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Publications


Structural Biology

Journal Papers

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors

           S. Moitra, K.C. Tirupula, J. Klein-Seetharaman, C.J. Langmead

BMC Biophysics pp. (in press), 2012

PDF, Bibtex

 

Learning Generative Models of Molecular Dynamics

           N. S. Razavian, H. Kamisetty, C.J. Langmead

BMC Genomics 13 pp. Suppl 1, S5. 2012

PDF, Bibtex

 

On-the-fly Identification of Conformational Sub-states from Molecular Dynamics Simulations

           A. Ramanathan, J.O. Yoo, C.J. Langmead

Journal of Chemical Theory and Computation, 2011 7(3) pp. 778-789

PDF, Bibtex

 

Learning Generative Models for Protein Fold Families

           S. Balakrishnan, H. Kamisetty, J.C. Carbonell, S.I. Lee, C.J. Langmead

Proteins: Structure, Function, and Bioinformatics, 2011 79(6) pp. 1061–1078

PDF, Bibtex

 

Accounting for Conformational Entropy in Predicting Binding Free Energies of Protein-protein Interactions

           H. Kamisetty, A. Ramanathan, C. Bailey-Kellogg, C. J. Langmead

Proteins: Structure, Function, and Bioinformatics, 79(2) pp. 444-462, 2011

PDF, Bibtex

 

Discovering Conformational Sub-States Relevant to Protein Function

           A. Ramanathan, et al

PLoS One, 6(1) pp. e15827

PDF, Bibtex

 

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations

           A. Ramanathan, P. K. Agarwal, M. Kurnikova, C. J. Langmead

Journal of Computational Biology, 17(3), pp. 309-324, 2010 (invited submission)

PDF, Bibtex

 

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

Learning Generative Models of Molecular Dynamics

           N. S. Razavian, H. Kamisetty, C.J. Langmead

Proceedings of 10th Asia Pacific Bioinformatics Conference, (APBC) pp. (in press), 2012

Melbourne, Australia. January 17-19, 2012  

PDF, Bibtex

 

Synthesis of Insulin Pump Controllers from Safety Specifications using Bayesian Model Validation

           S. K. Jha, R.G. Datta C.J. Langmead, S. Jha, E. Sassano

Proceedings of 10th Asia Pacific Bioinformatics Conference, (APBC) pp. (in press), 2012

Melbourne, Australia. January 17-19, 2012

PDF, Bibtex

 

Structure and Parameter Learning for von Mises Graphical Models

           N. S. Razavian, H. Kamisetty, C.J. Langmead

Proceedings of NIPS workshop on Machine Learning in Computatioanl Biology, (MLCB) pp. (in press), 2011

also accepted for oral presentation

PDF, Bibtex

 

Approximating Correlated Equilibria using Relaxations on the Marginal Polytope

           H. Kamisetty, X.P. Xing, C.J. Langmead

Proceedings of 28th International Conference on Machine Learning, (ICML) pp. 1153-1160, 2011

Bellevue, WA. June 28-July 2, 2011

PDF, Bibtex

 

Time-Varying Gaussian Graphical Models of Molecular Dynamics Data

           N.S. Razavian, S. Moitra, H. Kamisetty, A. Ramanathan, C.J. Langmead

Proceedings of 3DSIG 2010 Structural Bioinformatics and Computational Biophysics

Boston, MA. July 9-10, 2010

PDF, Bibtex

 

Learning Networks of Statistical Couplings in Protein Fold Families using L1-regularization

           S. Balakrishnan, H. Kamisetty, J.C. Carbonell, S.I. Lee, C.J. Langmead

Proceedings of 3DSIG 2010 Structural Bioinformatics and Computational Biophysics

Boston, MA. July 9-10, 2010  

PDF, Bibtex

 

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

The von Mises Graphical Model: Expectation Propagation for Inference

           N.S. Razavian, H. Kamisetty, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-11-130

Sept 2011

PDF, Bibtex

 

The von Mises Graphical Model: Regularized Structure and Parameter Learning

           N.S. Razavian, H. Kamisetty, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-11-129

Sept 2011

PDF, Bibtex

 

The von Mises Graphical Model: Structure Learning

           N.S. Razavian, H. Kamisetty, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-11-108

March 2011

PDF, Bibtex

 

Time-Varying Gaussian Graphical Models of Molecular Dynamics Data

           N.S. Razavian, S. Moitra, H. Kamisetty, A. Ramanathan, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-10-119

May 2010

PDF, Bibtex

 

Learning Generative Models of Protein Fold Families

           S. Balakrishnan, H. Kamisetty, J.C. Carbonell, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-10-113

March 2010

PDF, Bibtex

 

