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ORCIDChris Bailey-Kellogg
Christopher Bailey-Kellogg
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- affiliation: Dartmouth College, Hanover, USA
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Journal Articles
- 2021
[j43]Bowen Dai, Chris Bailey-Kellogg
:
Protein interaction interface region prediction by geometric deep learning. Bioinform. 37(17): 2580-2588 (2021)- [j42]Brahm J. Yachnin, Vikram Khipple Mulligan, Sagar D. Khare, Chris Bailey-Kellogg:
MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. J. Chem. Inf. Model. 61(5): 2368-2382 (2021) - [j41]Spencer J. Mitchell, Deeptak Verma, Karl E. Griswold, Chris Bailey-Kellogg:
Building blocks and blueprints for bacterial autolysins. PLoS Comput. Biol. 17(4) (2021) - [j40]Daniel E. Mattox, Chris Bailey-Kellogg:
Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity. PLoS Comput. Biol. 17(10) (2021) - 2020
- [j39]Srivamshi Pittala, Chris Bailey-Kellogg:
Learning context-aware structural representations to predict antigen and antibody binding interfaces. Bioinform. 36(13): 3996-4003 (2020) - [j38]Yoonjoo Choi, Sukyo Jeong, Jung-Min Choi, Christian NDong, Karl E. Griswold, Chris Bailey-Kellogg, Hak-Sung Kim:
Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination. PLoS Comput. Biol. 16(8) (2020) - 2019
- [j37]Neerja Thakkar, Chris Bailey-Kellogg:
Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity. BMC Bioinform. 20(1): 241:1-241:14 (2019) - [j36]Deeptak Verma, Gevorg Grigoryan, Chris Bailey-Kellogg:
Pareto Optimization of Combinatorial Mutagenesis Libraries. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1143-1153 (2019) - 2018
- [j35]Yoonjoo Choi, Jacob M. Furlon, Ryan B. Amos, Karl E. Griswold, Chris Bailey-Kellogg:
DisruPPI: structure-based computational redesign algorithm for protein binding disruption. Bioinform. 34(13): i245-i253 (2018) - 2015
- [j34]Andres H. Gutiérrez, William D. Martin, Chris Bailey-Kellogg, Frances Terry, Leonard Moise, Anne S. De Groot:
Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method. BMC Bioinform. 16: 290:1-290:11 (2015) - [j33]Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg:
Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. J. Comput. Biol. 22(6): 474-486 (2015) - [j32]Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold:
Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate. PLoS Comput. Biol. 11(1) (2015) - [j31]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, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg:
Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j30]Lu He, Anne S. De Groot, Andres H. Gutiérrez, William D. Martin, Lenny Moise, Chris Bailey-Kellogg:
Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. BMC Bioinform. 15(S-4): S1 (2014) - 2013
- [j29]Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg:
Ballast: A Ball-based Algorithm for Structural Motifs. J. Comput. Biol. 20(2): 137-151 (2013) - [j28]Andrew S. Parker, Yoonjoo Choi, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-Guided Deimmunization of Therapeutic Proteins. J. Comput. Biol. 20(2): 152-165 (2013) - [j27]Yoonjoo Choi, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-based redesign of proteins for minimal T-cell epitope content. J. Comput. Chem. 34(10): 879-891 (2013) - [j26]K. S. M. Tozammel Hossain, Debprakash Patnaik, Srivatsan Laxman, Prateek Jain, Chris Bailey-Kellogg, Naren Ramakrishnan:
Improved Multiple Sequence Alignments Using Coupled Pattern Mining. IEEE ACM Trans. Comput. Biol. Bioinform. 10(5): 1098-1112 (2013) - 2012
- [j25]Tuobin Wang, Arminja N. Kettenbach, Scott A. Gerber, Chris Bailey-Kellogg:
MMFPh: a maximal motif finder for phosphoproteomics datasets. Bioinform. 28(12): 1562-1570 (2012) - [j24]Tuobin Wang, Arminja N. Kettenbach, Scott A. Gerber, Chris Bailey-Kellogg:
Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'. Bioinform. 28(16): 2213 (2012) - [j23]Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. BMC Bioinform. 13(S-3): S3 (2012) - 2011
- [j22]Fei Xiong, Alan M. Friedman, Chris Bailey-Kellogg:
Planning combinatorial disulfide cross-links for protein fold determination. BMC Bioinform. 12(S-12): S5 (2011) - [j21]Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions. J. Bioinform. Comput. Biol. 9(2): 207-229 (2011) - [j20]Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald:
