Spatial Aggregation: Language and Applications. - Christopher Bailey-Kellogg; Feng Zhao 001; Kenneth Yip (AAAI/IAAI, Vol. 1, 1996)

Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis. - Christopher Bailey-Kellogg; Feng Zhao 001 (AAAI/IAAI, 1998)

Influence-Based Model Decomposition. - Christopher Bailey-Kellogg; Feng Zhao 001 (AAAI/IAAI, 1999)

Intelligent Simulation Tools for Mining Large Scientific Data Sets. - Feng Zhao 001; Christopher Bailey-Kellogg; Xingang Huang; Iván Ordóñez (New Gener. Comput., 1999)

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data. - Christopher Bailey-Kellogg; Alik Widge; John J. Kelley 001; Marcelo J. Berardi; John H. Bushweller; Bruce Randall Donald (J. Comput. Biol., 2000)

Physical Geometric Algorithms for Structural Molecular Biology. - Bruce Randall Donald; Christopher Bailey-Kellogg; Jack Kelley; Ryan H. Lilien (ICRA, 2001)

Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially-Distributed Physical Systems. - Christopher Bailey-Kellogg; Naren Ramakrishnan (IJCAI, 2001)

Influence-based model decomposition for reasoning about spatially distributed physical systems. - Christopher Bailey-Kellogg; Feng Zhao 001 (Artif. Intell., 2001)

Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. - Christopher Bailey-Kellogg; John J. Kelley 001; Clifford Stein 001; Bruce Randall Donald (J. Comput. Biol., 2001)

Qualitative Analysis of Correspondence for Experimental Algorithmics - Christopher Bailey-Kellogg; Naren Ramakrishnan (CoRR, 2002)

Sampling strategies for mining in data-scarce domains. - Naren Ramakrishnan; Chris Bailey-Kellogg (Comput. Sci. Eng., 2002)

Service Learning in Software Engineering and Maintenance. - Panagiotis K. Linos; Chris Bailey-Kellogg (ICSM, 2003)

Gaussian Process Models of Spatial Aggregation Algorithms. - Naren Ramakrishnan; Christopher Bailey-Kellogg (IJCAI, 2003)

Physics-based encapsulation in embedded software for distributed sensing and control applications. - Feng Zhao 001; Christopher Bailey-Kellogg; Markus P. J. Fromherz (Proc. IEEE, 2003)

Spatial Aggregation for Qualitative Assessment of Scientific Computations. - Chris Bailey-Kellogg; Naren Ramakrishnan (AAAI, 2004)

Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. - Shobha Potluri; Aly Azeem Khan; A. Kuzminykh; Janusz M. Bujnicki; Alan M. Friedman; Chris Bailey-Kellogg (Pacific Symposium on Biocomputing, 2004)

Qualitative Spatial Reasoning Extracting and Reasoning with Spatial Aggregates. - Christopher Bailey-Kellogg; Feng Zhao 001 (AI Mag., 2004)

Reconsidering complete search algorithms for protein backbone NMR assignment. - Olga Vitek; Chris Bailey-Kellogg; Bruce A. Craig; Paul Kuliniewicz; Jan Vitek (ECCB/JBI, 2005)

Gaussian Processes for Active Data Mining of Spatial Aggregates. - Naren Ramakrishnan; Chris Bailey-Kellogg; Satish Tadepalli; Varun Pandey (SDM, 2005)

A Random Graph Approach to NMR Sequential Assignment. - Chris Bailey-Kellogg; Sheetal Chainraj; Gopal Pandurangan (J. Comput. Biol., 2005)

Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints. - Shobha Potluri; Anthony K. Yan; James J. Chou; Bruce Randall Donald; Chris Bailey-Kellogg (WAFR, 2006)

An efficient randomized algorithm for contact-based NMR backbone resonance assignment. - Hetunandan Kamisetty; Chris Bailey-Kellogg; Gopal Pandurangan (Bioinform., 2006)

Spatial data mining to support pandemic preparedness. - Chris Bailey-Kellogg; Naren Ramakrishnan; Madhav V. Marathe (SIGKDD Explor., 2006)

