Computational Biology

• X. Ye, A.M. Friedman, and C. Bailey-Kellogg, "Optimizing Bayes error for protein structure model selection by stability mutagenesis", Proc. CSB, 2008, to appear. abstract.
• F. Xiong, G. Pandurangan, and C. Bailey-Kellogg, "Contact replacement for NMR resonance assignment", Proc. ISMB, 2008, to appear. abstract. preprint.
• 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, pp. 300-314. abstract. official version. preprint.
• 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., in press. abstract.
• 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., 10:63-68, 2008. abstract. paper.
• F. Xiong and C. Bailey-Kellogg, "A hierarchical grow-and-match algorithm for backbone resonance assignments given 3D structure", Proc. IEEE BIBE, 2007, pp. 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, pp. 31-40. abstract. preprint.
• J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical models of residue coupling in protein families", IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press. 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. Computational Biology, 2007, 14:777-790. abstract. official version. preprint.
• 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. official version. preprint.
• 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. official version. preprint.
• O. Vitek, C. Bailey-Kellogg, B. Craig, and J. Vitek, "Inferential backbone assignment for sparse data", J. Biomolecular NMR, 2006, 35:187-208. abstract. official version.
• 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. official version. preprint.
• 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. official version.
• 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. official version. preprint.
• 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. official abstract. paper.
• J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical models of residue coupling in protein families", Proc. BioKDD, 2005. abstract. pdf. Copyright 2005, ACM.
• O. Vitek, C. Bailey-Kellogg, B. Craig, P. Kuliniewicz, J. Vitek, "Reconsidering complete search algorithms for protein backbone NMR assignment", Proc. ECCB, 2005, published in Bioinformatics, 2005, 21:ii230-236. abstract. pdf.
• C. Bailey-Kellogg, S. Chainraj, and G. Pandurangan, "A Random Graph Approach to NMR Sequential Assignment", J. Comp. Biol., 2005, 12:569-583. paper.
• 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.
• 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.
• 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. paper. local pdf. Copyright © International Union of Crystallography.
• O. Vitek, J. Vitek, B. Craig, and C. Bailey-Kellogg, "Model-based assignment and inference of protein backbone nuclear magnetic resonances", Statistical Applications in Genetics and Molecular Biology, 2004, 3(1), article 6, 1-33. abstract. paper. local pdf.
• C. Bailey-Kellogg, S. Chainraj, and G. Pandurangan, "A Random Graph Approach to NMR Sequential Assignment", Proc. RECOMB, 2004, pp. 58-67. abstract. pdf.
• 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. Pacific Symposium on Biocomputing (PSB), 2004. abstract. pdf.
• C. Bailey-Kellogg, J.J. Kelley, III, R. Lilien, and B.R. Donald, "Physical geometric algorithms for structural molecular biology," invited paper at the Special Session on Computational Biology and Chemistry, International Conference on Robotics and Automation (ICRA), 2001. abstract. pdf.
• 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. Computational Biology, 2001, 8:19-36. abstract. pdf.
• 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. Computational Biology, 2000, 7:537-558. abstract. pdf.
• 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, pp. 13-24. abstract. postscript.
• 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, pp. 33-44. abstract. postscript.

