The investigation of genetic differences among humans has given evidence that mutations
in DNA sequences are responsible for some genetic diseases. The most common mutation …

We present an O (mn) algorithm to determine whether a graph G with m edges and n
vertices has an odd cycle transversal of order at most k, for any fixed k. We also obtain an …

Motivation: The goal of the haplotype assembly problem is to reconstruct the two haplotypes
(chromosomes) for an individual using a mix of sequenced fragments from the two …

Genome sequencing studies to date have generally sought to assemble consensus
genomes by merging sequence contributions from multiple homologous copies of each …

Determining the underlying haplotypes of individual human genomes is an essential, but
currently difficult, step toward a complete understanding of genome function. Fosmid pool …

Genome assembly methods produce haplotype phase ambiguous assemblies due to
limitations in current sequencing technologies. Determining the haplotype phase of an …

In comparison to genotypes, knowledge about haplotypes (the combination of alleles
present on a single chromosome) is much more useful for whole-genome association …

Motivation: Haplotype reconstruction based on aligned single nucleotide polymorphism
(SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered …

This is a survey designed for mathematical programming people who do not know molecular
biology and want to learn the kinds of combinatorial optimization problems that arise. After a …

Motivation: Haplotypes have been attracting increasing attention because of their
importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing …