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WABI
2001
Springer
142views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Pattern Matching and Pattern Discovery Algorithms for Protein Topologies
We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgrap...
Juris Viksna, David Gilbert
WABI
2001
Springer
112views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Finding an Optimal Inversion Median: Experimental Results
We derive a branch-and-bound algorithm to find an optimal inversion median of three signed permutations. The algorithm prunes to manageable size an extremely large search tree usi...
Adam C. Siepel, Bernard M. E. Moret
WABI
2001
Springer
110views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Boosting EM for Radiation Hybrid and Genetic Mapping
Radiation hybrid (RH) mapping is a somatic cell technique that is used for ordering markers along a chromosome and estimating physical distances between them. It nicely complements...
Thomas Schiex, Patrick Chabrier, Martin Bouchez, D...
WABI
2001
Springer
13 years 8 months ago
A Chemical-Distance-Based Test for Positive Darwinian Selection
There are very few instances in which positive Darwinian selection has been convincingly demonstrated at the molecular level. In this study, we present a novel test for detecting p...
Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Sham...
WABI
2001
Springer
13 years 8 months ago
The Performance of Phylogenetic Methods on Trees of Bounded Diameter
We study the convergence rates of neighbor-joining and several new phylogenetic reconstruction methods on families of trees of bounded diameter. Our study presents theoretically ob...
Luay Nakhleh, Usman Roshan, Katherine St. John, Je...
WABI
2001
Springer
124views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Computing Linking Numbers of a Filtration
We develop fast algorithms for computing the linking number of a simplicial complex within a filtration. We give experimental results in applying our work toward the detection of...
Herbert Edelsbrunner, Afra Zomorodian
WABI
2001
Springer
134views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Comparing Assemblies Using Fragments and Mate-Pairs
Using current technology, large consecutive stretches of DNA (such as whole chromosomes) are usually assembled from short fragments obtained by shotgun sequencing, or from fragment...
Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eu...
WABI
2001
Springer
138views Bioinformatics» more  WABI 2001»
13 years 8 months ago
Algorithms for Finding Gene Clusters
Abstract. Comparing gene orders in completely sequenced genomes is a standard approach to locate clusters of functionally associated genes. Often, gene orders are modeled as permut...
Steffen Heber, Jens Stoye
WABI
2001
Springer
162views Bioinformatics» more  WABI 2001»
13 years 8 months ago
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
A central issue in molecular biology is understanding the regulatory mechanisms that control gene expression. The recent flood of genomic and postgenomic data opens the way for co...
Yoseph Barash, Gill Bejerano, Nir Friedman