A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. - Fei Xiong; Chris Bailey-Kellogg (BIBE, 2007)

Structure Discovery from Massive Spatial Data Sets Using Intelligent Simulation Tools. - Feng Zhao 001; Chris Bailey-Kellogg; Xingang Huang; Iván Ordóñez (Computational Discovery of Scientific Knowledge, 2007)

Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. - Xiaoduan Ye; Alan M. Friedman; Chris Bailey-Kellogg (J. Comput. Biol., 2007)

Contact replacement for NMR resonance assignment. - Fei Xiong; Gopal Pandurangan; Chris Bailey-Kellogg (ISMB, 2008)

Graphical Models of Residue Coupling in Protein Families. - John Thomas; Naren Ramakrishnan; Chris Bailey-Kellogg (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Gaussian Process Models in Spatial Data Mining. - Naren Ramakrishnan; Chris Bailey-Kellogg (Encyclopedia of GIS, 2008)

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. - Wei Zheng 009; Alan M. Friedman; Chris Bailey-Kellogg (J. Comput. Biol., 2009)

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints. - John Thomas; Naren Ramakrishnan; Chris Bailey-Kellogg (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Optimization algorithms for functional deimmunization of therapeutic proteins. - Andrew S. Parker; Wei Zheng 009; Karl E. Griswold; Chris Bailey-Kellogg (BMC Bioinform., 2010)

Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data. - Paritosh A. Kavathekar; Bruce A. Craig; Alan M. Friedman; Chris Bailey-Kellogg; Devin J. Balkcom (J. Bioinform. Comput. Biol., 2010)

Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. - Wei Zheng 009; Karl E. Griswold; Chris Bailey-Kellogg (J. Comput. Biol., 2010)

Using physicochemical properties of amino acids to induce graphical models of residue couplings. - K. S. M. Tozammel Hossain; Chris Bailey-Kellogg; Alan M. Friedman; Michael J. Bradley; Nathan A. Baker; Naren Ramakrishnan (BIOKDD, 2011)

Planning combinatorial disulfide cross-links for protein fold determination. - Fei Xiong; Alan M. Friedman; Chris Bailey-Kellogg (BMC Bioinform., 2011)

Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions. - Andrew S. Parker; Karl E. Griswold; Chris Bailey-Kellogg (J. Bioinform. Comput. Biol., 2011)

NMR Structural Inference of Symmetric Homo-Oligomers. - Himanshu Chandola; Anthony K. Yan; Shobha Potluri; Bruce Randall Donald; Chris Bailey-Kellogg (J. Comput. Biol., 2011)

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; Pei Zhou 001; Bruce Randall Donald (J. Comput. Biol., 2011)

Optimization of Combinatorial Mutagenesis. - Andrew S. Parker; Karl E. Griswold; Chris Bailey-Kellogg (J. Comput. Biol., 2011)

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations. - Andres H. Gutiérrez; Leonard Moise; Frances Terry; Kristen Dasilva; Chris Bailey-Kellogg; William D. Martin; Anne S. De Groot (BCB, 2012)

Structure-Guided Deimmunization of Therapeutic Proteins. - Andrew S. Parker; Karl E. Griswold; Chris Bailey-Kellogg (RECOMB, 2012)

MMFPh: a maximal motif finder for phosphoproteomics datasets. - Tuobin Wang; Arminja N. Kettenbach; Scott A. Gerber; Chris Bailey-Kellogg (Bioinform., 2012)

Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'. - Tuobin Wang; Arminja N. Kettenbach; Scott A. Gerber; Chris Bailey-Kellogg (Bioinform., 2012)

Algorithms for optimizing cross-overs in DNA shuffling. - Lu He; Alan M. Friedman; Chris Bailey-Kellogg (BMC Bioinform., 2012)

Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data. - Himanshu Chandola; Bruce Randall Donald; Chris Bailey-Kellogg (BCB, 2013)

