Chris Bailey-Kellogg

发表

Probabilistic cross‐link analysis and experiment planning for high‐throughput elucidation of protein structure

Chris Bailey-Kellogg, Xiaoduan Ye, Patrick K O'Neil, 2004, Protein science : a publication of the Protein Society.

Structure-Guided Deimmunization of Therapeutic Proteins

Chris Bailey-Kellogg, Andrew S. Parker, Yoonjoo Choi, 2012, RECOMB.

Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination

Chris Bailey-Kellogg, Xiaoduan Ye, Alan M. Friedman, 2006, RECOMB.

Physical geometric algorithms for structural molecular biology

Chris Bailey-Kellogg, Bruce Randall Donald, Ryan H. Lilien, 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).

Spatial Aggregation : Modeling and controllingphysical fields

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 2015 .

Graphical Models of Residue Coupling in Protein Families

Chris Bailey-Kellogg, Naren Ramakrishnan, John Thomas, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Structure‐based design of combinatorial mutagenesis libraries

Chris Bailey-Kellogg, Gevorg Grigoryan, Deeptak Verma, 2015, Protein science : a publication of the Protein Society.

An efficient randomized algorithm for contact-based NMR backbone resonance assignment

Chris Bailey-Kellogg, Gopal Pandurangan, Hetunandan Kamisetty, 2006, Bioinform..

Planning combinatorial disulfide cross-links for protein fold determination

Chris Bailey-Kellogg, Fei Xiong, Alan M. Friedman, 2011, BMC Bioinformatics.

Spatial Aggregation: Language and Applications

Chris Bailey-Kellogg, Feng Zhao, Kenneth Yip, 1996, AAAI/IAAI, Vol. 1.

Site‐directed combinatorial construction of chimaeric genes: General method for optimizing assembly of gene fragments

Chris Bailey-Kellogg, Alan M Friedman, Liz Saftalov, 2006, Proteins.

Gaussian Process Models of Spatial Aggregation Algorithms

Chris Bailey-Kellogg, Naren Ramakrishnan, 2003, IJCAI.

Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data

Chris Bailey-Kellogg, Devin J. Balkcom, Alan M. Friedman, 2010, J. Bioinform. Comput. Biol..

Influence-based model decomposition for reasoning about spatially distributed physical systems

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 2001, Artif. Intell..

Structure Discovery from Massive Spatial Data Sets Using Intelligent Simulation Tools

Chris Bailey-Kellogg, Feng Zhao, Iván Ordóñez, 2007, Computational Discovery of Scientific Knowledge.

A divide‐and‐conquer approach to determine the Pareto frontier for optimization of protein engineering experiments

Chris Bailey-Kellogg, Alan M Friedman, Lu He, 2012, Proteins.

Spatial Aggregation for Qualitative Assessment of Scientific Computations

Chris Bailey-Kellogg, Naren Ramakrishnan, 2004, AAAI.

Reconsidering complete search algorithms for protein backbone NMR assignment

Chris Bailey-Kellogg, Jan Vitek, Bruce A. Craig, 2005, ECCB/JBI.

A graphical model approach for predicting free energies of association for protein-protein interactions under backbone and side-chain flexibility

Chris Bailey-Kellogg, Hetunandan Kamisetty, Christopher J. Langmead, 2008 .

Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination

Chris Bailey-Kellogg, Wei Zheng, Karl E. Griswold, 2009, RECOMB.

A random graph approach to NMR sequential assignment.

Chris Bailey-Kellogg, Gopal Pandurangan, Sheetal Chainraj, 2005 .

Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data

Chris Bailey-Kellogg, Bruce Randall Donald, Himanshu Chandola, 2013, BCB.

Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions

Chris Bailey-Kellogg, Andrew S. Parker, Karl E. Griswold, 2011, J. Bioinform. Comput. Biol..

Physics-based encapsulation in embedded software for distributed sensing and control applications

Chris Bailey-Kellogg, Feng Zhao, Markus P. J. Fromherz, 2003, Proceedings of the IEEE.

