Chittaranjan Tripathy (please call me Chittu)

Department of Computer Science
Duke University
Update: Currently, I work as a Research Scientist at Amazon
The best way to contact me is via email.
Contact Information:
D240 LSRC
Department of Computer Science
Duke University
Durham, NC 27708-0129
Phone: (919) 660-4017, Fax: (919) 660-6519
Email: chittu [at] cs.duke.edu



Welcome to my homepage! I completed my Ph.D. from the Department of Computer Science at Duke University. I was extremely fortunate to be advised by Prof. Bruce Donald. Previously, I obtained a Master's degree in Computer Science from the School of Computer Science, the University of Oklahoma, Norman. Earlier, I obtained my B.Tech in Instrumentation and Electronics Engineering from Orissa University of Agriculture and Technology.

I am broadly interested in Computational Structural Biology, Bioinformatics, Data Mining, Machine Learning and Applied Algorithms. My current research focuses on developing efficient and robust algorithms for (i) Protein Structure Determination from a minimal amount of data recorded using Nuclear Magnetic Resonance (NMR) spectroscopy, and (ii) the Protein Loop Modeling Problem. My research interests also include Protein Design, and the study of protein dynamics and Intrinsically Disordered Proteins (IDPs), with an emphasis on sparse-data algorithms that use the knowledge mined from the big data involving protein structures, functions and experimental measurements, available to the scientific community. My research draws on tools and techniques from the biophysics and biochemistry of proteins, algebraic geometry, graph theory, combinatorial optimization, data mining, machine learning and robotics. Most recently, I have been working on planning and optimization problems in logistics planning and transportation systems.

I like the stimulating research milieu of the Donald Laboratory so much that I plan to hang around here this academic year! Meanwhile, I am also teaching in the Duke Computer Science Department.

Teaching

COMPSCI 230: Discrete Mathematics for Computer Science, Spring 2013, Summer 2013 (undergraduate course)

COMPSCI 330: Algorithms, Fall 2012, Summer 2013 (undergraduate and co-listed as non-CS graduate course)

CPS 130: Algorithms, Summer 2012 (undergraduate course)


Publications

Thesis:

Novel Algorithms for Protein Structure Determination from Sparse NMR Data. Chittaranjan Tripathy. Duke University, May 2012. (Need a copy? Please email me.)

Published:

Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure. PDF
Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou and Bruce R. Donald.
The 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Beijing, China, 2013.

Protein Loop Closure using Orientational Restraints from NMR Data. PDF
Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, and Bruce Randall Donald.
Proteins: Structure, Function, and Bioinformatics, 80(2):433-453, 2012. (Cover Article)
Software: POOL
Note: The journal version contains a wealth of new stuffs (e.g. dynamics and comparison with other state-of-the-art protocols) not present in the conference version.

Protein Loop Closure using Orientational Restraints from NMR Data. PDF
Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, and Bruce Randall Donald.
In Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI/LNCS 6577, pp. 483-498, 2011. (Conference Version)

Algorithms and Analytic Solutions using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR. PDF
Anna Yershova,* Chittaranjan Tripathy,* Pei Zhou, and Bruce Randall Donald.
In proceedings of the Ninth International Workshop on the Algorithmic Foundations of Robotics (WAFR, 2010), Springer Tracts in Advanced Robotics, 68:355-372, 2011.
*These authors contributed equally to the work.

Cover Article
Solution Structure of the FF Domain 2 of Human Transcription Elongation Factor CA150. PDF
Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
Structural Coordinates Deposited in the Protein Data Bank (PDB), PDB id: 2KIQ, 2009.

High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations. PDF
Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
Journal of Biomolecular NMR, 45(3):265-281, 2009.
Software: RDC-ANALYTIC and RDC-PANDA

A Hausdorff-Based NOE Assignment Algorithm Using Protein Backbone Determined from Residual Dipolar Couplings and Rotamer Patterns. PDF
Jianyang Zeng, Chittaranjan Tripathy, Pei Zhou, and Bruce Randall Donald.
Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB), 7:169-181, 2008.

Solution Structure of FF2

Submitted and In Preparation:

Analytic Solutions to Peptide Plane Orientations from Residual Dipolar Coupling and Residual Chemical Shift Anisotropy.
Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou and Bruce R. Donald.
In Preparation for a journal.

A Hybrid Algorithm to Determine Protein Fragment Conformations and Orientations from Residual Chemical Shift Anisotropy and Residual Dipolar Coupling Data: Applications to Computing the Protein Global-Fold.
Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou and Bruce R. Donald.
In Preparation for a journal.

Selected Posters and Workshop Presentations:

NMR Structure Determination of GrsA Epimerase Domain by Residual Dipolar Couplings (RDCs), Sparse NOEs and PREs.
Cheng-Yu Chen, Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, and Bruce Randall Donald.
Duke Biochemistry Department Retreat. Wrightsville Beach, NC, October 05-07, 2012. (Winner of the Best Poster Award)

RDC-PANDA: a High-Resolution NMR Structure Determination Algorithm Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations.
Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce R. Donald.
51st Experimental Nuclear Magnetic Resonance (ENC) Conference. Daytona Beach, FL, April 18 - 23, 2010.

Protein Structure Determination using Sparse Orientational Restraints from NMR Data.
Chittaranjan Tripathy, Anna Yershova, Pei Zhou, and Bruce R. Donald.
Duke Biochemistry Department Retreat. NC Biotech Center, September 26, 2009. (Winner of the Kamin Poster Award)

Bridging the Protein Gap: Using a Fragment Library with Incomplete NMR Models.
Vincent B. Chen, Chittaranjan Tripathy, Pei Zhou, Bruce R. Donald, David C. Richardson, and Jane S. Richardson.
Duke Biochemistry Department Retreat, Wrightsville Beach, NC, October 12-14, 2007.

Automated Structure Determination from Sparse NMR Data.
Jianyang Zeng, Lincong Wang, Chittaranjan Tripathy, Pei Zhou, and Bruce R. Donald.
6th NIH/NIGMS Protein Structure Initiative “Bottlenecks” Workshop, Natcher Conference Center, NIH, Bethesda, Maryland. March 19-20, 2007.