The following list is in roughly reverse chronological order; recent papers are also listed in their appropriate projects. There are abstracts posted for most of these, and pdfs when possible.

2009

  • H. Kamisetty, B. Ghosh, C. Bailey-Kellogg, and C.J. Langmead, "Modeling and inference of sequence-structure specificity", Proc. CSB, 2009. abstract. paper.
  • 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. abstract. paper.
  • 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.
  • W. Zheng, K.E. Griswold, and C. Bailey-Kellogg, "Protein fragment swapping: a method for asymmetric, selective site-directed recombination", Proc. RECOMB, 2009, pp. 321-338. abstract. preprint. official version.
  • J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Protein design by sampling an undirected graphical model of residue constraints", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 6:505-516. 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, pp. 99-108. abstract. paper.
  • F. Xiong, G. Pandurangan, and C. Bailey-Kellogg, "Contact replacement for NMR resonance assignment", Proc. ISMB, 2008; published in Bioinformatics, 2008, 24:i105-i213. abstract. official version. 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.
  • J. Thomas, N. Ramakrishnan, and C. Bailey-Kellogg, "Graphical models of residue coupling in protein families", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008, 5:183-197. 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., 2008, 94:4906-4923. abstract. official version.
  • 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.

2007

  • 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.
  • 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.

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. official version. preprint.
  • A. Kuzminykh and C. Bailey-Kellogg, "Polyhedral approximations of the sphere and representations of graphs", Geombinatorics, 2006, 15(4):183-190.
  • 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.
  • 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.

2005

  • 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.
  • 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.
  • 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. 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).
  • 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.
  • 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).
  • 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.

2003

  • 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.

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. pdf.

2001

  • 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, 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.

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. 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.

1999

  • 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.

1998

1997

  • C. Bailey-Kellogg and F. Zhao, "Spatial aggregation: modeling and controlling physical fields," Proc. 11th International Workshop on Qualitative Reasoning, Italy, 1997. abstract. postscript.

1996

Proceedings Edited