PublicationsStructural BiologyJournal PapersFree Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H. Kamisetty, E.P. Xing, C.J. Langmead Journal of Computational Biology 15(7), pp. 755-766, 2008 (invited submission)
A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology A.K. Yan C.J. Langmead, B.R. Donald The International Journal of Robotics Research Special Issue on Robotics Techniques Applied to Computational Biology 24 (2-3), pp.165-182, 2005
An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments C.J. Langmead, B.R. Donald Journal of Biomolecular NMR, 29, pp. 111-138, 2004
A Polynomial Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments C.J. Langmead, A.K. Yan, L. Wang, R. Lilien, B.R. Donald Journal of Computational Biology, 11(2-3), pp. 277-298, 2004 (invited submission) Conference PapersA Graphical Model Approach for Predicting Free Energies of Association for Protein-Protein Interactions Under Backbone and Side-Chain Flexibility H. Kamisetty, C. Bailey-Kellogg, C. J. Langmead Proceedings of 3DSIG 2009 Structural Bioinformatics and Computational Biophysics pp. 67-68, 2009 Also accepted for oral presentation * Winner Best Contribution PDF, Bibtex
A Bayesian Approach to Protein Model Quality Assessment H. Kamisetty and C.J. Langmead Proceedings of 26th International Conference on Machine Learning, (ICML) pp. 481-488, 2009
Modeling and Inference of Sequence-Structure Specificity H. Kamisetty, B. Ghosh, C. Bailey-Kellogg, C. J. Langmead Proceedings of The 8th Annual International Conference on Computational Systems Bioinformatics (CSB) pp. 91-101, 2009
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations A. Ramanathan, P. K. Agarwal, M. Kurnikova, C. J. Langmead Proceedings of The 13th Annual International Conference on Computational Molecular Biology (RECOMB) pp. 138-154, 2009
Conformational Free Energy of Protein Structures: Computing Upper and Lower bounds H. Kamisetty, C.J. Langmead Proceedings of 3DSIG 2008 Structural Bioinformatics and Computational Biophysics pp. 23-24, 2008 Also accepted for oral presentation PDF, Bibtex
Using Bit Vector Decision Procedures for Analysis of Protein Folding Pathways C.J. Langmead, S. K. Jha Fourth Workshop on Constraints in Formal Verification In press, 2007
Predicting Protein Folding Kinetics via Model Checking C.J. Langmead, S.K. Jha, Lecture Notes in Bioinformatics The 7th Workshop on Algorithms in Bioinformatics (WABI) pages 252-264, 2007
Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H. Kamisetty, E.P. Xing, C.J. Langmead Proceedings of The Eleventh Annual International Conference on Computational Molecular Biology (RECOMB) , pp 366-380, 2007
Structure based chemical shift prediction using Random Forests non-linear regression K. Arun and C.J. Langmead Proceedings of The Forth Asia-Pacific Bioinformatics Conference, (APBC) 2006. pp 317-326, 2006
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment C.J. Langmead, B.R. Donald Proceedings of The IEEE Computer Society Bioinformatics Conference (CSB), pp. 278-289, 2004
3D-Structural Homology Detection via Unassigned Residual Dipolar Couplings C.J. Langmead, B.R. Donald Proceedings of The IEEE Computer Society Bioinformatics Conference (CSB), pp. 209-217, 2003 PDF, Bibtex
A Polynomial Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments C.J. Langmead, A.K. Yan, L. Wang, R. Lilien, B.R. Donald Proceedings of The Seventh Annual International Conference on Computational Molecular Biology (RECOMB), pp. 176-187, 2003
Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data C.J. Langmead, B.R. Donald Proceedings of The Fifth Annual International Conference on Computational Molecular Biology (RECOMB), pp. 164-175, 2001 Ph.D. DissertationMolecular Replacement for Nuclear Magnetic Resonance: Application to NMR Resonance Assignment and Protein Structure Determination C.J. Langmead Doctorial Thesis: Dartmouth College Dept. of Computer Science, December 2003 Tech ReportsA graphical model approach for predicting free energies of association for protein-protein interactions under backbone and side-chain flexibility H. Kamisetty, C. Bailey-Kellogg, C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-08-162 December 2008
Using Tensor Analysis to Characterize Contact-Map Dynamics of Proteins A. Ramanathan, P.K. Agarwal, C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-08-109 January 2008
Detecting Protein-Protein Interaction Decoys using Fast Free Energy Calculations C.J. Langmead, H. Kamisetty Carnegie Mellon University School of Computer Science Technical Report CMU-CS-07-156 October 2007
