Object Recognition Using Subspace Methods. - Daniel P. Huttenlocher; Ryan H. Lilien; Clark F. Olson (ECCV (1), 1996)

View-Based Recognition Using an Eigenspace Approximation to the Hausdorff Measure. - Daniel P. Huttenlocher; Ryan H. Lilien; Clark F. Olson (IEEE Trans. Pattern Anal. Mach. Intell., 1999)

Physical Geometric Algorithms for Structural Molecular Biology. - Bruce Randall Donald; Christopher Bailey-Kellogg; Jack Kelley; Ryan H. Lilien (ICRA, 2001)

An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings. - Lincong Wang; Ramgopal R. Mettu; Ryan H. Lilien; Bruce Randall Donald (CSB, 2003)

Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. - Christopher James Langmead; Anthony K. Yan; Ryan H. Lilien; Lincong Wang; Bruce Randall Donald (RECOMB, 2003)

Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum. - Ryan H. Lilien; Hany Farid; Bruce Randall Donald (J. Comput. Biol., 2003)

A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. - Christopher James Langmead; Anthony K. Yan; Ryan H. Lilien; Lincong Wang; Bruce Randall Donald (J. Comput. Biol., 2004)

Optimization and dynamics of protein-protein complexes using B-splines. - Richard E. Gillilan; Ryan H. Lilien (J. Comput. Chem., 2004)

High-throughput inference of protein-protein interfaces from unassigned NMR data. - Ramgopal R. Mettu; Ryan H. Lilien; Bruce Randall Donald (ISMB (Supplement of Bioinformatics), 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 Randall Donald (J. Comput. Biol., 2005)

Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. - Ivelin Georgiev; Ryan H. Lilien; Bruce Randall Donald (ISMB (Supplement of Bioinformatics), 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 Randall Donald (RECOMB, 2006)

Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. - Clifton Forlines; Ryan H. Lilien (AVI, 2008)

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 H. Lilien; Bruce Randall Donald (J. Comput. Chem., 2008)

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. - Izhar Wallach; Ryan H. Lilien (Bioinform., 2009)

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. - Izhar Wallach; Ryan H. Lilien (Bioinform., 2009)

Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses. - Izhar Wallach; Ryan H. Lilien (J. Chem. Inf. Model., 2009)

A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy. - Navdeep Jaitly; Marcus A. Brubaker; John L. Rubinstein; Ryan H. Lilien (Bioinform., 2010)

Restricted dead-end elimination: Protein redesign with a bounded number of residue mutations. - Maria Safi; Ryan H. Lilien (J. Comput. Chem., 2010)

Applying Medicinal Chemistry Transformations and Multiparameter Optimization to Guide the Search for High-Quality Leads and Candidates. - Matthew D. Segall; Edmund J. Champness; Chris Leeding; Ryan H. Lilien; Ramgopal R. Mettu; Brian W. Stevens (J. Chem. Inf. Model., 2011)

Normalizing Molecular Docking Rankings using Virtually Generated Decoys. - Izhar Wallach; Navdeep Jaitly; Kong T. Nguyen; Matthieu Schapira; Ryan H. Lilien (J. Chem. Inf. Model., 2011)

Virtual Decoy Sets for Molecular Docking Benchmarks. - Izhar Wallach; Ryan H. Lilien (J. Chem. Inf. Model., 2011)

Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA. - Maria Safi; Ryan H. Lilien (J. Chem. Inf. Model., 2012)