E-mail: mchaisso@bioinf.ucsd.edu
Phone: (858) 822-5004
FAX:    (858) 534-7029
Office: CSE 4254

Mailing address:
Bioinformatics Program
University of California, San Diego
La Jolla, CA 92093-0412

Brief Biography:

• Ph.D. Student, Computer Science, University of California San Diego, 2002-present

Current projects:



• Fragment assembly with short reads: EULER v3.0.
• Phylogenetic reconstruction with rare characters: micro-inversions and indels.

Publications:


Mark J Chaisson, Haixu Tang, and Pavel A. Pevzner "Fragment assembly with short reads". Bioinformatics 20(13). (2004) pp 2067-74.

Mark J Chaisson, Benjamin J Raphael, and Pavel A. Pevzner "Microinversions in mammalian evolution". PNAS 103(52) (2006) pp 19824-9.

Mark J Chaisson and Pavel A Pevzner "Short Read Fragment Assembly of Bacterial Genomes". Genome Research. 18:324-330, 2008.

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Posters:


Mark J. Chaisson, Benjamin Raphael, Pavel A Pevzner. Micro-inversions in Mammalian Evolution. Algorithmic Biology. 2007. Best poster award.

Mark J. Chaisson, Dumitru Brinza, Pavel A Pevzner. Fragment Assembly with Short and Error-Prone Reads. ISMB 2008.

Presentations:


Fragment assembly with EULER-SR. Next Generation Sequencing SIG, ISMB 2008.