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Some Collabrators

Bernard Moret
Tandy Warnow
Jim Zheng
Lisan Wang
Todd Vision
 

 

Jijun Tang
Associate Professor
Deptartment of Computer Science and Engineering
University of South Carolina, Columbia, SC 29208



3A61 Swearingen Engineering Center
jtang at cse.sc.edu
803-777-8923(voice)
Name in Chinese: 唐继?BR>


Education

July 2004 Ph.D., Computer Science, University of New Mexico

May 2002 M.S., Computer Science, University of New Mexico

June 1996 M.S., Offshore Engineering, Tianjin University, China

June 1994 B.S., Naval Architecture, Tianjin University, China


Research Interests

Algorithm development and high performance computing, with emphasis on phylogenetic analysis from genome rearrangement and sequence data. My other research interests are high-performance computing and engineering simulation. I am also interested in computer game development, but mainly focused on teaching. It is possible that I will later develop educational games for computational biology.

Publication [back to top]

2014

  • Hu, F., Lin, Y. and Tang, J., "MLGO: phylogeny reconstruction and ancestral inference from gene-order data," BMC Bioinformatics, accepted
  • Yang, N., Hu, F., Zhou, L. and Tang, J., "Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches," PLOS ONE 9 (10), e108796 PDF
  • Qin, T., Matmati, N., Tsoi, L., Mohanty, B., Gao, N., Tang, J., Lawson, A;, Hannun, Y. and Zheng, W., "Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network," Nucl. Acids Res. (2014) PDF
  • Shepherd, J., Zhou, L., Arndt, W., Zhang, Y., Zheng, W. and Tang, J., "Exploring genomes with a game engine," Faraday DiscussionsPDF
  • Hu, F., Zhou, J., Zhou, L. and Tang, J., Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions. IEEE/ACM Trans. Comput. Biology Bioinform. 11(4): 667-672 (2014) PDF
  • Yin, Z., Tang, J., Schaeffer, S. and Bader, D., "A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents," The 20th International Computing and Combinatorics Conference (COCOON 2014): 227-238

2013

  • Shepherd, J., Zhou, L., Zhang, Y., Zheng, W. and Tang, J., "Exploring genomes with a game engine," BIBM 2013: 26-30
  • 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. PDF
  • Du, F., Xu, F., Qu, H., Feng, S., Tang, J. and Wu, R., "Exploiting the Transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to Develop and Characterize New EST-SSR Markers and Construct an EST-SSR Database," PLoS ONE 8(4):e61337 PDF
  • 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 2013): 561-570.
  • Gao, N., Hu, F. and Tang, J., "A Genetic Algorithm for the Reversal Median Problem," 5th International Conference on Bioinformatics and Computational Biology (BICoB), 145-151, 2013.
  • Gao, N., Yang, N. and Tang, J., "Ancestral Genome Inference using a Genetic Algorithm Approach," PLoS one, 8(5) e62156, 2013PDF.
  • 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), 17-27, 2013PDF
  • 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)PDF

2012

  • 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. PDF
  • 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
  • Zhang, Y., Hu, F. and Tang, J., "A Mixture Framework for Inferring Ancestral Gene Orders," APBC 2012, in BMC Genomics 2012, 13(Suppl 1):S7 (PDF)

2011

  • Sakib, M., Tang, J., Zheng, W. and Huang, C., "Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files," PLoS ONE, 6(12): e28251. PDF.
  • Zhang, M., Zhang, Y., Tang, J. and Bai, X.," Multi-pattern Matching with Wildcards," Journal of Software 6(12): 2391-2398.
  • 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.
  • 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 (2) 343-348.PDF
  • 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.
  • 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 PDF.
  • 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.
  • 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 Abstract.
  • Hu, F., Gao, N., Zhang, M. and Tang, J., "Maximum Likelihood Phylogenetic Reconstruction Using Gene Order Encodings", The 8th Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'11), 117-122. PDF
  • Shi, J., Arndt, W. and Tang, J., "Isolating - A New Resampling Method for Gene Order Data," The 8th Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'11), 135-140. PDF
  • 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.
  • 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 2011), 258-265.
  • 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 2011), 271-276.
  • Zhang, T., Dougal, R., Shepherd, J. and Tang, J., "The Simulation Tool for Mission-Optimized System Design," Grand Challenges in Modeling and Simulation (GCMS 2011), 348-355.

2010

  • 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), 169-174.
  • Zhang, Y., Hu, F. and Tang, J., "Pylogenetic Reconstruction with Gene Rearrangements and Gene Losses," 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'10), 35-38.PDF
  • 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.PDF
  • Shi, J., Zhang, Y., Luo, H. and Tang, J., "Using Jackknife to Assess the Quality of Gene Order Phylogenies," BMC Bioinformatics, 11 (168).PDF
  • Shepherd, J., Dougal, R. and Tang, J., "The Simulation and Data Visualization Potential of Microsoft's XNA," 2010 Grand Challenges in Modeling Simulation, pp. 306-310, Ottawa, Canada, July 2010.
  • 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.

