| 2014 | RECOMB | Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. | Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg |
| 2012 | RECOMB | Ballast: A Ball-Based Algorithm for Structural Motifs. | Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2012 | RECOMB | Structure-Guided Deimmunization of Therapeutic Proteins. | Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2011 | KDD | Using physicochemical properties of amino acids to induce graphical models of residue couplings. | K. S. M. Tozammel Hossain, Chris Bailey-Kellogg, Alan M. Friedman, Michael J. Bradley, Nathan A. Baker, Naren Ramakrishnan |
| 2011 | RECOMB | A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. | Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald |
| 2011 | RECOMB | Optimization of Combinatorial Mutagenesis. | Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2009 | RECOMB | Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. | Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg |
| 2008 | ISMB | Contact replacement for NMR resonance assignment. | Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2008 | RECOMB | Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. | Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg |
| 2007 | BIBE | A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. | Fei Xiong, Chris Bailey-Kellogg |
| 2006 | RECOMB | Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. | Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg |
| 2006 | WAFR | Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints. | Shobha Potluri, Anthony K. Yan, James J. Chou, Bruce Randall Donald, Chris Bailey-Kellogg |
| 2005 | ECCB | Reconsidering complete search algorithms for protein backbone NMR assignment. | Olga Vitek, Chris Bailey-Kellogg, Bruce A. Craig, Paul Kuliniewicz, Jan Vitek |
| 2005 | KDD | Graphical models of residue coupling in protein families. | John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg |
| 2005 | SDM | Gaussian Processes for Active Data Mining of Spatial Aggregates. | Naren Ramakrishnan, Chris Bailey-Kellogg, Satish Tadepalli, Varun Pandey |
| 2004 | AAAI | Spatial Aggregation for Qualitative Assessment of Scientific Computations. | Chris Bailey-Kellogg, Naren Ramakrishnan |
| 2004 | PSB | Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. | Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg |
| 2004 | RECOMB | A random graph approach to NMR sequential assignment. | Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan |