2012
- L. He, F. Vandin, G. Pandurangan, and C. Bailey-Kellogg, "Ballast: A ball-based algorithm for structural motifs", Proc. RECOMB, 2012, to appear. [abstract] [preprint]
- A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, "Structure-guided deimmunization of therapeutic proteins", Proc. RECOMB, 2012, to appear. [abstract] [preprint]
2011
- F. Xiong, A.M. Friedman, and C. Bailey-Kellogg, "Planning combinatorial disulfide cross-links for protein fold determination", BMC Bioinf., 2011, 12(Suppl 12):S5. [abstract] [paper]
- L. He, A.M. Friedman, and C. Bailey-Kellogg, "A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments'", Proteins, 2011, epub. [abstract] [paper]
- A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, "Optimization of combinatorial mutagenesis", J. Comp. Biol., 2011, 18:1745-1756. [abstract] [paper]
- K.S.M.T. Hossain, C. Bailey-Kellogg, A.M. Friedman, M.J. Bradley, N. Baker, and N. Ramakrishnan, "Using physicochemical properties of amino acids to induce graphical models of residue couplings", Proc. BioKDD, 2011. [abstract] [preprint]
- L. He, A.M. Friedman, and C. Bailey-Kellogg, "Algorithms for optimizing cross-overs in DNA shuffling", Proc. ACM-BCB, 2011, 143-152. [abstract] [preprint]
- H. Chandola, A.K. Yan, S. Potluri, B.R. Donald, and C. Bailey-Kellogg, "NMR structural inference of symmetric
homo-oligomers", J. Comp. Biol., 2011, 18:1757-1775. [abstract] [paper]
- J. Martin, A.K. Yan, C. Bailey-Kellogg, P. Zhou, and B.R. Donald, "A graphical method for analyzing distance restraints for
structure determination of symmetric protein homo-oligomers", Protein Sci., 2011, 20:970-985. [abstract] [paper]
- A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, "Optimization of therapeutic proteins to delete T-cell epitopes
while maintaining beneficial residue interactions", J. Bioinf. Comp. Biol., 2011, 9:207-229. [abstract] [paper] [software]
- J. Martin, A.K. Yan, C. Bailey-Kellogg, P. Zhou, and B.R. Donald, "A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs", Proc. RECOMB, 2011, 222-237. [abstract]
- A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, "Optimization of combinatorial mutagenesis", Proc. RECOMB, 2011, 321-335. [abstract] [preprint]
- H. Kamisetty, A. Ramanathan, C. Bailey-Kellogg, and C.J. Langmead, "Accounting for conformational entropy in predicting binding free energies of
protein-protein interactions", Proteins, 2011, 79:444-462. [abstract] [paper]
2010
- P. Kavethekar, B. Craig, A.M. Friedman, C. Bailey-Kellogg, and D. Balkcom, "Characterizing the space of interatomic distance distribution functions consistent with solution scattering data", J. Bioinf. Comp. Biol., 2010, 8:315-335. [abstract] [paper]
- A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, "Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions", Proc. CSB, 2010, 100-113. [abstract] [paper] [software]
- W. Zheng, K.E. Griswold, and C. Bailey-Kellogg, "Protein fragment swapping: A method for asymmetric, selective site-directed recombination", J. Comp. Biol., 2010, 17:459-475. [abstract] [paper]
- F. Xiong, A.M. Friedman, and C. Bailey-Kellogg, "Planning combinatorial disulfide cross-links for protein fold determination", Proc. BioKDD, 2010. [abstract] [preprint]
- A.S. Parker, W. Zheng, K.E. Griswold, and C. Bailey-Kellogg, "Optimization algorithms for functional deimmunization of therapeutic proteins", BMC Bioinf., 2010, 0.583333333. [abstract] [paper] [software]
2009
- W. Zheng, A.M. Friedman, and C. Bailey-Kellogg, "Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins", J. Comp. Biol, 2009, 16:1151-1168. [abstract] [paper]