PyTensor: A Python based Tensor Library

           J. O. Yoo, A. Ramanathan, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-10-102

December 2010

PDF, Bibtex

 

Structure Learning for Generative Models of Protein Fold Families

           S. Balakrishnan, H. Kamisetty, J.C. Carbonell, C.J. Langmead

Carnegie Mellon University School of Computer Science Technical Report CMU-CS-09-177

December 2009

PDF, Bibtex

 

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

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

 

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

Mechanistic Interpretation of the Binding Energy Landscape of Ubiquitin

           A. Ramanathan, X. Gao, C. J. Langmead

From Computational Biophysics to Systems Biology (CBSB10)

Traverse City, MI. June 6-8, 2010

 

Incorporating Configurational Entropy into Binding Free Energy Calculations via Statistical Inference

           H. Kamisetty, X. Gao, C. J. Langmead

Keystone Symposium on Computer Aided Drug Design

Whistler, BC. April 20-25, 2010

            * Also invited for oral presentation

 

 

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 invited 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 and Medicine

Journal Papers

A Head-to-Head Comparison of Available Clinical Scores in Predicting Persistent Organ Failure in Acute Pancreatitis

           R. Mounzer*, C.J. Langmead*, A. Evans, F. Bishezari, V. Muddana, A. Slivka, D. C. Whitcomb, D. Yadav, G.I. Papachristou

Gasteroenterology, 2012, pp. (in press)

* Joint first authorship

 

Serum Biomarker Profiles as Screening Tools in Lung Cancer

           B.M. Nolen,  C.J. Langmead, S, Choi, A. Lomakin, A. Marrangoni, W. L. Bigbee, J. L. Weissfeld, D. O. Wilson, S. Dacic, J. M. Siegfried, and A. E. Lokshin

Cancer Biomarkers 10(1) pp. 3--12, 2012

PDF, Bibtex

 

Synthesis of Insulin Pump Controllers from Safety Specifications using Bayesian Model Validation

           S. K. Jha,  R.G. Datta, C.J. Langmead, S, Jha, E. Sassano

Int. J. Bioinformatics Research and Applications 2012, pp. (in press)

PDF, Bibtex

 

Exploring Behaviors of SDE Models of Biological Systems using Change of Measures

           S. K. Jha,  C.J. Langmead

BMC Bioinformatics 2012, pp. (in press)

PDF, Bibtex

 

Using Optical Markers of Normal-Appearing Rectal Epithelial Cells to Identify Patients With Ulcerative Colitis (UC) - Associated Neoplasia

R. K. Bista, T. A. Brentnall, M. P. Bronner,  C.J. Langmead, R. E. Brand, and Y. Liu

Inflammatory Bowel Diseases, 17(12) pp. 2427--2435, 2011

PDF, Bibtex

 

Serum Biomarker Panels for the Detection of Pancreatic Cancer

R. E. Brand, C.J. Langmead, B. M. Nolen, H. J. Zeh, P. J. Allen, M. A. Eloubeidi, M. Goldberg, E. Elton, J. P. Arnoletti,  J. D. Christein, S. M. Vickers, D. P. Landsittel, D. C. Whitcomb, W. E. Grizzle, and A. E. Lokshin

Clinical Cancer Research, 2011 17(4):805-816

PDF, Bibtex

 

Synthesis and Infeasibility Analysis for Stochastic Models of Biochemical Systems using Statistical Model Checking and Abstraction Refinement

            S. K. Jha,  C. J. Langmead

Journal of Theoretical Computer Science, 412(21), pp. 2162-2187, 2011 (invited submission)

PDF, Bibtex

 

Angiopoietin-2, a regulator of vascular permeability in inflammation, is associated with persistent organ failure in patients with acute pancreatitis from the US and Germany

           D. C. Whitcomb, V. Muddana,  C. J. Langmead, F.D. Houghton, A. Guenther,

           P.K. Eagon, J. Mayerle, A. A. Aghdassi, F. Ulrich, A. Evans, J. Lamb,

           G. Clermont, M.M. Lerch, G. I. Papachristou

American Journal of Gastroenterology, 105(10), pp. 2287–2292, 2010

PDF, Bibtex

  

Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology

           A. Donze, G. Clermont,  C. J. Langmead

Journal of Computational Biology, 17(3), pp. 325-336, 2010 (invited submission)

PDF, Bibtex

 

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

Decision Procedure Based Discovery of Rare Behaviors in SDE Models of Biological Systems: Applications to Minimal Cell Cycle Model

           A.K. Ghosh, S. K. Jha,   C.J. Langmead, S. Jha, E. Sassano

Proceedings of the 2nd  International Conference on Bio and Medical Sciences (ICCABS), 2012, (in press)