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs. J. Comput. Biol. 18(11): 1507-1523 (2011) - [j19]Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Combinatorial Mutagenesis. J. Comput. Biol. 18(11): 1743-1756 (2011) - [j18]Himanshu Chandola, Anthony K. Yan, Shobha Potluri, Bruce Randall Donald, Chris Bailey-Kellogg:
NMR Structural Inference of Symmetric Homo-Oligomers. J. Comput. Biol. 18(12): 1757-1775 (2011) - 2010
- [j17]Andrew S. Parker, Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinform. 11: 180 (2010) - [j16]Paritosh A. Kavathekar, Bruce A. Craig, Alan M. Friedman, Chris Bailey-Kellogg, Devin J. Balkcom:
Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data. J. Bioinform. Comput. Biol. 8(2): 315-335 (2010) - [j15]Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. J. Comput. Biol. 17(3): 459-475 (2010) - 2009
- [j14]Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. J. Comput. Biol. 16(8): 1151-1168 (2009) - [j13]John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg:
Protein Design by Sampling an Undirected Graphical Model of Residue Constraints. IEEE ACM Trans. Comput. Biol. Bioinform. 6(3): 506-516 (2009) - 2008
- [j12]John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg:
Graphical Models of Residue Coupling in Protein Families. IEEE ACM Trans. Comput. Biol. Bioinform. 5(2): 183-197 (2008) - 2007
- [j11]Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg:
Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. J. Comput. Biol. 14(6): 777-790 (2007) - 2006
- [j10]Hetunandan Kamisetty, Chris Bailey-Kellogg, Gopal Pandurangan:
An efficient randomized algorithm for contact-based NMR backbone resonance assignment. Bioinform. 22(2): 172-180 (2006) - [j9]Chris Bailey-Kellogg, Naren Ramakrishnan, Madhav V. Marathe:
Spatial data mining to support pandemic preparedness. SIGKDD Explor. 8(1): 80-82 (2006) - 2005
- [j8]Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan:
A Random Graph Approach to NMR Sequential Assignment. J. Comput. Biol. 12(6): 569-583 (2005) - 2004
- [j7]Christopher Bailey-Kellogg, Feng Zhao:
Qualitative Spatial Reasoning Extracting and Reasoning with Spatial Aggregates. AI Mag. 24(4): 47-60 (2004) - 2003
- [j6]Feng Zhao, Christopher Bailey-Kellogg, Markus P. J. Fromherz:
Physics-based encapsulation in embedded software for distributed sensing and control applications. Proc. IEEE 91(1): 40-63 (2003) - 2002
- [j5]Naren Ramakrishnan, Chris Bailey-Kellogg:
Sampling strategies for mining in data-scarce domains. Comput. Sci. Eng. 4(4): 31-43 (2002) - 2001
- [j4]Christopher Bailey-Kellogg, Feng Zhao:
Influence-based model decomposition for reasoning about spatially distributed physical systems. Artif. Intell. 130(2): 125-166 (2001) - [j3]Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald:
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. J. Comput. Biol. 8(1): 19-36 (2001) - 2000
- [j2]Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald:
The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data. J. Comput. Biol. 7(3-4): 537-558 (2000) - 1999
- [j1]Feng Zhao, Christopher Bailey-Kellogg, Xingang Huang, Iván Ordóñez:
Intelligent Simulation Tools for Mining Large Scientific Data Sets. New Gener. Comput. 17(4): 333-347 (1999)
Conference and Workshop Papers
- 2021
- [c33]Lisa Oh, Bowen Dai, Chris Bailey-Kellogg:
A multi-resolution graph convolution network for contiguous epitope prediction. BCB 2021: 38:1-38:10 - 2016
- [c32]Deeptak Verma, Gevorg Grigoryan, Chris Bailey-Kellogg:
OCoM-SOCoM: Combinatorial Mutagenesis Library Design Optimally Combining Sequence and Structure Information. BCB 2016: 307-316 - 2014
- [c31]Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg:
Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. RECOMB 2014: 129-143 - 2013
- [c30]Himanshu Chandola, Bruce Randall Donald, Chris Bailey-Kellogg:
Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data. BCB 2013: 171 - 2012
- [c29]K. S. M. Tozammel Hossain, Debprakash Patnaik, Srivatsan Laxman, Prateek Jain, Chris Bailey-Kellogg, Naren Ramakrishnan:
Improved multiple sequence alignments using coupled pattern mining. BCB 2012: 28-35 - [c28]Andres H. Gutiérrez, Leonard Moise, Frances Terry, Kristen Dasilva, Chris Bailey-Kellogg, William D. Martin, Anne S. De Groot:
Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations. BCB 2012: 637-642 - [c27]Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg:
Ballast: A Ball-Based Algorithm for Structural Motifs. RECOMB 2012: 79-93 - [c26]Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-Guided Deimmunization of Therapeutic Proteins. RECOMB 2012: 184-198 - 2011