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins

Chris Bailey-Kellogg, Wei Zheng, Alan M. Friedman, 2008, RECOMB.

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations

Chris Bailey-Kellogg, Leonard Moise, William D. Martin, 2012, BCB.

Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models

Chris Bailey-Kellogg, Christopher James Langmead, Bornika Ghosh, 2014, RECOMB.

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints

Chris Bailey-Kellogg, Naren Ramakrishnan, John Thomas, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints

Anthony K. Yan, Chris Bailey-Kellogg, Bruce Randall Donald, 2006, WAFR.

Graphical Models of Residue Coupling in Protein Families

Chris Bailey-Kellogg, Naren Ramakrishnan, John Thomas, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'

Chris Bailey-Kellogg, Scott A. Gerber, Tuobin Wang, 2012, Bioinform..

Geometric Analysis of Cross-Linkability for Protein Fold Discrimination

Chris Bailey-Kellogg, Janusz M. Bujnicki, Alan M. Friedman, 2003, Pacific Symposium on Biocomputing.

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data

Chris Bailey-Kellogg, Bruce Randall Donald, Alik Widge, 2000, J. Comput. Biol..

Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models

Chris Bailey-Kellogg, Christopher James Langmead, Bornika Ghosh, 2015, J. Comput. Biol..

Optimization of Combinatorial Mutagenesis

Chris Bailey-Kellogg, Andrew S. Parker, Karl E. Griswold, 2011, RECOMB.

Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially-Distributed Physical Systems

Chris Bailey-Kellogg, Naren Ramakrishnan, C. Bailey-Kellogg, 2001, IJCAI.

Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling

Chris Bailey-Kellogg, Bruce Randall Donald, Clifford Stein, 2000, J. Comput. Biol..

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method

Chris Bailey-Kellogg, Leonard Moise, William D. Martin, 2015, BMC Bioinformatics.

Gaussian Processes for Active Data Mining of Spatial Aggregates

Chris Bailey-Kellogg, Naren Ramakrishnan, Satish Tadepalli, 2005, SDM.

A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure

Chris Bailey-Kellogg, Fei Xiong, C. Bailey-Kellogg, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Gaussian Process Models in Spatial Data Mining

Chris Bailey-Kellogg, Naren Ramakrishnan, C. Bailey-Kellogg, 2008, Encyclopedia of GIS.

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins

Chris Bailey-Kellogg, Wei Zheng, Alan M. Friedman, 2008, RECOMB.

Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination

Chris Bailey-Kellogg, Wei Zheng, Karl E. Griswold, 2010, J. Comput. Biol..

Qualitative Analysis of Correspondence for Experimental Algorithmics

Chris Bailey-Kellogg, Naren Ramakrishnan, 2002, ArXiv.

Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage

Chris Bailey-Kellogg, William D. Martin, Anne S. De Groot, 2014, BMC Bioinformatics.

Intelligent simulation tools for mining large scientific data sets

Chris Bailey-Kellogg, Feng Zhao, Iván Ordóñez, 2009, New Generation Computing.

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints

Chris Bailey-Kellogg, Naren Ramakrishnan, John Thomas, 2009, TCBB.

Improved Multiple Sequence Alignments Using Coupled Pattern Mining

Chris Bailey-Kellogg, Naren Ramakrishnan, Prateek Jain, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Influence-Based Model Decomposition

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 1999, AAAI/IAAI.

Optimization of Combinatorial Mutagenesis

Chris Bailey-Kellogg, Andrew S. Parker, Karl E. Griswold, 2011, RECOMB.

Service learning in software engineering and maintenance

Chris Bailey-Kellogg, Panagiotis K. Linos, 2003, International Conference on Software Maintenance, 2003. ICSM 2003. Proceedings..

A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs

Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, 2011, J. Comput. Biol..

Contact replacement for NMR resonance assignment

Chris Bailey-Kellogg, Gopal Pandurangan, Fei Xiong, 2008, ISMB.