PDF, Bibtex

 

Discovering Rare Behaviors of Stochastic Models of Biological Systems using Decision Procedures based Design Tool

           A.K. Ghosh, S. K. Jha,  F. Hussain,  C.J. Langmead, S. Jha

Proceedings of the 49th Annual Design Automation Conference (DAC), 2012, (in press)

PDF, Bibtex

 

Exploring Behaviors of SDE Models of Biological Systems using Change of Measures * Winner Best Paper

           S. K. Jha,  C.J. Langmead

Proceedings of the 1st International Conference on Bio and Medical Sciences (ICCABS), Orlando FL, 2011, pp. 111-117

PDF, Bibtex

 

Analogies between Structural and Systems Biology and Systems Engineering in Dynamic Environments

           S. Moitra, N. Yanamala, O. Tastan, I. Singh,  C.J. Langmead, J. Klein-Seetharaman

Proceedings of The 5th International Conference on Systems of Systems Engineering (SoSE), Leicestershire, UK, June 22-24, 2010 (in press) (invited submission)

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, August, 2009

PDF, Bibtex

 

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, September 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

Hematocrit, Creatinine, and Blood Urea Nitrogen in the assesment of Pancreatic Necrosis in Acute Pancreatitis: An International Study

           R. Mounzer, C.J. Langmead, A. Evans, F. Bishezari, J. Nasr, D. C. Whitcomb, G. I. Papachristou

           Gasteroenterology, 2011, Abstracts from Digestive Disease Week 2011

          * Also invited for oral presentation

 

Admission clinical scores in predicting Persistent Organ Failure in Acute Pancreatitis: a head-to-head comparison and design of novel step-up classification rules

           R. Mounzer, C.J. Langmead, A. Evans, F. Bishezari, J. Nasr, D. Yadav, D. C. Whitcomb, G. I. Papachristou

           Gasteroenterology, 2011, Abstracts from Digestive Disease Week 2011

          * Also invited for oral presentation

 

Prevalence of and factors determining prolonged length of stay in mild acute pancreatitis

           R. Mounzer, C.J. Langmead, D. Yadav, J. Nasr, M. Sanders, A. Geldrud, A. Slivka, D. C. Whitcomb, G. I. Papachristou

           Gasteroenterology, 2011, Abstracts from Digestive Disease Week 2011

 

Synthesis of Biochemical Models Using Signatures

           S. K. Jha,  C.J. Langmead

1st International Conference on Bio and Medical Sciences (ICCABS), Orlando FL, 2011, page 248

PDF, Bibtex

 

Parameter Estimation and Synthesis for Systems Biology: New Algorithms for Nonlinear and Stochastic Models           

          S.K. Jha, A. Donze, R. Paul, J. Dutta-Moscato, Q. Mi, G. Clermont, Y. Vodovotz, C.J. Langmead

          9th International Conference on Complexity in Acute Illness (ICCAI), Atlanta, GA, Sept 10-12, 2010

 

Efficient Inference: Perturbagen Effect on Protein Subcellular Location Pattern

           A. Naik, J. Kangas, C.J. Langmead, R. F. Murphy

          18th Conference on Intelligent Systems in Molecular Biology (ISMB), Boston, MA, July 11-13, 2010

 

Efficient Characterization of the Dependency of Protein Subcellular Location Pattern on Perturbagens           

           A. Naik, J. Kangas, C.J. Langmead, R. F. Murphy

           NIBIB Trainee Meeting, 2010, Bethesda, MD, June 24-25, 2010

 

Using Optical Markers of Normal-appearing Rectal Epithelial Cells to Identify Patients with Ulcerative Colitis (UC)-associated Neoplasia

           T. Bretnall, R.K. Bista, M.P. Bronner, C. J. Langmead, R. Brand, Y. Liu

           Gasteroenterology, 2010, Abstracts from Digestive Disease Week 2010

 

Resistin, a potent adipokine, is associated with acute pancreatitis: Assessment of functional genetic polymorphisms and serum levels

           D.C. Whitcomb, V.N. Muddana, C. J. Langmead, G. I. Papachristou

           Gasteroenterology, 2010, Abstracts from Digestive Disease Week 2010

         * Also invited for oral presentation

 

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

          * Also invited for oral presentation

 

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

When to Stop Verification? Statistical Trade-off between Expected Loss and Simulation Cost

S. K. Jha , C.J. Langmead, S. Ramesh, and S. Mohalik

Proceedings of Design Automation and Test in Europe (DATE), pp. 1309-1314

Grenoble, France, March, 2011

 

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

PDF, 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