- H. Kamisetty, B. Ghosh, C. Bailey-Kellogg, and C.J. Langmead, "Modeling and inference of sequence-structure specificity", Proc. CSB, 2009, 91-101. [abstract] [preprint]
- P. Kavethekar, B. Craig, A.M. Friedman, C. Bailey-Kellogg, and D. Balkcom, "Characterizing the space of interatomic distance distribution functions consistent with solution scattering data", Proc. CSB, 2009, 239-250. [abstract] [preprint]
- J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical models of protein-protein interaction specificity from correlated mutations and interaction data", Proteins, 2009, 76:911-929. [abstract] [paper]
- J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Protein design by sampling an undirected graphical model of residue constraints", IEEE/ACM Trans. Comp. Biol. Bioinf., 2009, 6:505-516. [abstract] [preprint] [paper]
- W. Zheng, K.E. Griswold, and C. Bailey-Kellogg, "Protein fragment swapping: a method for asymmetric, selective site-directed
recombination", Proc. RECOMB, 2009, 321-338. [abstract] [preprint] [paper]
2008
- X. Ye, A.M. Friedman, and C. Bailey-Kellogg, "Optimizing Bayes error for protein structure model selection by stability mutagenesis", Proc. CSB, 2008, 99-108. [abstract] [preprint]
- F. Xiong, G. Pandurangan, and C. Bailey-Kellogg, "Contact replacement for NMR resonance assignment", Bioinformatics (Proc. ISMB), 2008, 24:i105-i213. [abstract] [preprint] [paper]
- W. Zheng, A.M. Friedman, and C. Bailey-Kellogg, "Algorithms for joint optimization of stability and diversity in planning
combinatorial libraries of chimeric proteins", Proc. RECOMB, 2008, 300-314. [abstract] [preprint] [paper]
- J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical Models of Residue Coupling in Protein Families", IEEE/ACM Trans. Comp. Biol. Bioinf., 2008, 5:183-197. [abstract] [preprint] [paper]
- T.E. Williamson, B.A. Craig, E. Kondrashkina, C. Bailey-Kellogg, and A.M. Friedman, "Analysis of self-associating proteins by singular value decomposition of solution scattering data", Biophys. J., 2008, 94:4906-4923. [abstract] [paper]
- L.V. Avramova, J. Desai, S. Weaver, A.M. Friedman, and C. Bailey-Kellogg, "Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules", J. Comb. Chem., 2008, 10:63-68. [abstract] [paper]
2007
- F. Xiong and C. Bailey-Kellogg, "A hierarchical grow-and-match algorithm for backbone resonance assignments
given 3D structure", Proc. IEEE BIBE, 2007, 403-410. [abstract] [preprint]
- W. Zheng, X. Ye, A.M. Friedman, and C. Bailey-Kellogg, "Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination", Proc. CSB, 2007, 31-40. [abstract] [preprint]
- X. Ye, A.M. Friedman, and C. Bailey-Kellogg, "Hypergraph model of multi-residue interactions in proteins: sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination", J. Comp. Biol., 2007, 14:777-790. [abstract] [preprint] [paper]
- S. Potluri, A.K. Yan, B.R. Donald, and C. Bailey-Kellogg, "A complete algorithm to resolve ambiguity for inter-subunit NOE assignment in structure determination of symmetric homo-oligomers", Protein Science, 2007, 16:69-81. [abstract] [preprint] [paper]
2006
- S. Potluri, A.K. Yan, J.J. Chou, B.R. Donald, and C. Bailey-Kellogg, "Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space using NMR restraints and van der Waals packing", Proteins, 2006, 65:203-219. [abstract] [preprint] [paper]
- O. Vitek, C. Bailey-Kellogg, B. Craig, and J. Vitek, "Inferential backbone assignment for sparse data", J. Biomol. NMR, 2006, 35:187-208. [abstract] [paper]
