Chakra Chennubhotla

I am an Assistant Professor in the Department of Computational and Systems Biology at the School of Medicine, University of Pittsburgh. My research focuses on issues in structural biology and bioimaging, with an emphasis on understanding molecular basis of enzyme function, establishing organizational principles for conformational ensembles, mining molecular dynamics simulations for biologically relevant substates and automated reconstruction of neuronal structure from histological data.

Links to: Students and Collaborators; TECBio; Ph.D. Program; Contact information.

Recent Teaching

• Algorithms for Computational Structural Biology (with Chris Langmead, Spring 2010)

Ph.D. Thesis

• Spectral Methods for Multi-Scale Feature Extraction and Data Clustering.
  Department of Computer Science, University of Toronto.

Research Papers

• C. Chennubhotla*, J. Appavoo*, J. Ayoob, H. Katz. Computational microscope: supercomputer-driven bioimaging for neuronal reconstruction. (2010)
• A. Ramanathan, A. Savol, C. Langmead, P. Agarwal, C. Chennubhotla. Higher-order correlations in internal protein motions and energetics. (2010)
• A. Savol, C. Chennubhotla. Structure-from-FRET: protein trajectory reconstruction from FRET-derived distance constraints. (2010)
• C. Chennubhotla. Distance Geometry for Elastic Network Interpolation. (2010)
• C. Chennubhotla, Y. Zheng, I. Bahar Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol Bio Syst. 4, 287-292, 2008.
• I. Bahar, C. Chennubhotla, D. Tobi. (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol. 17:633-40.
• C. Chennubhotla, I. Bahar. Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol. Sep 21;3(9):1716-26. (2007)
• C. Chennubhotla & I. Bahar Markov Methods for Hierarchical Coarse Graining of Large Protein Dynamics. J Comput Biol. 14:765-76. (2007) (Also appeared in RECOMB06, Lecture Notes in Computer Science 3909, 379-393.) (2006)
• L.-W. Yang, E. Eyal, C. Chennubhotla, J. Jee, A. Gronenborn, I. Bahar. Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray data with Computational Predictions. Structure 15, 741-749. (2007)
• I. Bahar, C. Chennubhotla, B. Erman. "Reply to Comment on Elastic Network Models and Proteins" Physical Biology 4, 64-65. (2007)
• E. Eyal, C. Chennubhotla, L.-W. Yang, I. Bahar. Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models. Bioinformatics 23: i175-184. (2007)
• I. Farkas, C. Wu, C. Chennubhotla, I. Bahar, Z. Oltvai. Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics 7, 478. (2006)
• C. Chennubhotla, I. Bahar. Markov Propagation of Allosteric Effects in Biomolecular Systems. Molecular Systems Biology 2, 36. (2006)
• C. Chennubhotla, A. Rader, L.-W. Yang, I. Bahar. Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Physical Biology 2, S173-S180. (2005)
• C. Chennubhotla, A. Jepson. Hierarchical Eigensolver for Transition Matrices in Spectral Methods. Advances in Neural Information Processing Systems (NIPS) (2005)
• P. Estrada, A. Jepson, C. Chennubhotla. Spectral Embedding and Min-Cut for Image Segmentation. British Machine Vision Conference (2004)
• C. Chennubhotla, A. Jepson. Perceptual Distance Normalization for Appearance Detection. International Conference on Pattern Recognition (2004)
• C. Chennubhotla, A. Jepson. EigenCuts: Half-Lives of EigenFlows for Spectral Clustering. Advances in Neural Information Processing Systems (NIPS), 689-696. (2003)
• C. Chennubhotla, A. Paccanaro. Markov Analysis of Protein Sequence Similarities. Lecture Notes in Computer Science, 2859:278-286. (2003)
• A. Paccanaro, C. Chennubhotla, J. Casbon, M. Saqi. Spextral Clustering of Protein Sequences. International Joint Conference on Neural Networks (2003)
• C. Chennubhotla, A. Jepson., J. Midgley. Robust Contrast Invariant EigenDetection. International Conference on Pattern Recognition (2002)
• C. Chennubhotla, A. Jepson. Sparse-PCA: Extracting Multi-Scale Structure from Data. International Conference on Computer Vision (ICCV) 641-647. (2001)
• C. Chennubhotla, A. Jepson. Sparse Coding in Practice. SCTV (2001)

Students and Collaborators

• Andrej Savol (Ph.D., 2008- )
• Virginia Burger (Ph.D., Fall 2010- )

• Hilary Katz (Mt. Holyoke, TECBio Student 2010)
• Kim Schneider (Carlow College, TECBio Student 2010)
• Jonathan Gibbons (Duquesne, TECBio Student 2010)
• Jessica Dzurek (CS@Pitt, Moye Fellowship, Summer 2010)
• Shannon Quinn (Murphy Lab, Summer 2010, EigenCuts on Apache Mahout)

• Prof. Jonathan Appavoo (Boston University)
• Dr. Joseph Ayoob (CSB, Pitt)
• Dr. Pratul Agarwal (Oakridge National Labs)
• Dr. Ivet Bahar (CSB, Pitt)
• Prof. Takis Benos (CSB, Pitt)
• Dr. Tridib Dutta (Benos Lab, CSB, Pitt)
• Prof. Sanford Leuba (Cell Biology and Physiology, Pitt)
• Prof. Cecilia Lo (Developmental Biology, Pitt)
• Prof. Sandra Murray (Cell Biology and Physiology, Pitt)
• Dr. Arvind Ramanathan (Oakridge National Labs)
• Dr. John Vries (CSB, Pitt)

Contact Information