2009 Research Reports

BICB 2009/01
Incorporating Functional Inter-relationships into Protein Function Prediction Algorithms
Pandey, G., Myers, C.L., and Kumar, V.

BICB 2009/02
An Association Analysis Approach to Bioclustering
Pandey, G., Alturi, G., Steinbach, M., Myers, C.L., and Kumar, V.

BICB 2009/03
Threshold Occupancy and Specific Cation Binding Modes in the Hammerhead Ribozyme Active Site are Required for Active Conformation
Lee, T.S., Giambasu, G.M., Sosa, C.P., Martick, M., Scott, W.G., and York, D.M.

BICB 2009/04
Predictive Learning Using Group Information
Cherkassky, V. and Cai, F.

BICB 2009/05
Selective and Irreversible Inhibitors of Aphid Acetylcholinesterases: Steps Toward Human-safe Insecticides
Pang, Y.-P., Singh, S.K., Gao, Y., Lassiter, T.L., Mishra, R.K., Zhu,K.Y., Brimijoin, S.
PLoS ONE, 4(2): e4349 (2009).

BICB 2009/06
Structure of HI-6•Sarin-Acetylcholinesterase Determined by X-ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design
Ekström, F., Hörnberg, A., Artursson, E., Hammarström, L.-G., Schneider, G., and Pang, Y.-P.

BICB 2009/07
Selective and Irreversable Inhibitors of Mosquito Acetylcholinesterases for Controlling Malaria and Other Mosquito-Borne Diseases
Pang, Y.-P., Ekström, F., Polsinelli, Y.G., Rana, S., Hua, D.H., Andersson, B., Andersson, P.O., Peng, L., Singh, S.K., Mishra, R.K., Zhu, K.Y., Fallon, A.M., Ragsdale, D.W., Brimijoin, S.
PLoS ONE, 4(8): e6851 (2009).

BICB 2009/08
Crystal structures of oxime-bound fenamiphos-acetylcholinesterases: Reactivation involving flipping of the His447 ring to form a reactive Glu334-His447-oxime triad
Hörnberg, A., Artursson, E., Wärme, R., Pang, Y.-P., Ekström, F.
Biochem Pharmacol (2009), doi:10.1016/

BICB 2009/09
A Hypergraph-based Learning Algorithm for Classifying Gene Expression and ArrayCGH Data with Prior Knowledge
Tian, Z., Hwang, T., and Kuang, R.
Bioinformatics In Press (2009), doi:10:10.93/bioinformatics/btp467

BICB 2009/10
A Hypergraph-based Learning Algorithm for Classifying ArrayCGH Data with Spatial Prior
Tian, Z., Hwang, T., and Kuang, R.
Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009 Aug

BICB 2009/11
Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction
Hwang, T., Tian, Z., Kocher, J.-P. and Kuang, R.
Proc. of Eighth IEEE International Conference on Data Mining (ICDM), pages 293-302, 2008 Nov

BICB 2009/12
Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs
Hwang, T., Hugues, S., Tian, Z., Wu, B., Wigle, D., Kocher, J.-P., Kumar, V., and Kuang, R.
Bioinformatics, Vol. 24, No. 18, pages 2023-2029, 2008 Aug

BICB 2009/13
A Regulatory Mechanism for RSK2 NH₂-Terminal Kinase Activity
Cho, Y.-Y., Yao, K., Pugliese, A., Malakhova, M., Bode, A., and Dong, Z.
Cancer Res 2009; 69: (10).  May 15, 2009

BICB 2009/14
Predictive Modeling of Transplant-Related Mortality
Cherkassky, V. and Cai, F.

BICB 2009/15
Predictive Learning With Structured (Grouped) Data
Liang, L., Cai, F., and Cherkassky, V.
Neural Networks (2009), doi:10.1016/j.neunet.2009.06.030

BICB 2009/16
A Simple Rank Test to Distinguish Extreme Pathways from Elementary Modes in Metabolic Networks
Jevremovic, D., Trinh, C., Srienc, F., and Boley, D.

BICB 2009/17
On Algebraic Properties of Extreme Pathways in Metabolic Networks
Jevremovic, D., Trinh, C., Srienc, F., and Boley, D.

BICB 2009/18
Predictive Learning With Sparse Heterogenous Data
Cherkassky, V., Cai, F., and Ling, L.
2009 International Conference on Neural Networks, Atlanta

BICB 2009/19
Subspace Differential Coexpression Analysis: Problem Definition and A General Approach
Fang, G., Kuang, R., Pandey, G., Steinbach, M., Myers, C., and Kumar, V.
Proceedings of the 15th Pacific Symposium on Biocomputing (PSB), pp. 145-156, 2010.

BICB 2009/20
Mining Low-Support Discriminative Patterns from Dense and High-Dimensional Data
Fang, G., Pandey, G., Gupta, M., Steinbach, M., and Kumar, V.
Tech Report 09-011, Department of Computer Science, University of Minnesota, 2009.