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WABI
2010
Springer
168views Bioinformatics» more  WABI 2010»
10 years 1 months ago
The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree
Abstract. A recursive algorithm by Aho, Sagiv, Szymanski, and Ullman [1] forms the basis for many modern rooted supertree methods employed in Phylogenetics. However, as observed by...
Jesper Jansson, Richard S. Lemence, Andrzej Lingas
WABI
2010
Springer
178views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Haplotype Inference on Pedigrees with Recombinations and Mutations
Abstract. Haplotype Inference (HI) is a computational challenge of crucial importance in a range of genetic studies, such as functional genomics, pharmacogenetics and population ge...
Yuri Pirola, Paola Bonizzoni, Tao Jiang
WABI
2010
Springer
141views Bioinformatics» more  WABI 2010»
10 years 2 months ago
An Experimental Study of Quartets MaxCut and Other Supertree Methods
Although many supertree methods have been developed in the last few decades, none has been shown to produce more accurate trees than the popular Matrix Representation with Parsimon...
M. Shel Swenson, Rahul Suri, C. Randal Linder, Tan...
WABI
2010
Springer
188views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
Abstract. We present three heuristic strategies for folding RNA sequences into secondary structures including kissing hairpin motifs. The new idea is to construct a kissing hairpin...
Corinna Theis, Stefan Janssen, Robert Giegerich
WABI
2010
Springer
170views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Haplotypes versus Genotypes on Pedigrees
Abstract. Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping...
Bonnie Kirkpatrick
WABI
2010
Springer
160views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Genomic Distance with DCJ and Indels
The double cut and join (DCJ) operation, introduced by Yancopoulos, Attie and Friedberg in 2005, allows one to represent most rearrangement events in genomes. However, a DCJ cannot...
Marília D. V. Braga, Eyla Willing, Jens Sto...
WABI
2010
Springer
177views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data
In this paper we present a novel expectation-maximization algorithm for inference of alternative splicing isoform frequencies from high-throughput transcriptome sequencing (RNA-Seq...
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Al...
WABI
2010
Springer
124views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Improved Orientations of Physical Networks
Abstract. The orientation of physical networks is a prime task in deciphering the signaling-regulatory circuitry of the cell. One manifestation of this computational task is as a m...
Iftah Gamzu, Danny Segev, Roded Sharan
WABI
2010
Springer
128views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Sparsification of RNA Structure Prediction Including Pseudoknots
Background: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space con...
Mathias Möhl, Raheleh Salari, Sebastian Will,...
WABI
2010
Springer
143views Bioinformatics» more  WABI 2010»
10 years 2 months ago
Swiftly Computing Center Strings
The center string (or closest string) problem is a classical computer science problem with important applications in computational biology. Given k input strings and a distance thr...
Franziska Hufsky, Léon Kuchenbecker, Kathar...
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