Ballast: A Ball-based Algorithm for Structural Motifs. - Lu He; Fabio Vandin; Gopal Pandurangan; Chris Bailey-Kellogg (J. Comput. Biol., 2013)

Structure-Guided Deimmunization of Therapeutic Proteins. - Andrew S. Parker; Yoonjoo Choi; Karl E. Griswold; Chris Bailey-Kellogg (J. Comput. Biol., 2013)

Structure-based redesign of proteins for minimal T-cell epitope content. - Yoonjoo Choi; Karl E. Griswold; Chris Bailey-Kellogg (J. Comput. Chem., 2013)

Improved Multiple Sequence Alignments Using Coupled Pattern Mining. - K. S. M. Tozammel Hossain; Debprakash Patnaik; Srivatsan Laxman; Prateek Jain 002; Chris Bailey-Kellogg; Naren Ramakrishnan (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. - Lu He; Anne S. De Groot; Andres H. Gutiérrez; William D. Martin; Lenny Moise; Chris Bailey-Kellogg (BMC Bioinform., 2014)

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method. - Andres H. Gutiérrez; William D. Martin; Chris Bailey-Kellogg; Frances Terry; Leonard Moise; Anne S. De Groot (BMC Bioinform., 2015)

Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. - Hetunandan Kamisetty; Bornika Ghosh; Christopher James Langmead; Chris Bailey-Kellogg (J. Comput. Biol., 2015)

Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees. - Ickwon Choi; Amy W. Chung; Todd J. Suscovich; Supachai Rerks-Ngarm; Punnee Pitisuttithum; Sorachai Nitayaphan; Jaranit Kaewkungwal; Robert J. O'Connell; Donald Francis; Merlin L. Robb; Nelson Michael; Jerome H. Kim; et al. (PLoS Comput. Biol., 2015)

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate. - Regina S. Salvat; Andrew S. Parker; Yoonjoo Choi; Chris Bailey-Kellogg; Karl E. Griswold (PLoS Comput. Biol., 2015)

OCoM-SOCoM: Combinatorial Mutagenesis Library Design Optimally Combining Sequence and Structure Information. - Deeptak Verma; Gevorg Grigoryan; Chris Bailey-Kellogg (BCB, 2016)

Gaussian Process Models in Spatial Data Mining. - Naren Ramakrishnan; Chris Bailey-Kellogg (Encyclopedia of GIS, 2017)

DisruPPI: structure-based computational redesign algorithm for protein binding disruption. - Yoonjoo Choi; Jacob M. Furlon; Ryan B. Amos; Karl E. Griswold; Chris Bailey-Kellogg (Bioinform., 2018)

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity. - Neerja Thakkar; Chris Bailey-Kellogg (BMC Bioinform., 2019)

Pareto Optimization of Combinatorial Mutagenesis Libraries. - Deeptak Verma; Gevorg Grigoryan; Chris Bailey-Kellogg (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Learning context-aware structural representations to predict antigen and antibody binding interfaces. - Srivamshi Pittala; Chris Bailey-Kellogg (Bioinform., 2020)

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination. - Yoonjoo Choi; Sukyo Jeong; Jung-Min Choi; Christian NDong; Karl E. Griswold; Chris Bailey-Kellogg; Hak-Sung Kim (PLoS Comput. Biol., 2020)

A multi-resolution graph convolution network for contiguous epitope prediction. - Lisa Oh; Bowen Dai; Chris Bailey-Kellogg (BCB, 2021)

Protein interaction interface region prediction by geometric deep learning. - Bowen Dai; Chris Bailey-Kellogg (Bioinform., 2021)

MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. - Brahm J. Yachnin; Vikram Khipple Mulligan; Sagar D. Khare; Chris Bailey-Kellogg (J. Chem. Inf. Model., 2021)

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity. - Daniel E. Mattox; Chris Bailey-Kellogg (PLoS Comput. Biol., 2021)

Building blocks and blueprints for bacterial autolysins. - Spencer J. Mitchell; Deeptak Verma; Karl E. Griswold; Chris Bailey-Kellogg (PLoS Comput. Biol., 2021)