Paul Medvedev

Postdoctoral Scholar University of California, San Diego Department of Computer Science and Engineering 9500 Gilman Drive, MC0404 La Jolla, CA, 92093-0404, USA Office: EBU3b 4212 (CSE Building) Email: pmedvedev at cs dot ucsd dot edu Phone : (858) 534-5340

• I am on the job market, let me know if you are interested!
• Please consider submitting to RECOMB-seq, a satellite workshop on sequencing which I am co-chairing.

About

My research falls at the interface of biology and theoretical computer science, specifically in problems where rigorous algorithms and analysis can have a demonstrated impact in the biological sciences. My main focus has been on genome assembly and variation detection, though I am interested in a variety of areas such as phylogenetics, graph theory, computational complexity, on-line algorithms, and networking.

Currently, I am a postdoc with Pavel Pevzner in UC San Diego. I received my Ph.D. at the University of Toronto under the supervision of Michael Brudno and Allan Borodin. During that time, I also visited Bielefeld University for a year, working with Jens Stoye. Prior to that, I did my M.Sc. at the University of Southern Denmark under the supervision of Joan Boyar.

Curriculum Vitae

Software

• Hammer : error-correction of high-throughput sequencing datasets
• CNVer : method for detecting copy number variation
• Bidirected network flow solver (download).

Selected Publications

• Paul Medvedev, Eric Scott, Boyko Kakaradov, and Pavel Pevzner, Error correction of high-throughput sequencing datasets with non-uniform coverage, ISMB 2011.
• Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler and Pavel Pevzner, Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers, RECOMB 2011.
• The Plane-Width of Graphs, with Marcin Kaminski and Martin Milanic, Journal of Graph Theory, 2011.
• Paul Medvedev, Marc Fiume, Misko Dzamba, Tim Smith, Michael Brudno, Detecting Copy Number Variation with Mated Short Reads, Genome Research, 2010.
• Paul Medvedev, Monica Stanciu, Michael Brudno, Computational Methods for Discovering Structural Variation with Next Generation Sequencing, Nature Methods, 2009.

See the full list here