MAXAMIZE. A DNA sequencing strategy advisor. - René Bach; Peter Friedland; Douglas L. Brutlag; Laurence H. Kedes (Nucleic Acids Res., 1982)

SEQ: a nucleotide sequence analysis and recombination system. - Douglas L. Brutlag; J. Clayton; Peter Friedland; Laurence H. Kedes (Nucleic Acids Res., 1982)

GENESIS, a knowledge-based genetic engineering simulation system for representation of genetic data and experiment planning. - Peter Friedland; Laurence H. Kedes; Douglas L. Brutlag; Yumi Iwasaki; René Bach (Nucleic Acids Res., 1982)

Rapid searches for complex patterns in biological molecules. - R. M. Abarbanel; Paul R. Wieneke; E. Mansfield; David A. Jaffe; Douglas L. Brutlag (Nucleic Acids Res., 1984)

BIONET: national computer resource for molecular biology. - Dennis H. Smith; Douglas L. Brutlag; Peter Friedland; Laurence H. Kedes (Nucleic Acids Res., 1986)

Improved sensitivity of biological sequence database searches. - Douglas L. Brutlag; Jean-Pierre Dautricourt; S. Maulik; J. Relph (Comput. Appl. Biosci., 1990)

Knowledge-based simulation of DNA metabolism: prediction of enzyme action. - Douglas L. Brutlag; A. R. Galper; D. H. Millis (Comput. Appl. Biosci., 1991)

On Suboptimal Alignments of Biological Sequences. - Dalit Naor; Douglas L. Brutlag (CPM, 1993)

Detection of Correlations in tRNA Sequences with Structural Implications. - Tod M. Klingler; Douglas L. Brutlag (ISMB, 1993)

BLAZETM: An Implementation of the Smith-Waterman Sequence Comparison Algorithm on a Massively Parallel Computer. - Douglas L. Brutlag; Jean-Pierre Dautricourt; Ron Diaz; Jeff Fier; Bruce Moxon; Richard Stamm (Comput. Chem., 1993)

Discovering Side-Chain Correlations In alpha-Helices. - Tod M. Klingler; Douglas L. Brutlag (ISMB, 1994)

On Near-Optimal Alignments of Biological Sequences. - Dalit Naor; Douglas L. Brutlag (J. Comput. Biol., 1994)

Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning Techniques. - Thomas D. Wu; Douglas L. Brutlag (ISMB, 1995)

Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families. - Thomas D. Wu; Douglas L. Brutlag (ISMB, 1996)

Enumerating and Ranking Discrete Motifs. - Craig G. Nevill-Manning; Komal S. Sethi; Thomas D. Wu; Douglas L. Brutlag (ISMB, 1997)

Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations. - Amit Pal Singh; Douglas L. Brutlag (ISMB, 1997)

Viewpoint: Directions for Clinical Research and Genomic Research into the Next Decade: Implications for Informatics. - Thomas C. Rindfleisch; Douglas L. Brutlag (J. Am. Medical Informatics Assoc., 1998)

Regression Analysis of Multiple Protein Structures. - Thomas D. Wu; Scott C. Schmidler; Trevor Hastie; Douglas L. Brutlag (J. Comput. Biol., 1998)

A Motion Planning Approach to Flexible Ligand Binding. - Amit Pal Singh; Jean-Claude Latombe; Douglas L. Brutlag (ISMB, 1999)

Minimal-Risk Scoring Matrices for Sequence Analysis. - Thomas D. Wu; Craig G. Nevill-Manning; Douglas L. Brutlag (J. Comput. Biol., 1999)

Fast probabilistic analysis of sequence function using scoring matrices. - Thomas D. Wu; Craig G. Nevill-Manning; Douglas L. Brutlag (Bioinform., 2000)

Bayesian Segmentation of Protein Secondary Structure. - Scott C. Schmidler; Jun S. Liu; Douglas L. Brutlag (J. Comput. Biol., 2000)

Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps. - Mehmet Serkan Apaydin; Amit Pal Singh; Douglas L. Brutlag; Jean-Claude Latombe (ICRA, 2001)

BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. - X. Liu; Douglas L. Brutlag; Jun S. Liu (Pacific Symposium on Biocomputing, 2001)

The EMOTIF database. - Jimmy Y. Huang; Douglas L. Brutlag (Nucleic Acids Res., 2001)

Stochastic roadmap simulation for the study of ligand-protein interactions. - Mehmet Serkan Apaydin; Carlos Guestrin; Chris Varma; Douglas L. Brutlag; Jean-Claude Latombe (ECCB, 2002)

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 (ECCB, 2002)

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 (RECOMB, 2002)

Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion. - Mehmet Serkan Apaydin; Douglas L. Brutlag; Carlos Guestrin; David Hsu; Jean-Claude Latombe (WAFR, 2002)

Automatic Construction of 3D Structural Motifs for Protein Function Prediction. - Mike P. Liang; Douglas L. Brutlag; Russ B. Altman (CSB, 2003)

Remote homology detection: a motif based approach. - Asa Ben-Hur; Douglas L. Brutlag (ISMB (Supplement of Bioinformatics), 2003)

Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. - Mike P. Liang; Douglas L. Brutlag; Russ B. Altman (Pacific Symposium on Biocomputing, 2003)

3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. - Steven P. Bennett; Craig G. Nevill-Manning; Douglas L. Brutlag (Bioinform., 2003)

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; Chris Varma (J. Comput. Biol., 2003)

3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. - Steven P. Bennett; Lin Lu; Douglas L. Brutlag (Nucleic Acids Res., 2003)

WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures. - Mike P. Liang; D. Rey Banatao; Teri E. Klein; Douglas L. Brutlag; Russ B. Altman (Nucleic Acids Res., 2003)

Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale. - Haidong Wang; Eran Segal; Asa Ben-Hur; Daphne Koller; Douglas L. Brutlag (NIPS, 2004)

A suite of web-based programs to search for transcriptional regulatory motifs. - Yueyi Liu; Liping Wei; Serafim Batzoglou; Douglas L. Brutlag; Jun S. Liu; Xiaole Shirley Liu (Nucleic Acids Res., 2004)

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. - Jessica Shapiro; Douglas L. Brutlag (Nucleic Acids Res., 2004)

Computational functional genomics. - Mike P. Liang; Olga G. Troyanskaya; Alain Laederach; Douglas L. Brutlag; Russ B. Altman (IEEE Signal Process. Mag., 2004)

Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site. - Edward J. Bertaccini; Jessica Shapiro; Douglas L. Brutlag; James R. Trudell (J. Chem. Inf. Model., 2005)

eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. - Qiaojuan Jane Su; Lin Lu; Serge Saxonov; Douglas L. Brutlag (Nucleic Acids Res., 2005)

Sequence Motifs: Highly Predictive Features of Protein Function. - Asa Ben-Hur; Douglas L. Brutlag (Feature Extraction, 2006)

MotifCut: regulatory motifs finding with maximum density subgraphs. - Eugene Fratkin; Brian T. Naughton; Douglas L. Brutlag; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2006)

Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. - Tsung-Han Chiang 001; Mehmet Serkan Apaydin; Douglas L. Brutlag; David Hsu; Jean-Claude Latombe (RECOMB, 2006)

Development and validation of a consistency based multiple structure alignment algorithm. - Jessica Ebert; Douglas L. Brutlag (Bioinform., 2006)

Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values. - Tsung-Han Chiang 001; Mehmet Serkan Apaydin; Douglas L. Brutlag; David Hsu; Jean-Claude Latombe (J. Comput. Biol., 2007)