Chakra Chennubhotla

Chakra Chennubhotla, Ph.D.
Associate Professor

Ph.D. in Computer Science, University of Toronto

Phone: (412)648-7794

Research Summary

Developing computational models and methods to improve the understanding of major interactions and allosteric mechanisms that underlie the proper functioning of biomolecular systems. In particular (i) developing information-theoretic concepts for determining the probabilistic rates and pathways of information flow in biomolecular systems both within multicomponent structures and at the cellular level (protein-protein interaction networks); and studying the sequence of events possibly induced by information flow; (ii) designing and interpreting FRET based experiments to explore molecular interactions and correlations and assessing their functional implications; and finally (iii) developing novel methods originating from computer vision for analyzing, refining and interpreting biomolecular images in terms of the structure, dynamics and function of the observed systems, focusing on cryo-electron microscopic measurements.

Recent Publications
Benos PV, Tosun BA, Manatakis DV, Vukmirovic M, Nguyen L, Yan X, Hu B, Deluliis G, Woolard T, Maya JD, Homer R, Kaminski N, Chennubhotla CS (2017) Towards Understanding Spatial Lung Tissue Heterogeneity In Idiopathic Pulmonary Fibrosis (IPF) A72. Mechanisms Driving Fibrosis.

Narayanan C, Bernard DN, Bafna K, Choudhary OP, Chennubhotla CS, Agarwal PK, Doucet N (2017) Conformational Motions Impacting Function in an Enzyme Superfamily The FASEB Journal. 31(1 supplement): 762.6

Jones T, Nguyen L, Tosun BA, Chennubhotla CS, Fine JL (2017) Computational Pathology versus Manual Microscopy: Comparison Based on Workflow Simulations of Breast Core Biopsies Laboratory Investigation. 97: 398A


Project title Proj Start Date Proj End Date Funding Source
Assaying Heterotaxy Patient Genes in Cilia Motility and Left-Right Patterning 9/1/2014 8/31/2018 NIGMS-R01
Training and Experimentation in Computational Biology (TECBio): Simulation and Visualization of Biological Systems at Multiple Scales 3/1/2013 1/31/2017 NSF
Informatics Tools for Tumor Heterogeneity in Multiplexed Flourescence Images 5/4/2016 4/30/2019 NCI-U01
Conformational sub-states in enzyme catalysis: Applications to the ribonuclease family 4/1/2014 3/31/2019 NIGMS-R01
Large-scale Analysis of the Evolution of Organellar Social Networks 8/14/2015 7/31/2018 NSF
Center for Causal Modeling and Discovery of Biomedical Knowledge from Big Data 9/29/2014 8/31/2018 NHGRI-U54
Incorporating Spatial Heterogeneity Analytics to Impact the Ability to Predict the Progression of Barrett’s Esophagus 5/1/2017 4/30/2018 Cernostics