Spatial Aggregation

• C. Bailey-Kellogg, N. Ramakrishnan, and M. Marathe, "Spatial Data Mining to Support Pandemic Preparedness", ACM SIGKDD Explorations, 8:80-82, 2006. (Report on SIAM DM 2006 Workshop on Spatial Data Mining.) local pdf. official version.
• N. Ramakrishnan, C. Bailey-Kellogg, S. Tadepalli, and V.N. Pandey, "Gaussian Processes for Active Data Mining of Spatial Aggregates", Proc. SIAM Data Mining Conference, 2005. Selected among "Best of SIAM Data Mining 2005" for presentation at Interface 2005. abstract. pdf.
• N. Ramakrishnan, C. Bailey-Kellogg, S. Tadepalli, and V.N. Pandey, "Gaussian Processes for Active Data Mining of Spatial Aggregates", Proc. 18th International Workshop on Qualitative Reasoning, Chicago, 2004. (Preliminary version of SIAM-DM-05 paper above.) abstract. pdf.
• C. Bailey-Kellogg and N. Ramakrishnan, "Spatial Aggregation for Qualitative Assessment of Scientific Computations", Proc. AAAI, 2004. abstract. pdf. Copyright 2004, American Association for Artificial Intelligence (www.aaai.org).
• C. Bailey-Kellogg and F. Zhao, "Qualitative spatial reasoning: extracting and reasoning with spatial aggregates", AI Magazine, 2004, 24:47-60. abstract. pdf. Copyright 2004, American Association for Artificial Intelligence (www.aaai.org).
• C. Bailey-Kellogg and N. Ramakrishnan, "Active data mining of correspondence for qualitative assessment of scientific computations," Proc. 17th International Workshop on Qualitative Reasoning, Brasilia, 2003, pp. 23-30. abstract. pdf.
• N. Ramakrishan and C. Bailey-Kellogg, "Gaussian process models of spatial aggregation algorithms", Proc. Int'l Joint Conf. on Artificial Intelligence (IJCAI), 2003, pp. 1045-1051. abstract. pdf. Copyright 2003, IJCAI (www.ijcai.org).
• 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. postscript.
• 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. pdf.
• C. Bailey-Kellogg and F. Zhao, "Influence-based model decomposition," Artificial Intelligence, 2001, 130:125-166. abstract. pdf.
• C. Bailey-Kellogg and N. Ramakrishnan, "Ambiguity-directed sampling for qualitative analysis of sparse data from spatially-distributed physical systems," Proc. Int'l Joint Conf. on Artificial Intelligence (IJCAI), 2001, pp. 43-50. abstract. pdf. Copyright 2001, IJCAI (www.ijcai.org).
• F. Zhao, C. Bailey-Kellogg, and I. Ordóñez, "The spatial aggregation language: think globally, act locally," Dr. Dobb's Journal, April, 2001.
• C. Bailey-Kellogg, "The spatial aggregation language for modeling and controlling distributed physical systems," PhD thesis, Ohio State University, 1999. abstract. thesis.
• C. Bailey-Kellogg and F. Zhao, "Influence-based model decomposition," Proc. AAAI, 1999, pp. 402-409. abstract. postscript. Copyright 1999, American Association for Artificial Intelligence (www.aaai.org).
• C. Bailey-Kellogg and F. Zhao, "The SAL interpreter for large-scale optimization in distributed control systems," Proc. IEEE Symposium on Computer-Aided Control Systems Design, 1999. abstract. postscript.
• F. Zhao, C. Bailey-Kellogg, X. Huang, and I. Ordóñez, "Intelligent simulation for mining large scientific data sets," New Generation Computing, 1999, 17:333-347. abstract. postscript.
• C. Bailey-Kellogg and F. Zhao, "Qualitative analysis of distributed physical systems with applications to control synthesis," Proc. AAAI, 1998, pp. 232-239. abstract. postscript. Copyright 1998, American Association for Artificial Intelligence (www.aaai.org).
• F. Zhao and C. Bailey-Kellogg, "Intelligent simulation," AAAI Tutorial Forum, 1998. abstract. Slides handout (2 per page).
• C. Bailey-Kellogg and F. Zhao, "Reasoning about and optimizing distributed parameter physical systems using influence graphs," Proc. 12th International Workshop on Qualitative Reasoning, Cape Cod, 1998. abstract. postscript.
• C. Bailey-Kellogg and F. Zhao, "Spatial aggregation: modeling and controlling physical fields," Proc. 11th International Workshop on Qualitative Reasoning, Italy, 1997. abstract. postscript.
• C. Bailey-Kellogg, F. Zhao, and K. Yip, "Spatial aggregation: language and applications," Proc. AAAI, 1996, pp. 517-522. abstract. postscript. Copyright 1996, American Association for Artificial Intelligence (www.aaai.org).

Proceedings Edited

• C. Bailey-Kellogg and N. Ramakrishnan, co-chairs, 2006 SIAM Data Mining Workshop on Spatial Data Mining (papers on the agenda page).
• C. Bailey-Kellogg and B. Kuipers, co-chairs, 20th International Workshop on Qualitative Reasoning, QR-06. Web proceedings.

Other Fun Stuff

• A. Kuzminykh and C. Bailey-Kellogg, "Polyhedral approximations of the sphere and representations of graphs", Geombinatorics, 2006, 15(4):183-190.
• A. Kuzminykh and C. Bailey-Kellogg, "Polyhedral approximations of the sphere with unusual geometric and topological properties", Geombinatorics, 2004, 14(2):55-61. abstract.