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Structural Biology

Journal Papers

Free 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)

PDF, Bibtex

  

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

PDF, Bibtex

 

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

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

Journal of Computational Biology, 11(2-3), pp. 277-298, 2004 (invited submission)

PDF, Bibtex

Conference Papers

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

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

Ph.D. Dissertation

Molecular 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 Reports

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

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-08-162

December 2008

PDF, Bibtex

 

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

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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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

An Improved Nuclear Vector Replacement Algorithm for Nuclear Magnetic Resonance Assignment

C.J. Langmead, B.R. Donald

Dartmouth Technical Report TR2004-494

March 2004

PDF, Bibtex

 

High-Throughput 3D Homology Detection via NMR Resonance Assignment

C.J. Langmead, B.R. Donald

Dartmouth Technical Report TR2004-487

February 2004

PDF, Bibtex

 

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

PDF, Bibtex

Posters and Abstracts

Protein 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

PDF

 

Belief Propagation Reveals Allosteric Mechanisms in Proteins

H. Kamisetty, A. Ramanathan, C. J. Langmead

8th Annual International Conference on Computational Systems Bioinformatics (CSB), 2009

PDF

 

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 Biology

Journal Papers

Symbolic 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)

PDF, Bibtex

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 Papers

A 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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

PDF, Bibtex

 

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

Bibtex

 

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

PDF, Bibtex

Posters and Abstracts

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, 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 Reports

Structural 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

PDF, Bibtex

 

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

PDF, Bibtex

 


Miscellaneous

Conference Papers

Sound 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 Thesis

A 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 Reports

Bayesian 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

PDB, Bibtex

 

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

PDF, Bibtex