Using physicochemical properties of amino acids to induce graphical models of residue couplings

Chris Bailey-Kellogg, Naren Ramakrishnan, K. S. M. Tozammel Hossain, 2011, BIOKDD '11.

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

Chris Bailey-Kellogg, Neerja Thakkar, C. Bailey-Kellogg, 2019, BMC Bioinformatics.

A random graph approach to NMR sequential assignment

Chris Bailey-Kellogg, Gopal Pandurangan, Sheetal Chainraj, 2004, J. Comput. Biol..

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

Chris Bailey-Kellogg, Andrew S. Parker, Yoonjoo Choi, 2015, PLoS Comput. Biol..

OCoM-SOCoM: Combinatorial Mutagenesis Library Design Optimally Combining Sequence and Structure Information

Chris Bailey-Kellogg, Gevorg Grigoryan, Deeptak Verma, 2016, BCB.

Sampling strategies for mining in data-scarce domains

Chris Bailey-Kellogg, Naren Ramakrishnan, C. Bailey-Kellogg, 2002, Computing in Science & Engineering.

The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data

Chris Bailey-Kellogg, Bruce Randall Donald, Alik Widge, 2000, RECOMB '00.

Algorithms for optimizing cross-overs in DNA shuffling

Chris Bailey-Kellogg, Lu He, Alan M. Friedman, 2011, BMC Bioinformatics.

Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 1998, AAAI/IAAI.

Algorithms for optimizing cross-overs in DNA shuffling

Chris Bailey-Kellogg, Lu He, Alan M. Friedman, 2011, BCB.

Qualitative Spatial Reasoning Extracting and Reasoning with Spatial Aggregates

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 2004, AI Mag..

Structure-Guided Deimmunization of Therapeutic Proteins

Chris Bailey-Kellogg, Andrew S. Parker, Karl E. Griswold, 2012, RECOMB.

Nmr Structural Inference of Symmetric Homo-oligomers

Anthony K. Yan, Chris Bailey-Kellogg, Bruce Randall Donald, 2022 .

The spatial aggregation language for modeling and controlling distributed physical systems

Chris Bailey-Kellogg, Feng Zhao, 1999 .

Active Data Mining of Correspondence for Qualitative Assessment of Scientific Computations

Chris Bailey-Kellogg, Naren Ramakrishnan, 2003 .

Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination

Chris Bailey-Kellogg, Xiaoduan Ye, Alan M. Friedman, 2007, J. Comput. Biol..

Structure‐based redesign of proteins for minimal T‐cell epitope content

Chris Bailey-Kellogg, Yoonjoo Choi, Karl E. Griswold, 2013, J. Comput. Chem..

Ballast: A Ball-Based Algorithm for Structural Motifs

Chris Bailey-Kellogg, Gopal Pandurangan, Lu He, 2012, RECOMB.

Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees

Chris Bailey-Kellogg, Jaranit Kaewkungwal, Todd J. Suscovich, 2015, PLoS Comput. Biol..

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

Chris Bailey-Kellogg, Srivamshi Pittala, C. Bailey-Kellogg, 2019, bioRxiv.

Open Access Methodology Article Optimization Algorithms for Functional Deimmunization of Therapeutic Proteins

Chris Bailey-Kellogg, Wei Zheng, Andrew S. Parker, 2022 .

DisruPPI: structure-based computational redesign algorithm for protein binding disruption

Chris Bailey-Kellogg, Yoonjoo Choi, Karl E. Griswold, 2018, Bioinform..

The spatial aggregation language

Chris Bailey-Kellogg, Feng Zhao, Iván Ordóñez, 2001 .

MMFPh: a maximal motif finder for phosphoproteomics datasets

Chris Bailey-Kellogg, Scott A. Gerber, Tuobin Wang, 2012, Bioinform..

Reasoning About and Optimizing Distributed Parameter Physical Systems Using Influence Graphs

Chris Bailey-Kellogg, Feng Zhao, C. Bailey-Kellogg, 1998 .

