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FCCM
2007
IEEE
117views VLSI» more  FCCM 2007»
15 years 3 months ago
FPGA Acceleration of Gene Rearrangement Analysis
In this paper we present our work toward FPGA acceleration of phylogenetic reconstruction, a type of analysis that is commonly performed in the fields of systematic biology and co...
Jason D. Bakos
STOC
1995
ACM
194views Algorithms» more  STOC 1995»
15 years 1 months ago
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Genomes frequently evolve by reversals ␳(i, j) that transform a gene order ␲1 . . . ␲i␲iϩ1 . . . ␲jϪ1␲j . . . ␲n into ␲1 . . . ␲i␲jϪ1 . . . ␲iϩ1␲j . . ....
Sridhar Hannenhalli, Pavel A. Pevzner
RECOMB
2010
Springer
14 years 8 months ago
Limited Lifespan of Fragile Regions in Mammalian Evolution
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Althou...
Max A. Alekseyev, Pavel A. Pevzner
RECOMB
2006
Springer
15 years 10 months ago
A Parsimony Approach to Genome-Wide Ortholog Assignment
The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various...
Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang...
RECOMB
2002
Springer
15 years 10 months ago
Tests for gene clustering
Comparing chromosomal gene order in two or more related species is an important approach to studying the forces that guide genome organization and evolution. Linked clusters of si...
Dannie Durand, David Sankoff