Education

Ph. D (1998). Computational Biology

Shanghai Institute of Biochemistry, Academia Sinica

Doctoral Dissertation: “Structure-based protein ligand design.”

B. S. (1993) Condensed Matter Physics

Department of Physics, Nanjing University

Professional experience

1998-1999 Research Associate, Shanghai Institute of Biochemistry, Chinese Academy of Sciences.

1999-2001 Post-Doctoral Research Associate (with M. S. Waterman), Department of Mathematics, University of Southern California, CA

2001-now Assistant Project Scientist (with P. A. Pevzner), Department of Computer Science and Engineering, University of California at San Diego, CA.

Computational experiences

C/C++ on UNIX/PC, Perl, CGI & web programming

Scientific softwares: Splus, Matlab

Molecular biology softwares: GCG, blast, clustalX, MSI/Biosym, etc.

Algorithms: dynamic programming, branch & cut, HMM, NN, graph theory, etc.

Summary of previous research

Comparative protein modeling (1993-1995)

We build a new comparative protein modeling system “PMODELING”, with the new algorithms for protein structural comparison, backbone reconstruction and side-chain placement.

Structure-based protein ligand design (1995-1998)

We develop a novel flexible docking strategy based on the new optimization algorithm “reactive tabu searching” and an empirical binding energy formula.

Computational protein design (1997-1999)

We improve the “self-consistent ensemble optimization” (SCEO) method to automatic protein design. The novel design scheme, “hetero-SCEO” has been applied to different problems of protein design: designing protein cores, grafting protein active sites onto natural scaffolds and redesigning the protein interfaces.

Algorithms of sequence comparison (1993-1999)

(1) We improve the “divide and conquer” technique in sequence alignment and get the multiple solutions of that problem.

(2) We develop a fast algorithm to align two very long genomic sequence and apply it to the comparisons of the sequences of human, mouse and plants.

(3) We develop a novel algorithm to align a gene sequence and a protein sequence with the consideration of the frameshift errors.

Analysis of gene expression (1999-2000)

(1) We analyze the relation between the co-expression of genes and their adjacency in the genome.

(2) We establish a novel method to estimate the statistical significance of the correlation between the expression patterns of two genes.

EULER Project: Sequence fragment assembly (2000-now)

We abandon the classical "overlap-layout-consensus" paradigm in favor of a new approach that reduces the fragment assembly to a variation of the classical Eulerian path problem.

Selected Publications

D. Ding and H. Tang (1994) An improvement of Myers-Miller's algorithm for sequence alignment. J. Biomath., 9(2):1-10.

H. Tang and D. Ding (1995) A new structure comparison method for protein homologous modeling and tertiary structure prediction. Biophysica Sinica, 11(1):60-66.

B. Zhang, D. Ding and H. Tang (1995) A fast and accurate protein structure rigid superposition method. Biophysica, Sinica, 11(4):575-582.

D. Ding, H. Tang and B. Zhang (1995) A knowledge-based protein modeling system and its evaluation. Biophysica Sinica, 11:416-428.

H. Tang and D. Ding (1996) A knowledge-based protein modeling system and its evaluation. II. Side-chain placement. Biophysica Sinica, 12:125-134.

H. Tang and D. Ding (1996) Large-scale homologous analysis of genome sequence. Acta Biochimica et Biophysica Sinica, 28(6)686-693.

D. Ding, H. Tang, B. Zhang and J. Chen (1997) PMODELING: A new homologous protein modeling system. In "Theoretical Physics in biology. Symposium of XiangShan scientific conferences, tribute to Prof. Peng Hengwu". Shanghai Science and Technology Press.

J. Chen, H. Tang and D. Ding (1997) Sequence-independent protein structure comparison. Acta . Biophysica Sinica 13(4):216-222.

H. Tang and D. Ding (1997) A new algorithm for large-scale genome sequence alignment. J.Biomath. 12(2):94-101.

H. Tang and D. Ding (1997) Very long genome sequence analysis. In "Theoretical Physics in Biology. Symposium of XiangShan scientific conferences, tribute to Prof. Peng Hengwu". Shanghai Science and Technology Press.

H. Tang, J. Chen and D. Ding (1998) Empirical and semi-empirical binding free energy calculation for protein-protein complex. Acta Biochimica et Biophysica Sinica, 30(2):119-124.

Y. Ye, H. Tang and D. Ding (1998) Predicting the solvated structures of protein mutants by self-consistent ensemble optimization. Acat. Biophysica Sinica 14(2):311-317.

H. Tang, Y. Ye and D. Ding (1998) Flexible docking proteins and "Drug-like " ligands. Acta Biochimica et Biophysica Sinica 30(6):623-630.

Y. Ye, H. Tang and D. Ding (1998) Design of protein cores by screening combinatorial sequence library. Acta Biochimica et Biophysica Sinica 30(5):525-529.

H. Tang, J. Chen and D. Ding (1998) Structural prediction of flexible complex of proteins. Acat. Biophysica Sinica, 14(4):750-756.

Y. Ye, H. Tang, D. Ding (1999) Engineering novel functional proteins: grafting active sites into natural scaffolds. Acta Biochimica et Biophysica Sinica., 31(3):303-308.

W. Zhang, H. Tang and D. Ding (1999) Discussion about applicability of pharmacophore hypothesis in de novo design of ligands. Acta. Biophysica Sinica, 15(4):740-750.

W. Zhang, S. Zhang, H. Tang and D. Ding (2000) Reverse-translated alignment of EST sequence with protein sequence. Acta. Biophysica Sinica , 16(2):322-333.

S. Kruglyak and H. Tang (2000) Regulation of Adjecent Yeast Genes. Trends in Genetics, 16(3):109-111.

S. Kruglyak and H. Tang (2001) A New Estimator of Significance of Correlation in Time Series Data, J. Comp. Biol. (accepted).

P. A. Pevzner, H. Tang and M. S. Waterman (2001) A New Approach to Fragment Assembly in DNA Sequencing. Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, April 2001, Montreal, Canada, ACM Press.

P. A. Pevzner, H. Tang, M. S. Waterman (2001), An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA, 98(17):9748-53.

P. A. Pevzner, H. Tang, Fragment assembly with double-barreled data. Bioinformatics. 2001 Jun;17 Suppl 1:S225-33 (Special ISMB 2001 issue).