- [c25]Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. BCB 2011: 143-152 - [c24]K. S. M. Tozammel Hossain, Chris Bailey-Kellogg, Alan M. Friedman, Michael J. Bradley, Nathan A. Baker, Naren Ramakrishnan:
Using physicochemical properties of amino acids to induce graphical models of residue couplings. BIOKDD 2011: 3:1-3:10 - [c23]Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald:
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. RECOMB 2011: 222-237 - [c22]Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Combinatorial Mutagenesis. RECOMB 2011: 321-335 - 2009
- [c21]Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. RECOMB 2009: 321-338 - 2008
- [c20]Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg:
Contact replacement for NMR resonance assignment. ISMB 2008: 205-213 - [c19]Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. RECOMB 2008: 300-314 - 2007
- [c18]Fei Xiong, Chris Bailey-Kellogg:
A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. BIBE 2007: 403-410 - 2006
- [c17]Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg:
Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. RECOMB 2006: 15-29 - [c16]Shobha Potluri, Anthony K. Yan, James J. Chou, Bruce Randall Donald, Chris Bailey-Kellogg:
Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints. WAFR 2006: 335-340 - 2005
- [c15]Olga Vitek, Chris Bailey-Kellogg, Bruce A. Craig, Paul Kuliniewicz, Jan Vitek:
Reconsidering complete search algorithms for protein backbone NMR assignment. ECCB/JBI 2005: 236 - [c14]John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg:
Graphical models of residue coupling in protein families. BIOKDD 2005: 12-20 - [c13]Naren Ramakrishnan, Chris Bailey-Kellogg, Satish Tadepalli, Varun Pandey:
Gaussian Processes for Active Data Mining of Spatial Aggregates. SDM 2005: 427-438 - 2004
- [c12]Chris Bailey-Kellogg, Naren Ramakrishnan:
Spatial Aggregation for Qualitative Assessment of Scientific Computations. AAAI 2004: 585-591 - [c11]Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg:
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. Pacific Symposium on Biocomputing 2004: 447-458 - [c10]Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan:
A random graph approach to NMR sequential assignment. RECOMB 2004: 58-67 - 2003
- [c9]Panagiotis K. Linos, Chris Bailey-Kellogg:
Service Learning in Software Engineering and Maintenance. ICSM 2003: 336- - [c8]Naren Ramakrishnan, Christopher Bailey-Kellogg:
Gaussian Process Models of Spatial Aggregation Algorithms. IJCAI 2003: 1045-1051 - 2001
- [c7]Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien:
Physical Geometric Algorithms for Structural Molecular Biology. ICRA 2001: 940-947 - [c6]Christopher Bailey-Kellogg, Naren Ramakrishnan:
Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially-Distributed Physical Systems. IJCAI 2001: 43-50 - 2000
- [c5]Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald:
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. ISMB 2000: 13-24 - [c4]Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald:
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. RECOMB 2000: 33-44 - 1999
- [c3]Christopher Bailey-Kellogg, Feng Zhao:
Influence-Based Model Decomposition. AAAI/IAAI 1999: 402-409 - 1998
- [c2]Christopher Bailey-Kellogg, Feng Zhao:
Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis. AAAI/IAAI 1998: 232-239 - 1996
- [c1]Christopher Bailey-Kellogg, Feng Zhao, Kenneth Yip:
Spatial Aggregation: Language and Applications. AAAI/IAAI, Vol. 1 1996: 517-522
Parts in Books or Collections
- 2007
- [p1]Feng Zhao, Chris Bailey-Kellogg, Xingang Huang, Iván Ordóñez:
Structure Discovery from Massive Spatial Data Sets Using Intelligent Simulation Tools. Computational Discovery of Scientific Knowledge 2007: 158-174
Reference Works
- 2017
- [r2]Naren Ramakrishnan, Chris Bailey-Kellogg:
Gaussian Process Models in Spatial Data Mining. Encyclopedia of GIS 2017: 639-644 - 2008
- [r1]Naren Ramakrishnan, Chris Bailey-Kellogg:
Gaussian Process Models in Spatial Data Mining. Encyclopedia of GIS 2008: 325-329
Informal and Other Publications
- 2002
- [i2]Christopher Bailey-Kellogg, Naren Ramakrishnan:
Qualitative Analysis of Correspondence for Experimental Algorithmics. CoRR cs.AI/0204053 (2002) - [i1]Naren Ramakrishnan, Christopher Bailey-Kellogg:
Sampling Strategies for Mining in Data-Scarce Domains. CoRR cs.CE/0204047 (2002)
Coauthor Index
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