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Assistant Professor Phone:
435-797-2570 Fax:
435-797-3265 Office:
Old Main 401F Email:
Charles.Yan@usu.edu 4205
Old Main Hill |
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Education:
Teaching:
CS7960
Topics in Bioinformatics
CS 6670 Computer Science Applications In Bioinformatics With A Project
CS 6890 S.T. Bioinformatics--The Machine Learning Approach
CS 5890 Bioinformatics: Problems And Solutions
Research Topics:
- Bioinformatics, Computational Biology, Machine Learning
and Data Mining
My research mainly focuses on the
development of machine learning algorithms to solve specific bioinformatic problems, such as identification of protein
functional sites, protein function/structure prediction, gene finding, and
sequence classification. Other topics that I am interested in include protein
folding, protein docking, gene expression analysis, phylogenetic
inference and protein interaction network.
Recent Refereed
Journal Articles
1.
Hu,
J. and Yan, C. A Method for
discovering transmembrane beta-barrel proteins in
gram-negative bacterial proteomes. Computational
Biology and Chemistry 2008 32:298-301.
2.
Hu, J. and Yan, C.
Identification of deleterious non-synonymous single nucleotide polymorphisms
using sequence-derived information BMC
Bioinformatics 2008, 9:297.
3.
Yan, C., Hu, J. and Wang, Y. Discrimination
of outer membrane proteins using a K-nearest
neighbor method.
Amino Acids 2008 35(1):65-73.
4.
Yan, C., Hu, J. and Wang, Y.
Discrimination of outer membrane proteins with improved performance. BMC Bioinformatics 2008, 9:47.
5.
Yan, C., Wu, F., Jernigan, R.L., Dobbs, D., and Honavar V. Characterization of
protein-protein interfaces. The Protein Journal
2008 27(1):59-70.
6.
Hu,
J., and Yan, C. An improved method
for alpha-helical transmembrane protein topology
prediction. Bioinformatics and Biology
Insights 2008 2: 67-74.
7.
Yan, C., Terribilini, M., Wu, F., Jernigan,
R.L., Dobbs, D., and Honavar V. Predicting
DNA-binding sites of proteins from amino acid sequence. BMC
Bioinformatics, 2006, 7:262.
8.
Terribilini,
M. Lee, J.-H., Yan, C., Jernigan, R.,
Honavar, V., and Dobbs, D. Computational prediction of RNA-binding sites in
proteins based on amino acid sequence, RNA, 2006, 12 (8): 1450-1462.
9.
Yan, C. and Hu, J. An exploration to the
combining of solvent accessibility with amino acid sequence in the
identification of helix-turn-helix motifs, WSEAS
Transaction on Biology and Biomedicine, 2006, 6(3): 477-484.
10.
Yan, C.,
Burleigh, J.G. and Eulenstein, O. Identifying optimal
incomplete phylogenetic data sets from sequence
databases. Mol Phylogenet Evol.
2005, 35(3):528-35.
11.
Yan, C., Dobbs, D., and Honavar, V. A
two-stage classifier for identification of protein-protein interface residues. Bioinformatics,
2004, 20(S1): i371-i378.
12.
Yan, C., Honavar, V., and Dobbs, D. Identification of
interface residues in protease-inhibitor and antigen-antibody complexes: a
support vector machine approach. Neural Computing &
Applications, 2004,
13(2): 123 -129.
13.
Sen, T., Kloczkowski, A., Jernigan, R., Yan, C., Honavar, V., Ho,
K., Wang, C., Ihm, Y., Cao, H., Gu,
X., Dobbs, D. Prediction of protein binding sites by
combining several methods. BMC Bioinformatcs, 2004, 5:205.
Refereed
Conference Articles
1.
Hu,
J. and Yan, C. Predicting protein subcellular localizations using weighted Euclidian
distance. In Proceedings of IEEE 7th International Symposium on BioInformatics and BioEngineering,
2007, 1370-1373.
2.
Shan,
J., Wang, Y. and Yan, C. Toward the
recognition code of protein-DNA recognition. In Proceedings of IEEE 7th
International Symposium on BioInformatics and BioEngineering, 2007, 1290 - 1293.
3.
Shan,
J., Ju,
4.
Ju,
W., Shan, J. Yan, C., and Cheng, H.D. Discrimination of outer membrane proteins using fuzzy
support vector machines. In Proceedings of the 10th Joint Conference
on Information Sciences, 2007, 854-860.
5.
Yan, C. and Hu, J. Identification of
Helix-Turn-Helix motifs from amino acid sequence. In
Proceedings of IEEE Symposium on Computational Intelligence in
Bioinformatics and Computational Biology, 2006, 2006,
1-7.
6.
Yan, C. and Hu, J. A
Hidden Markov Model for the Identification of Helix-Turn-Helix Motifs. In
Proceedings of WSEAS International Conference on Cellular and Molecular
Biology-Biophysics and Bioengineering, 2006,14-19.
7.
Yan, C. A hidden Markov model approach to
model protein sequence and structural information: Identification of helix-turn-helix
DNA-binding motif. In Proceedings of IEEE International Conference on Granular
Computing, 2006, 385-388.
8.
Terribilini,
M., Lee, J., Yan, C., Jernigan, R.L., Carpenter, S., Honavar, V., and Dobbs, D. Identifying
Interaction Sites In "Recalcitrant" Proteins: Predicted protein and
RNA binding sites in Rev ProteinS of HIV-1 and EIAV agree with experimental data. In Proceedings of
Pacific Symposium on Biocomputing, 2006, 11:415-426.
9.
Yan, C., Dobbs, D., and Honavar, V.
Identification of surface residues in protein-protein interaction - a support
vector machine approach. In Proceedings of Intelligent Systems Design and
Application, 2003, 53-62.