Related papers: Robust haplotype-resolved assembly of diploid indi…
While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is only viable when variants are relatively rare and the bubbles…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…
We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require…
The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasing on pedigrees. Despite several algorithmic advances and…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
We propose a novel clustering pipeline that combines two classic clustering algorithms to better understand student problem-solving strategies. This unsupervised machine learning method helps uncover patterns in reasoning without…
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without…
Chromosome capture techniques like Hi-C have expanded our understanding of mammalian genome 3D architecture and how it influences gene activity. To analyze Hi-C data sets, researchers increasingly treat them as DNA-contact networks and use…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…