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BMCBI
2011
14 years 8 months ago
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
Background: The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progr...
Botond Sipos, Tim Massingham, Gregory E. Jordan, N...
IEEEPACT
2007
IEEE
15 years 8 months ago
Speculative Decoupled Software Pipelining
In recent years, microprocessor manufacturers have shifted their focus from single-core to multi-core processors. To avoid burdening programmers with the responsibility of paralle...
Neil Vachharajani, Ram Rangan, Easwaran Raman, Mat...
RECOMB
2006
Springer
16 years 2 months ago
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes
Micro-indels are small insertion or deletion events (indels) that occur during genome evolution. The study of micro-indels is important, both in order to better understand the unde...
Sagi Snir, Lior Pachter
HPCA
1999
IEEE
15 years 6 months ago
Instruction Recycling on a Multiple-Path Processor
Processors that can simultaneously execute multiple paths of execution will only exacerbate the fetch bandwidth problem already plaguing conventional processors. On a multiple-pat...
Steven Wallace, Dean M. Tullsen, Brad Calder
IPPS
2010
IEEE
15 years 7 days ago
Fast Smith-Waterman hardware implementation
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is alw...
Zubair Nawaz, Koen Bertels, Huseyin Ekin Sumbul