- L. Saftalov, P.A. Smith, A.M. Friedman, and C. Bailey-Kellogg, "Site-Directed Combinatorial Construction of Chimaeric Genes: General Method for Optimizing Assembly of Gene Fragments", Proteins, 2006, 64:629-642. [abstract] [preprint] [paper]
- S. Potluri, A.K. Yan, J.J. Chou, B.R. Donald, and C. Bailey-Kellogg, "Extended Abstract: Structure determination of symmetric protein complexes by a complete search of symmetry configuration space using NMR distance restraints", Proc. WAFR, 2006. [abstract] [preprint]
- X. Ye, A.M. Friedman, and C. Bailey-Kellogg, "Hypergraph model of multi-residue interactions in proteins: sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination", Proc. RECOMB, 2006, 15-29. [abstract] [paper]
- Z. Yi, O. Vitek, M. A. Qasim, S.M. Lu, W. Lu, M. Ranjbar, J. Li, M.C. Laskowski, C. Bailey-Kellogg, and M. Laskowski, Jr., "Functional evolution within a protein superfamily", Proteins, 2006, 63:697-708. [abstract] [preprint] [paper]
- H. Kamisetty, C. Bailey-Kellogg, and G. Pandurangan, "An efficient randomized algorithm for contact-based NMR backbone resonance assignment", Bioinformatics, 2006, 22:172-80. [abstract] [paper]
2005
- J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical models of residue coupling in protein families", Proc. BioKDD, 2005. [abstract] [preprint]
- C. Bailey-Kellogg, S. Chainraj, and G. Pandurangan, "A Random Graph Approach to NMR Sequential Assignment", J. Comp. Biol., 2005, 12:569-583. [abstract] [paper]
- O. Vitek, C. Bailey-Kellogg, B. Craig, P. Kuliniewicz, and J. Vitek, "Reconsidering complete search algorithms for protein backbone NMR assignment", Bioinformatics (Proc. ECCB), 2005, 21:ii230-236. [abstract] [preprint]
- N. Ramakrishnan, C. Bailey-Kellogg, S. Tadepalli, and V.N. Pandey, "Gaussian Processes for Active Data Mining of Spatial Aggregates", Proc. SIAM Data Mining, 2005. [abstract] [preprint]
- J. Li, Z.-P. Yi, M.C. Laskowski, M. Laskowski Jr., and C. Bailey-Kellogg, "Analysis of sequence-reactivity space for protein-protein interactions", Proteins, 2005, 58:661-671. [abstract] [paper]
2004
- X. Ye, P.K. O'Neil, A.N. Foster, M.J. Gajda, J. Kosinski, M.A. Kurowski, A.M. Friedman, and C. Bailey-Kellogg, "Probabilistic cross-link analysis and experiment planning for
high-throughput elucidation of protein structure", Protein Sci., 2004, 13:3298-3313. [abstract] [paper]
- A. Kuzminykh and C. Bailey-Kellogg, "Polyhedral approximations of the sphere with unusual geometric and topological
properties", Geombinatorics, 2004, 14(2):55-61. [abstract]
- N. Ramakrishnan, C. Bailey-Kellogg, S. Tadepalli, and V.N. Pandey, "Gaussian Processes for Active Data Mining of Spatial Aggregates", Proc. QR, 2004. [abstract] [preprint]
- C. Bailey-Kellogg and N. Ramakrishnan, "Spatial Aggregation for Qualitative Assessment of Scientific Computations", Proc. AAAI, 2004. [abstract] [preprint]
- R.H. Lilien, C. Bailey-Kellogg, A.A. Anderson, and B.R. Donald, "A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry", Acta Cryst., 2004, D60:1057-1067. [abstract] [preprint] [paper]
- O. Vitek, J. Vitek, B. Craig, and C. Bailey-Kellogg, "Model-based assignment and inference of protein backbone nuclear magnetic resonances", Stat. Appl. Gen. Mol. Biol., 2004, 3(1), article 6, 1-33. [abstract] [preprint] [paper]
- C. Bailey-Kellogg, S. Chainraj, and G. Pandurangan, "A Random Graph Approach to NMR Sequential Assignment", Proc. RECOMB, 2004, 58-67. [abstract] [preprint]
- C. Bailey-Kellogg and F. Zhao, "Qualitative spatial reasoning: extracting and reasoning with spatial aggregates", AI Magazine, 2004, 24:47-60. [abstract] [preprint]