Ballast: A Ball-Based Algorithm for Structural Motifs

Chris Bailey-Kellogg, Gopal Pandurangan, Lu He, 2012, RECOMB.

Spatial data mining to support pandemic preparedness

Chris Bailey-Kellogg, Madhav V. Marathe, Naren Ramakrishnan, 2006, SKDD.

A multi-resolution graph convolution network for contiguous epitope prediction

Chris Bailey-Kellogg, Lisa Oh, Bowen Dai, 2021, BCB.

Protein interaction interface region prediction by geometric deep learning

Chris Bailey-Kellogg, Bowen Dai, C. Bailey-Kellogg, 2021, Bioinform..

MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform

Chris Bailey-Kellogg, Vikram Khipple Mulligan, Sagar D. Khare, 2021, J. Chem. Inf. Model..

Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules.

Chris Bailey-Kellogg, Larisa V Avramova, Jairav Desai, 2008, Journal of combinatorial chemistry.

Reconsidering Complete Search Algorithms for Protein

Chris Bailey-Kellogg, Olga Vitek, Bruce A. Craig, 2005 .

Gene and Protein Sequence Optimization for High-Level Production of Fully Active and Aglycosylated Lysostaphin in Pichia pastoris

Chris Bailey-Kellogg, Yoonjoo Choi, Karl E. Griswold, 2014, Applied and Environmental Microbiology.

Design and analysis of immune-evading enzymes for ADEPT therapy.

Chris Bailey-Kellogg, Karl E Griswold, Andrew S. Parker, 2012, Protein engineering, design & selection : PEDS.

Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination.

Chris Bailey-Kellogg, Wei Zheng, Xiaoduan Ye, 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Protein deimmunization via structure‐based design enables efficient epitope deletion at high mutational loads

Chris Bailey-Kellogg, Yoonjoo Choi, Regina S. Salvat, 2015, Biotechnology and bioengineering.

Graphical models of protein–protein interaction specificity from correlated mutations and interaction data

Chris Bailey-Kellogg, Naren Ramakrishnan, C. Bailey-Kellogg, 2009, Proteins.

Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo.

Chris Bailey-Kellogg, Deeptak Verma, Karl E Griswold, 2015, Chemistry & biology.

Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate

Chris Bailey-Kellogg, Andrew S. Parker, Yoonjoo Choi, 2014, Cellular and Molecular Life Sciences.

Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity

Chris Bailey-Kellogg, Deeptak Verma, Karl E Griswold, 2017, Proceedings of the National Academy of Sciences.

A high throughput MHC II binding assay for quantitative analysis of peptide epitopes.

Chris Bailey-Kellogg, Karl E Griswold, Leonard Moise, 2014, Journal of visualized experiments : JoVE.

Optimizing Bayes error for protein structure model selection by stability mutagenesis.

Chris Bailey-Kellogg, Xiaoduan Ye, C. Bailey-Kellogg, 2008, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Antibody humanization by structure-based computational protein design

Chris Bailey-Kellogg, Yoonjoo Choi, C. Bailey-Kellogg, 2015, mAbs.

Inferential backbone assignment for sparse data

Chris Bailey-Kellogg, Jan Vitek, Olga Vitek, 2006, Journal of biomolecular NMR.

Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen

Chris Bailey-Kellogg, Deeptak Verma, C. Bailey-Kellogg, 2018, Protein engineering, design & selection : PEDS.

Analysis of sequence–reactivity space for protein–protein interactions

Chris Bailey-Kellogg, Michael C. Laskowski, Jiangtian Li, 2004, Proteins.

Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances

Chris Bailey-Kellogg, Jan Vitek, Olga Vitek, 2004, Statistical applications in genetics and molecular biology.

MODELING AND INFERENCE OF SEQUENCE-STRUCTURE SPECIFICITY

Chris Bailey-Kellogg, Bornika Ghosh, Hetunandan Kamisetty, 2009 .