JCVI: About / Bios / Brian Walenz
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Brian Walenz
Sr. Software Engineer

Research Interests and Accomplishments

Brian Walenz is a Senior Software Engineer at the J. Craig Venter Institute. He is the lead software engineer for the Celera Assembler, primarily responsible for developing algorithms to incorporate next generation sequencing data. He has developed genome comparison and high throughput cDNA/EST alignment software at Celera, and contributed to protein folding research at Sandia National Laboratories. Mr. Walenz received his Master's degree in computer science from the University of New Mexico and his Bachelor's degree in computer engineering and computer science from Iowa State University. 

Select Publications

Koren S, Schatz MC, et al.
Hybrid Error Correction and De Novo Assembly of Single-molecule Sequencing Reads.

Nature biotechnology. 2012 Jul 01; 30: 693-700.[more]

Gillespie, J. J., Joardar, V., et al.
A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight Into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle.

Journal of bacteriology. 2012 Jan 01; 194(2): 376-94.[more]

Walenz, B., Florea, L.
Sim4db and Leaff: Utilities for Fast Batch Spliced Alignment and Sequence Indexing

Bioinformatics. 2011 May 06;[more]

Koren, S., Miller, J. R., et al.
An Algorithm for Automated Closure During Assembly

BMC Bioinformatics. 2010 Sep 10; 11: 457.[more]

Miller, J. R., Delcher, A. L., et al.
Aggressive Assembly of Pyrosequencing Reads With Mates

Bioinformatics. 2008 Oct 28; 24(24): 2818-24.[more]

Denisov, G., Walenz, B., et al.
Consensus Generation and Variant Detection by Celera Assembler

Bioinformatics. 2008 Apr 15; 24(8): 1035-40.[more]

Levy, S., Sutton, G., et al.
The Diploid Genome Sequence of an Individual Human

PLoS Biol. 2007 Sep 04; 5(10): e254.[more]

Dew IM, Walenz B, et al.
A Tool for Analyzing Mate Pairs In Assemblies (TAMPA).

Journal of computational biology : a journal of computational molecular cell biology. 2005 Jun 01; 12: 497-513.[more]

Istrail, S., Sutton, G. G., et al.
Whole-genome Shotgun Assembly and Comparison of Human Genome Assemblies

Proc Natl Acad Sci U S A. 2004 Feb 17; 101(7): 1916-21.[more]