Predicting Protein Folding Kinetics via Model Checking C.J. Langmead, S.K. Jha, Carnegie Mellon University School of Computer Science Technical Report CMU-CS-07-132 May 2007
Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H. Kamisetty, E.P. Xing, C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-06-160 November 2006
Structure based chemical shift prediction using Random Forests non-linear regression K. Arun, C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-05-163 July 2005
Classifying Protein Structural Dynamics via Residual Dipolar Couplings Ruben Valas, C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-05-108 December 2004
An Improved Nuclear Vector Replacement Algorithm for Nuclear Magnetic Resonance Assignment C.J. Langmead, B.R. Donald Dartmouth Technical Report TR2004-494 March 2004
High-Throughput 3D Homology Detection via NMR Resonance Assignment C.J. Langmead, B.R. Donald Dartmouth Technical Report TR2004-487 February 2004
A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology A.K. Yan C.J. Langmead, B.R. Donald Dartmouth Technical Report TR2003-474 October 2003 PDF, Bibtex
3D-Structural Homology Detection via Unassigned Residual Dipolar Couplings C.J. Langmead, B.R. Donald Dartmouth Technical Report TR2003-439 January 2003 Posters and AbstractsProtein Flexibility and Energy Flow During Enzyme Catalysis A. Ramanathan, J.M. Borroguero, C. J. Langmead, P.K. Agarwal Computers in Chemistry, 238th ACS National Meeting, 2009 Also accepted for oral presentation
Dynamic Invariants in Protein Folding Pathways Revealed by Tensor Analysis A. Ramanathan, C. J. Langmead 8th Annual International Conference on Computational Systems Bioinformatics (CSB), 2009
Belief Propagation Reveals Allosteric Mechanisms in Proteins H. Kamisetty, A. Ramanathan, C. J. Langmead 8th Annual International Conference on Computational Systems Bioinformatics (CSB), 2009
A Graphical Model Approach for Predicting Free Energies of Association for Protein-Protein Interactions Under Backbone and Side-Chain Flexibility H. Kamisetty, C. Bailey-Kellogg, C. J. Langmead Intelligent Systems in Molecular Biology (ISMB), 2009
Identifying Allosteric Mechanisms via Message Passing H. Kamisetty, A. Ramanathan, C. J. Langmead Keystone Symposium on Protein Dynamics, Allostery, and Function Keystone, CO. June 5-10, 2009
Protein Flexibility and Energy Flow During Enzyme Catalysis A. Ramanathan, J.M. Borroguero, C. J. Langmead, P.K. Agarwal Keystone Symposium on Protein Dynamics, Allostery, and Function Keystone, CO. June 5-10, 2009
Identifying Energy Coupled Networks of Residues Mediating Allosteric Coupling in Proteins A. Ramanathan, A. Savol, C. J. Langmead, P.K. Agarwal, C. S. Chennubhotla Keystone Symposium on Protein Dynamics, Allostery, and Function Keystone, CO. June 5-10, 2009
Identifying Allosteric Mechanisms via Belief Propagation H. Kamisetty, A. Ramanathan, C. J. Langmead 13th Annual International Conference on Computational Molecular Biology (RECOMB) Tucson, AZ. May 18-21, 2009
Incorporating Protein Flexibility in Predicting Free Energies of Association for Protein-Protein Interactions H. Kamisetty, C. Bailey-Kellogg, C. J. Langmead 13th Annual International Conference on Computational Molecular Biology (RECOMB) Tucson, AZ. May 18-21, 2009
Conserved Protein Flexibility And Pathways Of Energy Flow In Enzyme Catalysis A. Ramanathan, J. Borreguero, C. J. Langmead, P. K. Agarwal Biophysical Journal, 2009 96(3) p. 71a
Large-Scale Testing of Chemical Shift Prediction Algorithms and Improved Machine Learning-Based Approaches to Shift Prediction K. Arun and C.J. Langmead IEEE Computer Society Bioinformatics Conference (CSB) Stanford University, Palo Alto, CA, August 2004
High-Throughput 3D Homology Detection via NMR Resonance Assignment C.J. Langmead, B.R. Donald The Eighth Annual International Conference on Computational Molecular Biology (RECOMB) March, CA, March 2004
A Framework for Automated NMR Resonance Assignment and 3D Structural Homology Detection C.J. Langmead, B.R. Donald Gordon Research Conference on Computational Aspects of Biomolecular NMR Ventura, CA, January 2004
Chemical Shifts Dynamics (CSD): Time-Frequency Analysis of Protein NMR Data C.J. Langmead, B.R. Donald Intelligent Systems in Molecular Biology (ISMB) San Diego, CA, August 2000 Systems BiologyJournal PapersSymbolic Approaches to Finding Control Strategies in Boolean Networks C.J. Langmead, S.K. Jha Journal of Bioinformatics and Computational Biology, 7(2) pp. 323 – 338, 2009 (invited submission) Supplemental Figure and Text Example 4x4 input file Example 32x32 input file
