• "Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA." Maria Safi, Ryan Lilien, Journal of Chemical Information and Modeling, 52(6):1529-41 (2012).
• "Applying Medicinal Chemistry Transformations and Multiparameter Optimization to Guide the Search for High-Quality Leads and Candidates." Matthew Segall, Ed Champness, Chris Leeding, Ryan Lilien, Ram Mettu, Brian Stevens, Journal of Chemical Information and Modeling, 51(11):2967-76 (2011).
• "Normalizing Molecular Docking Rankings using Virtually Generated Decoys." Izhar Wallach, Navdeep Jaitly, Kong Nguyen, Matthieu Schapira, Ryan Lilien, Journal of Chemical Information and Modeling, 51(8):1817-30 (2011).
• "Virtual Decoy Sets for Molecular Docking Benchmarks." Izhar Wallach, Ryan Lilien, Journal of Chemical Information and Modeling, 51(2):196-202 (2011).
• "A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy." Navdeep Jaitly, Marcus Brubaker, John Rubinstein, Ryan Lilien, Bioinformatics, 26(19):2406-15 (2010).
• "A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways." Izhar Wallach, Navdeep Jaitly, Ryan Lilien, PLoS ONE, 5(8):1-11 (2010).
• "LigAlign: Flexible Ligand-Based Active Site Alignment and Analysis." Abraham Heifets, Ryan Lilien, Journal of Molecular Modeling and Graphics, 29(1):93-101 (2010).
• "Restricted Dead-End Elimination: Protein Redesign with a Bounded Number of Residue Mutations." Maria Mirza, Ryan Lilien, Journal of Computational Chemistry, 31(6):1207-15 (2010).
• "Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses." Izhar Wallach, Ryan Lilien, Journal of Chemical Information and Modeling, 49(9):2116-28 (2009).
• "Prediction of Sub-Cavity Binding Preferences Using an Adaptive Physiochemical Structure Representation." Izhar Wallach, Ryan Lilien, Bioinformatics, 25:i296-304 (2009).
     Article also appeared as:
     "Prediction of Sub-Cavity Binding Preferences Using an Adaptive Physiochemical
     Structure Representation." Izhar Wallach, Ryan Lilien, Proc. International Conference
     on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, (2009).
• "The Protein-Small-Molecule Database: A Non-Redundant Structural Resource for the Analysis of Protein-Ligand Binding." Izhar Wallach, Ryan Lilien, Bioinformatics, 25(5):615-20 (2009).
• "The Minimized Dead-End Elimination Criterion and its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles." Ivelin Georgiev, Ryan Lilien, Bruce Donald, Journal of Computational Chemistry, 29(10):1527-42 (2008).
• "Adapting a Single-user, Single-display Molecular Visualization Application for Use in a Multi-user, Multi-display Environment." Clifton Forlines, Ryan Lilien, Proc. Advanced Visual Interfaces (AVI), Napoli, Italy, 367-71 (2008).
• "Allosteric Inhibition of the Protein-Protein Interaction between the Leukemia-Associated Proteins Runx1 and CBFB." Michael Gorczynski, Jolanta Grembecka, Yunpeng Zhou, Yali Kong, Liya Roudaia, Michael Douvas, Miki Newman, Izabela Bielnicka, Gwen Baber, Takeshi Corpora, Jianxia Shi, Mohini Sridharan, Ryan Lilien, Bruce Donald, Nancy Speck, Milton Brown, John Bushweller, Chemistry & Biology, 14(10):1186-97 (2007).
• "Redesigning the PheA Domain of Gramicidin Synthetase Leads to a New Understanding of the Enzyme's Mechanism and Selectivity." Brian Stevens, Ryan H. Lilien, Ivelin Georgiev, Bruce R. Donald, Amy C. Anderson, Biochemistry, 45(51):15495-15504 (2006).
• "Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End Elimination, with Application to Protein Design." Ivelin Georgiev, Ryan H. Lilien, Bruce R. Donald, Bioinformatics, 22(14):e174-183 (2006). [PDF]
     Article also appeared as:
     "Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End
     Elimination, with Application to Protein Design.", Proc. International Conference
     on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, (2006)
• "A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles." Ivelin Georgiev*, Ryan H. Lilien*, Bruce R. Donald, Proc. The Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy, pp 530-545 (2006). *contributed equally
• "High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data." Ramgopal R. Mettu, Ryan H. Lilien, Bruce R. Donald, Bioinformatics, 21(Suppl. 1):i292-i301 (2005). [PDF]
     Article also appeared as:
     "High-Throughput Inference of Protein-Protein Interfaces from Unassigned
     NMR Data." Proc. International Conference on Intelligent Systems for
     Molecular Biology (ISMB), Detroit, MI, (2005).
• "A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme." Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce R. Donald, Journal of Computational Biology, 12(6-7):740-761 (2005). [PDF]
     Article also appeared as:
     "A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign,
     and its Application to Modify the Substrate Specificity of the Gramicidin
     Synthetase A Phenylalanine Adenylation Enzyme." Proc. The Eighth Annual
     International Conference on Research in Computational Molecular Biology
     (RECOMB), San Diego, pp 46-57 (2004).
• "A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry." Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald, Acta Crystallographica D: Biological Crystallography, 60:1057-1067 (2004). [PDF]
• "Optimization and Dynamics of Protein-Protein Complexes Using B-Splines." Richard E. Gillilan, Ryan H. Lilien, Journal of Computational Chemistry, 25(13):1630-1646 (2004).
• "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments." Christopher J. Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce R. Donald, Journal of Computational Biology, 11:277-298 (2004).
     Article also appeared as:
     "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated
     NMR Resonance Assignments." Proc. The Seventh Annual International
     Conference on Research in Computational Molecular Biology (RECOMB),
     Berlin, pp 176-186 (2003). [PDF]
• "Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme dihydrofolate reductase-thymidylate synthase." Rob H. O'Neil, Ryan H. Lilien, Bruce R. Donald, Robert M. Stroud, Amy C. Anderson, Journal of Biological Chemistry, 278(52):52980-52987 (2003). [PDF]
• "The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme." Rob H. O'Neil, Ryan H. Lilien, Bruce R. Donald, Robert M. Stroud, Amy C. Anderson, Journal of Eukaryotic Microbiology, Supplement to Volume 50:555-556 (2003).
• "An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings." Lincong Wang, Ramgopal R. Mettu, Ryan H. Lilien, Bruce R. Donald, Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto CA, pp 611-612 (2003). (Poster) *Winner of Best Poster Award* [PDF]
• "Hemopericardium and Cardiac Tamponade as Presenting Findings of Dexamethasone-Induced Hypertrophic Cardiomyopathy Complicated by Transmural Myocardial Infarction." L.D. Lilien, R.H. Lilien, S. Setrakian, Pediatric Cardiology, 24:280-283 (2003).
• "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum." Ryan H. Lilien, Hany Farid, and Bruce R. Donald, Journal of Computational Biology, 10(6):925-946 (2003). [PDF]
• "Physical Geometric Algorithms for Structural Molecular Biology." Chris Bailey-Kellogg, John J. Kelley III, Ryan Lilien, and Bruce Randall Donald, Invited paper at the Special Session on Computational Biology and Chemistry, International Conference on Robotics and Automation Seoul, Korea, pp 940-947 (2001). [PDF]
• "View-Based Recognition Using an Eigenspace Approximation to the Hausdorff Measure." Daniel Huttenlocher, Ryan Lilien, and Clark Olson, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol 21:9:951-955 (Sept 1999). [PDF]
• "Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment." Trevor Hart, Richard Gillilan, Ryan Lilien, Steven Ness, and Randy Read, High Performance Computing Systems and Applications, pp 299-308. Kluwer Academic Publisher (Summer 1998).
• "Tetramerization of RXR: Dynamics of Molecular Assemblies at Atomic Resolution Using RIGIN Hierarchical B-Splines." Richard Gillilan, Ryan Lilien, BL Atancio, HV Shah, Journal of Molecular Graphics & Modeling, Vol 16(4-6):285-285 (1998).
• "Object Recognition Using Subspace Methods." Daniel Huttenlocher, Ryan Lilien, and Clark Olson, Proceedings of the European Conference on Computer Vision, pp 536-545 (1996).

