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  High-Performance Algorithm Engineering
  and Computational Molecular Biology

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Internal Use
Dr. Nick Pattengale is a former student of Prof. Bernard Moret in Computer Science.

  • Publications
    • Parallelized phylogenetic post-analysis on multi-core architectures - Journal of Computational Science
    • Uncovering Hidden Phylogenetic Consensus - Proc. 5th Int'l Symp. on Bioinformatics Research and Applications ISBRA'10, accepted, to appear - (available as a UNM Tech Report PDF)
    • Parallel Computation of Phylogenetic Consensus Trees - Proc. 10th Int'l Conf. Computational Science ICCS'10, accepted, to appear - (available as a rapid pre-release TUM Tech Report PDF)
    • How Many Bootstrap Replicates are Necessary? - Journal of Computational Biology, Special Issue for Best Papers from RECOMB 2009
    • How Many Bootstrap Replicates are Necessary? - Paper presented at RECOMB 2009 (PDF)
    • Higher Fidelity Subtree Merging for Disk-Covering Methods - Poster (PDF) and extended abstract (PDF) presented at Algorithmic Biology 2006
    • Efficiently Computing the Robinson-Foulds Metric - Journal of Computational Biology, August 12 2007 [vol 14 issue 6] (PDF)
    • A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric - Paper presented at RECOMB06 (PDF)
    • A Framework for Orthology Assignment from Gene Rearrangement Data - Paper presented at RECOMBCG 2005. (PDF)
    • Phylogenetic Postprocessing - Extended Abstract (two pages) for poster presented at CSB 2005 (PDF).
    • Tools For Phylogenetic Postprocessing - Master's Thesis (PDF or postscript)
    • Algorithmic Decomposition of Most Parsimonious Sets - Poster (PDF or postscript) and abstract (PDF or postscript ) presented at 2004 Mt. Baldy Conference on Geometry, Algebra, and Phylogenetic Trees
  • Software
    • Download FastRF, as mentioned in 'Efficiently Computing the Robinson-Foulds Metric' (above).
    • Download the Sublinear Robinson-Foulds Approximation, hopefully this will be integrated into TreeViz soon, as it was designed to do so.
  • Personal webpage

email: nickp@cs.unm.edu

Department of Computer Science
Farris Engineering Center
University of New Mexico
Albuquerque, NM 87131

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