hood (2012-2013)