Phase-Independent Analysis of Genome-Wide Expression Patterns C.J. Langmead, A.K. Yan, C.R. McClung, B.R. Donald Journal of Computational Biology 10(3-4), pp. 521-536, 2003 (invited submission) PDF, Bibtex Conference PapersA Bayesian Approach to Model Checking Biological Systems S. K. Jha, E.M. Clarke, C.J. Langmead, A. Legay, A. Platzer, A., P. Zuliani Proceedings of The Seventh Annual Conference on Computational Methods in Systems Biology, (CMSB). pp. 218-234, 2009
Generalized Queries and Bayesian Statistical Model Checking in Dynamic Bayesian Networks: Application to Personalized Medicine C. J. Langmead Proceedings of The 8th Annual International Conference on Computational Systems Bioinformatics (CSB) pp. 201-212, 2009
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology A. Donze, G. Clermont, A. Legay, C. J. Langmead Proceedings of The 13th Annual International Conference on Computational Molecular Biology (RECOMB) pp. 155-169, 2009
Angiopoietin-2, a regulator of vascular permeability in inflammation, is elevated in severe acute pancreatitis and and is associated with systemic organ failure D.C. Whitcomb, V.N. Muddana, C. J. Langmead, J. Lamb, G. I. Papachristou Pancreas, Abstracts of Papers for the 39th Annual Meeting of the American Pancreatic Association 37(4), pp. 500-501, 2008
Statistical Model Checking in BioLab: Application to the automated analysis of the T-Cell Receptor Signalling Pathway E.M. Clarke, J.R. Faeder. L.A. Harris, C.J. Langmead, A. Legay, S. K. Jha Proceedings of The Sixth Annual Conference on Computational Methods in Systems Biology, (CMSB) 2008. pp. 231-250, 2008
Symbolic Approaches to Finding Control Strategies in Boolean Networks C.J. Langmead, S.K. Jha Proceedings of The Sixth Asia-Pacific Bioinformatics Conference, (APBC) pp. 307-319, 2008. An extended version of the conference paper PDF, Bibtex
A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data C.J. Langmead Proceedings of The Forth Asia-Pacific Bioinformatics Conference, (APBC) pp. 217-226, 2006
A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns C.J. Langmead, C.R. McClung, B.R. Donald Proceedings of IEEE Computer Society Bioinformatics Conference (CSB), pp. 237-245, 2002 PDF, Bibtex
Phase-Independent Analysis of Genome-Wide Expression Patterns C.J. Langmead, A.K. Yan, C.R. McClung, B.R. Donald Proceedings of The Sixth Annual International Conference on Computational Molecular Biology (RECOMB), pp. 205-215, 2002 Posters and AbstractsAngiopoietin-2, a regulator of vascular permeability in inflammation, is elevated in severe acute pancreatitis and and is associated with systemic organ failure D.C. Whitcomb, V.N. Muddana, C. J. Langmead, F.D. Houghton, A. Guenther, P.K. Eagon, J. Mayerle, J. Lamb, G. Clermont, M.M. Lerch, G. I. Papachristou 41st Annual Meeting of the European Pancreatic Club, 2009
Multiplex Serum Marker Panel Accurately Predicts Systemic Complications of Acute Pancreatitis D.C. Whitcomb, V.N. Muddana, C. J. Langmead, J. Lamb, G. I. Papachristou Gasteroenterology, 2009, Abstracts from Digestive Disease Week 2009
Microarray Analysis of Circadian Gene Expression in Rat-1 Fibroblasts G.E. Duffield, J.D. Best, B. Meurers, C.J. Langmead, A. Bittner, J.J. Loros, J.C., Dunlap Gordon Research Conference on Chronobiology, 2001 Technical ReportsStructural Operational Semantics (SOS) description of the BioNetGen language E.M. Clarke, S.K. Jha, C.J. Langmead, J. Faeder
Symbolic Approaches to Finding Control Strategies in Boolean Networks C.J. Langmead, S.K. Jha Carnegie Mellon University School of Computer Science Technical Report CMU-CS-07-155R October 2007
Temporal Logics as query languages for Dynamic Bayesian Networks: Application to D. Melanogaster Embryo Development C.J. Langmead, S.K. Jha, E. M. Clarke Carnegie Mellon University School of Computer Science Technical Report CMU-CS-06-159 September 2006
MiscellaneousConference PapersSound Analysis, Comparison and Modification Based on a Perceptual Model of Timbre Perception C.J. Langmead Proceedings of International Computer Music Conference Alberta, Canada, August 1995 Master's ThesisA Theoretical Model of Timbre Perception Based on Morphological Representations of Time-Varying Spectra C.J. Langmead Masters Thesis: Dartmouth College Dept. of Electro-Acoustic Music, June 1995 Tech ReportsBayesian Sequential Model Checking S.K Jha, E.M. Clarke, C.J. Langmead, A. Platzer, P. Zuliani Carnegie Mellon University School of Computer Science Technical Report CMU-CS-09-110 March 2009
Towards Inference and Learning in Dynamic Bayesian Networks using Generalized Evidence C.J. Langmead Carnegie Mellon University School of Computer Science Technical Report CMU-CS-08-151 August 2008 |