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RECOMB
2006
Springer
10 years 11 months ago
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in
Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fu...
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H...
RECOMB
2006
Springer
10 years 11 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
RECOMB
2006
Springer
10 years 11 months ago
Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data
Permutation of class labels is a common approach to build null distributions for significance analyis of microarray data. It is assumed to produce random score distributions, which...
Stefanie Scheid, Rainer Spang
RECOMB
2006
Springer
10 years 11 months ago
A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric
The Robinson-Foulds (RF) metric is the measure most widely used in comparing phylogenetic trees; it can be computed in linear time using Day's algorithm. When faced with the n...
Nicholas D. Pattengale, Bernard M. E. Moret
RECOMB
2006
Springer
10 years 11 months ago
Alignment Statistics for Long-Range Correlated Genomic Sequences
It is well known that the base composition along eukaryotic genomes is long-range correlated. Here, we investigate the effect of such long-range correlations on alignment score sta...
Philipp W. Messer, Ralf Bundschuh, Martin Vingron,...
RECOMB
2006
Springer
10 years 11 months ago
Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence
Abstract. We describe and empirically evaluate machine learning methods for the prediction of zinc binding sites from protein sequences. We start by observing that a data set consi...
Sauro Menchetti, Andrea Passerini, Paolo Frasconi,...
RECOMB
2006
Springer
10 years 11 months ago
An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets
Steffen Grossmann, Sebastian Bauer, Peter N. Robin...
RECOMB
2006
Springer
10 years 11 months ago
Simple and Fast Inverse Alignment
For as long as biologists have been computing alignments of sequences, the question of what values to use for scoring substitutions and gaps has persisted. While some choices for s...
John D. Kececioglu, Eagu Kim
RECOMB
2006
Springer
10 years 11 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
2006
Springer
10 years 11 months ago
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies
Abstract. Pharmacogenomics and clinical studies that measure the temporal expression levels of patients can identify important pathways and biomarkers that are activated during dis...
Naftali Kaminski, Ziv Bar-Joseph
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