- S. Potluri, A.A. Khan, A. Kuzminykh, J.M. Bujnicki, A.M. Friedman, and C. Bailey-Kellogg, "Geometric analysis of cross-linkability for protein fold discrimination", Proc. Pac. Symp. Biocomp. (PSB), 2004. [abstract] [preprint]
2003
- C. Bailey-Kellogg and N. Ramakrishnan, "Active data mining of correspondence for qualitative assessment of scientific
computations", Proc. QR, 2003, 23-30. [abstract] [preprint]
- N. Ramakrishan and C. Bailey-Kellogg, "Gaussian process models of spatial aggregation algorithms", Proc. IJCAI, 2003, 1045-1051. [abstract] [preprint]
- F. Zhao, C. Bailey-Kellogg, and M. Fromherz, "Physics-based encapsulation in embedded software for distributed sensing and control applications", Proceedings of the IEEE, 2003, 91:40-63. [abstract] [preprint]
2002
- N. Ramakrishnan and C. Bailey-Kellogg, "Using physical properties for mining in data-scarce domains", IEEE Computing in Science & Engineering, 2002, 4:31-43. [abstract] [preprint]
2001
- C. Bailey-Kellogg and F. Zhao, "Influence-based model decomposition", Artificial Intelligence Journal, 2001, 130:125-166. [abstract] [preprint]
- C. Bailey-Kellogg and N. Ramakrishnan, "Ambiguity-directed sampling for qualitative analysis of sparse data from spatially-distributed physical systems", Proc. IJCAI, 2001, 43-50. [abstract] [preprint]
- C. Bailey-Kellogg, J.J. Kelley, III, R. Lilien, and B.R. Donald, "Physical geometric algorithms for structural molecular biology", Invited paper, ICRA, 2001. [abstract] [preprint]
- C. Bailey-Kellogg, J.J. Kelley, III, C. Stein, and B.R. Donald, "Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling", J. Comp. Biol., 2001, 8:19-36. [abstract] [preprint]
2000
- C. Bailey-Kellogg, A. Widge, M.J. Berardi, J.H. Bushweller, and B.R. Donald, "The NOESY Jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data", J. Comp. Biol., 2000, 7:537-558. [abstract] [preprint]
- C. Bailey-Kellogg, J.J. Kelley, III, C. Stein, and B.R. Donald, "Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling", Proc. ISMB, 2000, 13-24. [abstract] [preprint]
- C. Bailey-Kellogg, A. Widge, M.J. Berardi, J.H. Bushweller, and B.R. Donald, "The NOESY Jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data", Proc. RECOMB, 2000, 33-44. [abstract] [preprint]
1999
- C. Bailey-Kellogg and F. Zhao, "Influence-based model decomposition", Proc. AAAI, 1999, 402-409. [abstract] [preprint]
- C. Bailey-Kellogg, "The spatial aggregation language for modeling and controlling distributed physical systems", PhD thesis, Ohio State University, 1999. [abstract] [preprint]
- C. Bailey-Kellogg and F. Zhao, "The SAL Interpreter for Large-Scale Optimization in Distributed Control Systems", Proc. IEEE Symp. Comp.-Aided Control Syst. Design, 1999. [abstract] [preprint]
1998
- F. Zhao and C. Bailey-Kellogg, "Intelligent simulation", AAAI Tutorial Forum, 1998. [abstract] [preprint]
1999
- F. Zhao, C. Bailey-Kellogg, X. Huang, and I. Ordonez, "Intelligent simulation for mining large scientific data sets", New Generation Computing, 1999, 17:333-347. [abstract] [preprint]
1998
- C. Bailey-Kellogg and F. Zhao, "Qualitative analysis of distributed physical systems with applications to control
synthesis", Proc. AAAI, 1998, 232-239. [abstract] [preprint]
- C. Bailey-Kellogg and F. Zhao, "Reasoning about and optimizing distributed parameter physical systems using influence graphs", Proc. QR, 1998. [abstract] [preprint]
1997
- C. Bailey-Kellogg and F. Zhao, "Spatial aggregation: modeling and controlling physical fields", Proc. QR, 1997. [abstract] [preprint]
1996
- C. Bailey-Kellogg, F. Zhao, and K. Yip, "Spatial aggregation: language and applications", Proc. AAAI, 1996, 517-522. [abstract] [preprint]