Search Results - "Gusfield, Dan"

Linear time algorithms for finding and representing all the tandem repeats in a string by Gusfield, Dan, Stoye, Jens

“…A tandem repeat (or square) is a string αα, where α is a non-empty string. We present an O(| S|)-time algorithm that operates on the suffix tree T( S) for a…”
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Constructing perfect phylogenies and proper triangulations for three-state characters by Gysel, Rob, Lam, Fumei, Gusfield, Dan

“…: In this paper, we study the problem of constructing perfect phylogenies for three-state characters. Our work builds on two recent results. The first result…”
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A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem by Ding, Zhihong, Filkov, Vladimir, Gusfield, Dan

“…Since the introduction of the Perfect Phylogeny Haplotyping (PPH) Problem in RECOMB 2002 (Gusfield, 2002), the problem of finding a linear-time (deterministic,…”
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The Multi-State Perfect Phylogeny Problem with missing and removable data: solutions via integer-programming and chordal graph theory by Gusfield, Dan

“…The Multi-State Perfect Phylogeny Problem is an extension of the Binary Perfect Phylogeny Problem, allowing characters to take on more than two states. In this…”
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An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding by Frid, Yelena, Gusfield, Dan

“…The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known [Formula: see…”
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Partition-distance: A problem and class of perfect graphs arising in clustering by Gusfield, Dan

“…Partitioning of a set of elements into disjoint clusters is a fundamental problem that arises in many applications. Different methods produce different…”
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Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination by Gusfield, Dan

“…Phylogenetic networks are models of sequence evolution that go beyond trees, allowing biological operations that are not consistent with tree-like evolution…”
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Editorial by Gusfield, Dan, Tramontano, Anna

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Editorial by Gusfield, Dan, Tramontano, Anna

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Editorial by Gusfield, Dan, Tramontano, Anna

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Editorial by Gusfield, Dan, Tramontano, Anna

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Editorial by Gusfield, Dan, Tramontano, Anna

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A Resolution of the Static Formulation Question for the Problem of Computing the History Bound by Matsieva, Julia, Kelk, Steven, Scornavacca, Celine, Whidden, Chris, Gusfield, Dan

“…Evolutionary data has been traditionally modeled via phylogenetic trees; however, branching alone cannot model conflicting phylogenetic signals, so networks…”
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Faster algorithms for RNA-folding using the Four-Russians method by Venkatachalam, Balaji, Gusfield, Dan, Frid, Yelena

“…The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n3)…”
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Final, Five-Year End, Editorial by Gusfield, Dan

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Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics by Gusfield, Dan

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A simple, practical and complete O(n3/log n)-time algorithm for RNA folding using the Four-Russians speedup by Frid, Yelena, Gusfield, Dan

“…The problem of computationally predicting the secondary structure (or folding) of RNA molecules was first introduced more than thirty years ago and yet…”
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EIC Editorial by Gusfield, Dan

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Inference of haplotypes from samples of diploid populations: complexity and algorithms by Gusfield, D

“…The next phase of human genomics will involve large-scale screens of populations for significant DNA polymorphisms, notably single nucleotide polymorphisms…”
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An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study by Gusfield, Dan, Hickerson, Dean, Eddhu, Satish

“…Phylogenetic networks are models of sequence evolution that go beyond trees, allowing biological operations that are not tree-like. One of the most important…”
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