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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:
CS 2420 Data Structures and Algorithms
CS7960 Machine-Learning
Methods for Bioinformatics
CS 6670 Core Algorithms In Bioinformatics
CS 6890 S.T. The Machine Learning Methods--Applications in Bioinformatics
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.
Research tools developed
For
details, please visit my research group at http://yanbioinformatics.cs.usu.edu:8080/index.
Recent Refereed
Journal Articles
1.
Hu, J. and Yan, C., A tool for
calculating binding-site residues on proteins from PDB structures. BMC Struct Biol. 2009 Aug 3;9:52.
2.
Ju,
W., Shan, J., Yan, C., and Cheng, H. Discrimination of disease-related non-synonymous
single nucleotide polymorphisms using multi-scale RBF kernel fuzzy support
vector machine. Pattern Recognition Letters 2009, 30:391-396.
3.
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.
4.
Hu,
J. and Yan, C. Identification of
deleterious non-synonymous single nucleotide polymorphisms using
sequence-derived information BMC
Bioinformatics 2008, 9:297.
5.
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.
6.
Yan, C., Hu, J. and Wang, Y.
Discrimination of outer membrane proteins with improved performance. BMC Bioinformatics 2008, 9:47.
7.
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.
8.
Hu,
J., and Yan, C. An improved method
for alpha-helical transmembrane protein topology prediction. Bioinformatics and Biology Insights 2008
2: 67-74.
9.
Hu,
J., and Yan, C. Protein subcellular
localisation prediction with improved performance. Int. J. Functioinal Informatics and Personalised Medicine 2008
1(3): 321-328.
10.
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.
11.
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.
12.
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.
13.
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.
14.
Yan, C., Dobbs, D., and Honavar, V. A two-stage
classifier for identification of protein-protein interface residues. Bioinformatics,
2004, 20(S1): i371-i378.
15.
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.
16.
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. Mining sequence features for DNA-binding site prediction. In Proceedings of IEEE Symposium on Computational
Intelligence in Bioinformatics and Bioengineering. Sept 15-17, 2008.
2.
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.
3.
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.
4.
Shan,
J., Ju,
5.
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.
6.
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.
7.
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.
8.
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.
9.
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.
10.
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.