2009

  • Zhang, Y., Dougal, R., Langland, B., Shi, J. and Tang,J.,"Method for partitioning large system models when using latency insertion method tospeed network solution," 2009 Conference on Grand Challenges in Modeling and Simulation (GCMS'09), 259-263.
  • Luo, H., Sun, Z., Arndt, W., Shi, J., Friedman, R. and Tang, J., "Gene Order Phylogeny and the Evolution of Methanogens," PLoS ONE 2009, 4(6): e6069 PDF.
  • Shepherd, J., Tang, J. and O'Kane, J., "Path-finding with Motion Constraints in Real Time Strategies," Computer Games and Allied Technologies (CGAT) 2009, 83-90.
  • Zhang, M., Arndt, W. and Tang, J., "An Exact Median Solver for the DCJ Distance," Proc. 2009 Pacific Symposium on Biocomputing (PSB 2009), 138-149PDF.
  • 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., Shi, J. and Tang, J., "Simultaneous Phylogeny Reconstruction and Multiple Sequence Alignment," Proc. 7th Asia-Pacific Bioinformatics Conf. (APBC 2009), in BMC Bioinformatics 2009, 10(Suppl 1):S11.
  • Yue, F. and Tang, J., "A Space-Efficient Algorithm for Three Sequence Alignment and Ancestor Inference", International Journal of Data Mining and Bioinformatics 2009, 3(2) 192-204.

2008

  • Luo, H. Shi, J., Arndt, W., Tang, J. and Friedman, R., "Gene Order Phylogeny of the Genus Prochlorococcus," PLoS ONE 3(12): e3837 doi:10.1371/journal.pone.0003837. PDF
  • Guo, Y. and J. Tang, "Phylogenetic Reconstruction with Disk-Covering and Bayesian Approaches," 8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2008), accepted.
  • Zhang, M., W. Arndt and J. Tang, "A Branch-and-bound Method for the Multichromosomal Reversal Median Problem", 8th Workshop on Algorithms in Bioinformatics (WABI 2008), in Lecture Notes in Bioinformatics 5251, 14-24. PDF
  • Arndt, W. and J. Tang, "Improving Reversal Median Computation using Commuting Reversals and Cycle Information", Journal of Computational Biology, 15, 8 (2008) 1079-1092. PDF
  • Yue, F., Zhang, M. and Tang, J., "Phylogenetic Reconstruction from Transposition", BMC Genomics, 2008, 9 (suppl 2):S15. PDF
  • Yue, F. and Tang, J., "A New Approach For Tree Alignment Based on Local Re-Optimization", 2008 International Conference on BioMedical Engineering and Informatics, 34-38.
  • 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. PDF
  • 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, CD only, Scotland.
  • Swenson, K., W. Arndt, J. Tang and B.M.E. Moret, "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). PDF

2007

  • Yue, F. and J. Tang, "A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference with Affine Gap Costs", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), 143-150.PDF
  • Bakos, J., P. Elenis and J. Tang, "FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data," Proc. 7th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2007), 888-895. PDF
  • Yue, F., M. Zhang and J. Tang, "A Heuristic for Phylogenetic Reconstruction Using Transposition", Proc. 7th IEEE Conf. on Bioinformatics and Bioengineering (BIBE 2007), 802-808. PDF
  • Yue, F. and J. Tang, "Three Sequence Alignment and Ancestor Inference with Affine Gap Costs", Procedings of the 2007 International Conference on Bioinformatics and Computational Biology (Biocomp 2007), 731-737.
  • Arndt, W. and J. Tang, "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. PDF
  • Ye, F., Y. Guo, A. Lawson and J. Tang, "Improving Tree Search in Phylogenetic Reconstruction from Genome Rearrangement Data", 6th Workshop on Experimental Algorithms (WEA 2007), in Lecture Notes in Computer Science 4525, 352-364. PDF
  • 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), Minneapolis, 2007. PDF

2006

  • Cui, L., Yue, F., dePamphilis, C., Moret, B.M.E. and Tang, J., "Inferring Ancestral Chloroplast Genomes with Inverted Repeat," Procedings of the 2006 International Conference on Bioinformatics and Computational Biology (Biocomp'06), pp 75-81, Las Vegas, NV.PDF
  • Zhang, M., Tang, J.,Guo, D.,Hu L., and Li, Q. "Succinct Text Indexes on Large Alphabet," Third Annual Conference on Theory and Applications of Models of Computation (TAMC 2006), in Lecture Notes in Computer Science 3959, 528-537.PDF
  • 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. PDF

2005

  • 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. PDF
  • Liu, T., Tang, J., and Moret, B.M.E., "Quartet Methods for Phylogeny Reconstruction from Gene Orders," Proc. 11th Int'l Computing and Combinatorics Conference (COCOON 2005), in Lecture Notes in Computer Science 3595, 63-73. PDF
  • Tang, J., and Moret, B.M.E., "Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements," Proc. 16th Symp. on Combinatorial Pattern Matching, (CPM 2005), in Lecture Notes in Computer Science 3537, 406-416. PDF
  • 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. PDF

2004

  • 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, IEEE Press (2004). PDF

2003

  • Tang, J., and Moret, B.M.E., "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. PDF
  • Tang, J., and Moret, B.M.E., "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. PDF

2002

  • Moret, B.M.E., Siepel, A.C., 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), inLecture Notes in Computer Science2452, 521-536. PDF
  • Moret, B.M.E., 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. PS

Thesis

  • "Large Scale Phylogenetic Reconstruction from Arbitrary Gene-order Data" Ph.D. Dissertation, 05/2004 PS
  • "A Study of Bounding Methods for Reconstructing Phylogenies from Gene-Order Data" Master Thesis, 01/2002 PS

Others (none-reviewed conference and tech report)

  • Moret, B.M.E. and Tang, J., "Improved bounding and searching for phylogeny reconstruction from gene-order data," UNM CS techreport TR-CS-2001-30.PS
  • "Software Framework for Simulation of Deployable Optical Membrane Telescope Mirrors," Optical Society of America, Baltimore, 1998.HTML
  • Tang, J., Desjarlais, L., Gerstle, W., Panthaki, M. and Sahu, R., "Application of CoMeT/SoftLab To Simulation of Multidisciplinary Systems," WAC2000, Hawaii, 06/2000.MS Word DOC
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