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Chris Bailey-Kellogg

Christopher Bailey-Kellogg

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affiliation: Dartmouth College, Hanover, USA

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2021
[j43]
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Bowen Dai, Chris Bailey-Kellogg:
Protein interaction interface region prediction by geometric deep learning. Bioinform. 37(17): 2580-2588 (2021)
[j42]
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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]
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  - journals/ploscb/MitchellVGB21
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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]
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  - journals/ploscb/MattoxB21
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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]
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Srivamshi Pittala, Chris Bailey-Kellogg:
Learning context-aware structural representations to predict antigen and antibody binding interfaces. Bioinform. 36(13): 3996-4003 (2020)
[j38]
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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]
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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]
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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]
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  - journals/bioinformatics/ChoiFAGB18
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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]
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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]
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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]
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  - journals/ploscb/SalvatPCBG15
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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]
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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]
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  - journals/bmcbi/HeGGMMB14
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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]
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  - journals/jcb/HeVPB13
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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]
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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]
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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]
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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]
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  - journals/bioinformatics/WangKGB12
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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]
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  - journals/bioinformatics/WangKGB12a
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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]
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  - journals/bmcbi/HeFB12
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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]
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  - journals/bmcbi/XiongFB11
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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]
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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]
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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]
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Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Combinatorial Mutagenesis. J. Comput. Biol. 18(11): 1743-1756 (2011)
[j18]
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  - journals/jcb/ChandolaYPDB11
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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]
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  - journals/bmcbi/ParkerZGB10
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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]
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  - journals/jbcb/KavathekarCFBB10
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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]
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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]
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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]
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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]
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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]
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  - journals/jcb/YeFB07
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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]
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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]
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Chris Bailey-Kellogg, Naren Ramakrishnan, Madhav V. Marathe:
Spatial data mining to support pandemic preparedness. SIGKDD Explor. 8(1): 80-82 (2006)
2005
[j8]
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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]
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Christopher Bailey-Kellogg, Feng Zhao:
Qualitative Spatial Reasoning Extracting and Reasoning with Spatial Aggregates. AI Mag. 24(4): 47-60 (2004)
2003
[j6]
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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]
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Naren Ramakrishnan, Chris Bailey-Kellogg:
Sampling strategies for mining in data-scarce domains. Comput. Sci. Eng. 4(4): 31-43 (2002)
2001
[j4]
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Christopher Bailey-Kellogg, Feng Zhao:
Influence-based model decomposition for reasoning about spatially distributed physical systems. Artif. Intell. 130(2): 125-166 (2001)
[j3]
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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
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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]
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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

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2021
[c33]
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  - conf/bcb/OhDB21
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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]
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  - conf/bcb/VermaGB16
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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]
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  - conf/recomb/KamisettyGLB14
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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]
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  - conf/bcb/ChandolaDB13
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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]
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  - conf/bcb/HossainPLJBR12
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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]
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  - conf/bcb/GutierrezMTDBMG12
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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]
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Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg:
Ballast: A Ball-Based Algorithm for Structural Motifs. RECOMB 2012: 79-93
[c26]
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Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-Guided Deimmunization of Therapeutic Proteins. RECOMB 2012: 184-198
2011
[c25]
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Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. BCB 2011: 143-152
[c24]
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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]
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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
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Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Combinatorial Mutagenesis. RECOMB 2011: 321-335
2009
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Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. RECOMB 2009: 321-338
2008
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Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg:
Contact replacement for NMR resonance assignment. ISMB 2008: 205-213
[c19]
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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
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Fei Xiong, Chris Bailey-Kellogg:
A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. BIBE 2007: 403-410
2006
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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
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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
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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]
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John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg:
Graphical models of residue coupling in protein families. BIOKDD 2005: 12-20
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Naren Ramakrishnan, Chris Bailey-Kellogg, Satish Tadepalli, Varun Pandey:
Gaussian Processes for Active Data Mining of Spatial Aggregates. SDM 2005: 427-438
2004
[c12]
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Chris Bailey-Kellogg, Naren Ramakrishnan:
Spatial Aggregation for Qualitative Assessment of Scientific Computations. AAAI 2004: 585-591
[c11]
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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
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Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan:
A random graph approach to NMR sequential assignment. RECOMB 2004: 58-67
2003
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Panagiotis K. Linos, Chris Bailey-Kellogg:
Service Learning in Software Engineering and Maintenance. ICSM 2003: 336-
[c8]
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Naren Ramakrishnan, Christopher Bailey-Kellogg:
Gaussian Process Models of Spatial Aggregation Algorithms. IJCAI 2003: 1045-1051
2001
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Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien:
Physical Geometric Algorithms for Structural Molecular Biology. ICRA 2001: 940-947
[c6]
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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]
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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]
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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]
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Christopher Bailey-Kellogg, Feng Zhao:
Influence-Based Model Decomposition. AAAI/IAAI 1999: 402-409
1998
[c2]
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Christopher Bailey-Kellogg, Feng Zhao:
Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis. AAAI/IAAI 1998: 232-239
1996
[c1]
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Christopher Bailey-Kellogg, Feng Zhao, Kenneth Yip:
Spatial Aggregation: Language and Applications. AAAI/IAAI, Vol. 1 1996: 517-522

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2007
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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

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2017
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Naren Ramakrishnan, Chris Bailey-Kellogg:
Gaussian Process Models in Spatial Data Mining. Encyclopedia of GIS 2017: 639-644
2008
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Naren Ramakrishnan, Chris Bailey-Kellogg:
Gaussian Process Models in Spatial Data Mining. Encyclopedia of GIS 2008: 325-329

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2002
[i2]
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  - journals/corr/cs-AI-0204053
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Christopher Bailey-Kellogg, Naren Ramakrishnan:
Qualitative Analysis of Correspondence for Experimental Algorithmics. CoRR cs.AI/0204053 (2002)
[i1]
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  - journals/corr/cs-CE-0204047
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Naren Ramakrishnan, Christopher Bailey-Kellogg:
Sampling Strategies for Mining in Data-Scarce Domains. CoRR cs.CE/0204047 (2002)

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