• "The Dartmouth CPR Score: A New Clinical Prediction Rule to Determine In-Hospital CPR Survival Based on Patient’s Pre-Arrest Characteristics." Hilary F. Ryder, Ryan H. Lilien, Frances C. Brokaw, SGIM 30th Annual Meeting, Toronto ON (April 2007). Published in The Journal of General Internal Medicine, Vol 22(Suppl. 1):10-11 (2007).
• "Exact Solutions for Vectors and Dihedral Angles from Two RDCs and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure." Lincong Wang, Ramgopal R Mettu, Ryan H Lilien, Anthony Yan, Bruce R Donald, Computational Aspects - Biomolecular NMR (Gordon Research Conference), Ventura CA (January 2004).
• "Ensembles of active site conformations allow structure-based redesign and drug design." Amy C Anderson, Ryan H Lilien, Veljko Popov, Bruce R Donald, 225th American Chemical Society National Meeting, New Orleans LA (March 2003).
• "Modeling Protein Flexibility for Structure-Based Active Site Redesign." Ryan H. Lilien, Amy C. Anderson, and Bruce R. Donald, The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). In Currents in Computational Molecular Biology, 2002 (ed. L. Florea et al.) pp 122-123 (2002).
• "Modeling of Protein Flexibility for Computational Active Site Redesign." Ryan H Lilien, Amy C Anderson, and Bruce R. Donald, The 16th Annual MD/PhD Conference, Given Institute, Aspen CO (July 2001).
• "Computational Screening Studies for Core Binding Factor Beta: Use of Multiple Conformations to Model Receptor Flexibility." Ryan Lilien, Mohini Sridharan, Xuemei Huang, John Bushweller, and Bruce Donald, The 8th International Conference on Intelligent Systems for Molecular Biology (ISMB-2000), San Diego CA (August 2000).
• "Monte Carlo Docking of Flexible Ligands in a Virtual Reality Environment." Ryan H. Lilien, Carlos H. Faerman, Trevor N. Hart, and Richard E. Gillilan, Fall Symposium of the American Society for Biochemistry and Molecular Biology. Conference title: "Computational Biology - Methods in Biomolecular Imaging" Whistler, B.C. (October 25-28, 1996).

• Crystal structure of Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) from Cryptosporidium hominis, (R. O'Neil, R. Lilien, B. Donald, R. Stroud, and A. Anderson), PDB ID: [1QZF].

• "Identification of Novel Small Molecule Inhibitors of Core-Binding Factor Dimerization by Computational Screening against NMR Molecular Ensembles." Ryan H. Lilien, Mohini Sridharan, Bruce R. Donald, Dartmouth Computer Science Department Technical Report TR2004-492 (2004). [PDF]