Chris Bailey-Kellogg

According to our database1, Chris Bailey-Kellogg authored at least 62 papers between 1996 and 2021.

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PhD thesis 


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MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform.
J. Chem. Inf. Model., 2021

Learning context-aware structural representations to predict antigen and antibody binding interfaces.
Bioinform., 2020

Pareto Optimization of Combinatorial Mutagenesis Libraries.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity.
BMC Bioinform., 2019

DisruPPI: structure-based computational redesign algorithm for protein binding disruption.
Bioinform., 2018

Gaussian Process Models in Spatial Data Mining.
Proceedings of the Encyclopedia of GIS., 2017

OCoM-SOCoM: Combinatorial Mutagenesis Library Design Optimally Combining Sequence and Structure Information.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate.
PLoS Comput. Biol., 2015

Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees.
PLoS Comput. Biol., 2015

Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models.
J. Comput. Biol., 2015

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method.
BMC Bioinform., 2015

Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage.
BMC Bioinform., 2014

Improved Multiple Sequence Alignments Using Coupled Pattern Mining.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Structure-based redesign of proteins for minimal T-cell epitope content.
J. Comput. Chem., 2013

Structure-Guided Deimmunization of Therapeutic Proteins.
J. Comput. Biol., 2013

Ballast: A Ball-based Algorithm for Structural Motifs.
J. Comput. Biol., 2013

Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data.
Proceedings of the ACM Conference on Bioinformatics, 2013

Algorithms for optimizing cross-overs in DNA shuffling.
BMC Bioinform., 2012

Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'.
Bioinform., 2012

MMFPh: a maximal motif finder for phosphoproteomics datasets.
Bioinform., 2012

Structure-Guided Deimmunization of Therapeutic Proteins.
Proceedings of the Research in Computational Molecular Biology, 2012

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations.
Proceedings of the ACM International Conference on Bioinformatics, 2012

Optimization of Combinatorial Mutagenesis.
J. Comput. Biol., 2011

A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs.
J. Comput. Biol., 2011

NMR Structural Inference of Symmetric Homo-Oligomers.
J. Comput. Biol., 2011

Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions.
J. Bioinform. Comput. Biol., 2011

Planning combinatorial disulfide cross-links for protein fold determination.
BMC Bioinform., 2011

Using physicochemical properties of amino acids to induce graphical models of residue couplings.
Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, 2011

Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination.
J. Comput. Biol., 2010

Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data.
J. Bioinform. Comput. Biol., 2010

Optimization algorithms for functional deimmunization of therapeutic proteins.
BMC Bioinform., 2010

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins.
J. Comput. Biol., 2009

Gaussian Process Models in Spatial Data Mining.
Proceedings of the Encyclopedia of GIS., 2008

Graphical Models of Residue Coupling in Protein Families.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Contact replacement for NMR resonance assignment.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination.
J. Comput. Biol., 2007

Structure Discovery from Massive Spatial Data Sets Using Intelligent Simulation Tools.
Proceedings of the Computational Discovery of Scientific Knowledge, 2007

A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

Spatial data mining to support pandemic preparedness.
SIGKDD Explor., 2006

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.
Bioinform., 2006

Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints.
Proceedings of the Algorithmic Foundation of Robotics VII, 2006

A Random Graph Approach to NMR Sequential Assignment.
J. Comput. Biol., 2005

Gaussian Processes for Active Data Mining of Spatial Aggregates.
Proceedings of the 2005 SIAM International Conference on Data Mining, 2005

Reconsidering complete search algorithms for protein backbone NMR assignment.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Qualitative Spatial Reasoning Extracting and Reasoning with Spatial Aggregates.
AI Mag., 2004

Geometric Analysis of Cross-Linkability for Protein Fold Discrimination.
Proceedings of the Biocomputing 2004, 2004

Spatial Aggregation for Qualitative Assessment of Scientific Computations.
Proceedings of the Nineteenth National Conference on Artificial Intelligence, 2004

Physics-based encapsulation in embedded software for distributed sensing and control applications.
Proceedings of the IEEE, 2003

Gaussian Process Models of Spatial Aggregation Algorithms.
Proceedings of the IJCAI-03, 2003

Service Learning in Software Engineering and Maintenance.
Proceedings of the 19th International Conference on Software Maintenance (ICSM 2003), 2003

Sampling strategies for mining in data-scarce domains.
Comput. Sci. Eng., 2002

Qualitative Analysis of Correspondence for Experimental Algorithmics
CoRR, 2002

Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling.
J. Comput. Biol., 2001

Influence-based model decomposition for reasoning about spatially distributed physical systems.
Artif. Intell., 2001

Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially-Distributed Physical Systems.
Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, 2001

Physical Geometric Algorithms for Structural Molecular Biology.
Proceedings of the 2001 IEEE International Conference on Robotics and Automation, 2001

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data.
J. Comput. Biol., 2000

Intelligent Simulation Tools for Mining Large Scientific Data Sets.
New Gener. Comput., 1999

Influence-Based Model Decomposition.
Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, 1999

Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis.
Proceedings of the Fifteenth National Conference on Artificial Intelligence and Tenth Innovative Applications of Artificial Intelligence Conference, 1998

Spatial Aggregation: Language and Applications.
Proceedings of the Thirteenth National Conference on Artificial Intelligence and Eighth Innovative Applications of Artificial Intelligence Conference, 1996