Algorithmic strategies in combinatorial chemistry. - Deborah Goldman; Sorin Istrail; Giuseppe Lancia; Antonio Piccolboni; Brian Walenz (SODA, 2000)

Visualization challenges for a new cyberpharmaceutical computing paradigm. - Russell J. Turner; Kabir Chaturvedi; Nathan Edwards; Daniel P. Fasulo; Aaron L. Halpern; Daniel H. Huson; Oliver Kohlbacher; Jason R. Miller; Knut Reinert; Karin A. Remington; Russell Schwartz; Brian Walenz; et al. (IEEE Symposium on Parallel and Large-Data Visualization and Graphics, 2001)

101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. - Giuseppe Lancia; Robert D. Carr; Brian Walenz; Sorin Istrail (RECOMB, 2001)

1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap. - Alberto Caprara; Robert D. Carr; Sorin Istrail; Giuseppe Lancia; Brian Walenz (J. Comput. Biol., 2004)

A Tool for Analyzing Mate Pairs in Assemblies (TAMPA). - Ian M. Dew; Brian Walenz; Granger G. Sutton (J. Comput. Biol., 2005)

A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data. - Ross A. Lippert; Clark M. Mobarry; Brian Walenz (J. Comput. Biol., 2005)

Consensus generation and variant detection by Celera Assembler. - Gennady Denisov; Brian Walenz; Aaron L. Halpern; Jason R. Miller; Nelson Axelrod; Samuel Levy; Granger G. Sutton (Bioinform., 2008)

Aggressive assembly of pyrosequencing reads with mates. - Jason R. Miller; Arthur L. Delcher; Sergey Koren; Eli Venter; Brian Walenz; Anushka Brownley; Justin Johnson 002; Kelvin Li; Clark M. Mobarry; Granger G. Sutton (Bioinform., 2008)

An algorithm for automated closure during assembly. - Sergey Koren; Jason R. Miller; Brian Walenz; Granger G. Sutton (BMC Bioinform., 2010)

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. - Brian Walenz; Liliana Florea (Bioinform., 2011)

Integrating Hi-C links with assembly graphs for chromosome-scale assembly. - Jay Ghurye; Arang Rhie; Brian Walenz; Anthony D. Schmitt; Siddarth Selvaraj; Mihai Pop; Adam M. Phillippy; Sergey Koren (PLoS Comput. Biol., 2019)

Weighted minimizer sampling improves long read mapping. - Chirag Jain; Arang Rhie; Haowen Zhang; Claudia Chu; Brian Walenz; Sergey Koren; Adam M. Phillippy (Bioinform., 2020)