Resolving genomes at haplotype level is crucial for understanding the evolutionary history of
polyploid species and for designing advanced breeding strategies. Polyploid phasing still …

Phasing, and in particular polyploid phasing, have been challenging problems held back by
the limited read length of high-throughput short read sequencing methods which can't …

Understanding genetic variation, eg, through mutations, in organisms is crucial to unravel
their effects on the environment and human health. A fundamental characterization can be …

Reconstructing components of a genomic mixture from data obtained by means of DNA
sequencing is a challenging problem encountered in a variety of applications including …

Background Haplotypes, the ordered lists of single nucleotide variations that distinguish
chromosomal sequences from their homologous pairs, may reveal an individual's …

Resolving haplotypes in polyploid genomes using phase information from sequencing reads
is an important and challenging problem. We introduce two new mathematical formulations …

Background Single individual haplotype problem refers to reconstructing haplotypes of an
individual based on several input fragments sequenced from a specified chromosome …

Haplotype assembly and viral quasispecies reconstruction are challenging tasks concerned
with analysis of genomic mixtures using sequencing data. High-throughput sequencing …

We apply matrix completion methods for haplotype assembly from NGS reads to develop the
new HapSVT, HapNuc, and HapOPT algorithms. This is performed by applying a …

Reconstructing haplotypes of an organism from a set of sequencing reads is a
computationally challenging (NP-hard) problem. In reference-guided settings, at the core of …