Chakra Chennubhotla

Chakra Chennubhotla
Contact	Dept. of Computational Biology School of Medicine, University of Pittsburgh 3501 Fifth Avenue, Suite 3081, Biomedical Science Tower 3 (BST3) Pittsburgh, PA 15260 chakracs [AT] pitt [DOT] edu Tel: 412.648.7794 Fax: 412.648.3163
Research	COMPUTATIONAL BIOLOGY COMPUTER VISION AND MACHINE LEARNING
Focus	Spectral graph-theoretic methods for computational biology
Recent Work	Signal Propagation in Proteins and Relation to Equilibrium Fluctuations Chakra Chennubhotla and Ivet Bahar. PLoS Computational Biology (Accepted). 2007 Insights into Equilbrium Dynamics of Proteins from comparison of NMR and X-ray data with computational predictions Lee-Wei Yang, Eran Eyal, Chakra Chennubhotla, J. Jee, A. Gronenborn and Ivet Bahar. Structure, in press 2007 Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-ray crystallography and Elastic Network Models Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang and Ivet Bahar. Bioinformatics, in press 2007 Markov Propagation of Allosteric Effects in Biomolecular Systems Chakra Chennubhotla and Ivet Bahar. Molecular Systems Biology, 2:36, 2006 Topological Basis of Signal Integration in the Transcriptional-Regulatory Network of the Yeast, Saccharomyces Cerevisiae Illes Farkas, Chauang Wu, Chakra Chennubhotla, Ivet Bahar and Zoltan Oltvai. BMC Bioinformatics, 7:478, 2006 Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics Chakra Chennubhotla and Ivet Bahar. Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy (April 2-5, 2006). In Springer Berlin, Lecture Notes in Computer Science, RECOMB 2006, LNBI 3909, pp. 379-393, 2006. Also to appear in Journal of Computational Biology, 2007. The Gaussian Network Model: Theory and Applications A. J. Rader, Chakra Chennubhotla, Lee-Wei Yang and Ivet Bahar. Book chapter in Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, Eds. Qiang Cui and Ivet Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006 Elastic Network Models for Understanding Biomolecular Machinery: from enzymes to supramolecular assemblies Chakra Chennubhotla, A. J. Rader, Lee-Wei Yang and Ivet Bahar. Physical Biology, 2:S173-S180, 2005 Hierarchical Eigensolver for Transition Matrices in Spectral Methods Chakra Chennubhotla and Allan Jepson. NIPS 2004 Spectral Embedding and Min-Cut for Image Segmentation [Poster] Paco Estrada, Allan Jepson and Chakra Chennubhotla. BMVC 2004 Perceptual Distance Normalization for Appearance Detection Chakra Chennubhotla and Allan Jepson. ICPR 2004 Hierarchical Representation of Transition Matrices for Spectral Clustering Chakra Chennubhotla and Allan Jepson. 2003 Algorithm/Demo/FAQ. EigenCuts: Half-Lives of EigenFlows for Spectral Clustering Chakra Chennubhotla and Allan Jepson. NIPS 2002 Sparse PCA (S-PCA): Extracting Multi-Scale Structure from Data Chakra Chennubhotla and Allan Jepson. ICCV 2001 Algorithm/Demo/FAQ. Facelets, shown below, are multi-scale orthogonal S-PCA basis derived from a database of face images. Unlike Eigenfaces, facelets represent fine-scale information with spatially local support. S-PCA basis derived from a database of gesturing hand images. Sparse Coding in Practice Chakra Chennubhotla and Allan Jepson. SCTV 2001 Robust Contrast-Invariant EigenDetection Chakra Chennubhotla, Allan Jepson, and John Midgley. ICPR 2002 Spectral Clustering of Protein Sequences Alberto Paccanaro, Chakra Chennubhotla, James Casbon and Mansoor Saqi. IJCNN 2003 Markov Analysis of Protein Sequence Similarities Chakra Chennubhotla and Alberto Paccanaro. 2003