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Publications

Structural Biology

Journal Papers

Can Protein Structure Decoys Be Identified via Kinetics?

           C.J. Langmead

In preparation

 

An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments

C.J. Langmead, B.R. Donald

Journal of Biomolecular NMR, 29, 2004,  pp. 111-138

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), 2004, pp. 277-298 (invited submission)

PDF, Bibtex

 

Conference Papers

Using Bit Vector Decision Procedures for Analysis of Protein Folding Pathways

           C.J. Langmead, S. K. Jha

Fourth Workshop on Constraints in Formal Verification

Bremen, Germany, July 16, 2007

In press

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) (accepted)

Philadelphia, PA. September 8-9, 2007

            pages 252-264

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,

Oakland, CA. April 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

Taipei, Taiwan. Feb 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

Stanford University, Palo Alto, CA, August 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

Stanford University, Palo Alto, CA, August 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

Berlin, Germany, April 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

Montreal, Quebec, April 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

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

PDF, Bibtex

 

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

 

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

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

Conference Papers

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

submitted. May, 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) 2008. pp. 307-319

Kyoto, Japan. January 2008

Technical Reports

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-07-155

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

 

 

Functional Genomics

Journal Papers

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) 2003, pp. 521-536 (invited submission)

PDF, Bibtex

Conference Papers

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

Stanford University, Palo Alto, CA, August 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

Washington, DC, April 2002

PDF, Bibtex

 

Posters

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

Providence, RI, August 2001

 

Tech Reports

Machine Learning

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

 Bibtex

Tech Reports

 

A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data

C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-05-164

July 2005

PDF, Bibtex

 

Computational Geometry

Journal Papers

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), 2005, pp.165-182

PDF, Bibtex

Conference Papers

Tech Reports

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

 

Computer Music

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