Related papers: Robust haplotype-resolved assembly of diploid indi…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
Haplotyping is the bioinformatics problem of predicting likely haplotypes based on given genotypes. It can be approached using Gusfield's perfect phylogeny haplotyping (PPH) method for which polynomial and linear time algorithms exist.…
Motivation: Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin…
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…
Microarray technology is known as one of the most important tools for collecting DNA expression data. This technology allows researchers to investigate and examine types of diseases and their origins. However, microarray data are often…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
This paper presents a new clustering algorithm for space-time data based on the concepts of topological data analysis and in particular, persistent homology. Employing persistent homology - a flexible mathematical tool from algebraic…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Biclustering is an unsupervised machine-learning approach aiming to cluster rows and columns simultaneously in a data matrix. Several biclustering algorithms have been proposed for handling numeric datasets. However, real-world data mining…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Given a set of data, biclustering aims at finding simultaneous partitions in biclusters of its samples and of the features which are used for representing the samples. Consistent biclusterings allow to obtain correct classifications of the…
Recent matrix completion based methods have not been able to properly model the Haplotype Assembly Problem (HAP) for noisy observations. To cope with such a case, in this letter we propose a new Minimum Error Correction (MEC) based matrix…
Privacy computing involves the extensive exchange and processing of encrypted data. For the parties involved in these interactions, how to determine the consistency of exchanged data without accessing the original data, ensuring tamper…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…