| 2006 | ISMB | MotifCut: regulatory motifs finding with maximum density subgraphs. | Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou |
| 2006 | RECOMB | Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. | Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe |
| 2003 | ISMB | Remote homology detection: a motif based approach. | Asa Ben-Hur, Douglas L. Brutlag |
| 2003 | PSB | Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. | Mike P. Liang, Douglas L. Brutlag, Russ B. Altman |
| 2002 | ECCB | Stochastic roadmap simulation for the study of ligand-protein interactions. | Mehmet Serkan Apaydin, Carlos Guestrin, Chris Varma, Douglas L. Brutlag, Jean-Claude Latombe |
| 2002 | ECCB | Using robotics to fold proteins and dock ligands. | Douglas L. Brutlag, Mehmet Serkan Apaydin, Carlos Guestrin, David Hsu, Chris Varma, Amit Pal Singh, Jean-Claude Latombe |
| 2002 | RECOMB | Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. | Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe |
| 2002 | WAFR | Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion. | Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe |
| 2001 | ICRA | Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps. | Mehmet Serkan Apaydin, Amit Pal Singh, Douglas L. Brutlag, Jean-Claude Latombe |
| 2001 | PSB | BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. | X. Liu, Douglas L. Brutlag, Jun S. Liu |
| 1999 | ISMB | A Motion Planning Approach to Flexible Ligand Binding. | Amit Pal Singh, Jean-Claude Latombe, Douglas L. Brutlag |
| 1998 | RECOMB | Regression analysis of multiple protein structures. | Thomas D. Wu, Trevor Hastie, Scott C. Schmidler, Douglas L. Brutlag |
| 1997 | ISMB | Enumerating and Ranking Discrete Motifs. | Craig G. Nevill-Manning, Komal S. Sethi, Thomas D. Wu, Douglas L. Brutlag |
| 1997 | ISMB | Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations. | Amit Pal Singh, Douglas L. Brutlag |
| 1996 | ISMB | Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families. | Thomas D. Wu, Douglas L. Brutlag |
| 1995 | ISMB | Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning Techniques. | Thomas D. Wu, Douglas L. Brutlag |
| 1994 | ISMB | Discovering Side-Chain Correlations In alpha-Helices. | Tod M. Klingler, Douglas L. Brutlag |
| 1993 | CPM | On Suboptimal Alignments of Biological Sequences. | Dalit Naor, Douglas L. Brutlag |
| 1993 | ISMB | Detection of Correlations in tRNA Sequences with Structural Implications. | Tod M. Klingler, Douglas L. Brutlag |