Related papers: GenHap: A Novel Computational Method Based on Gene…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Homomorphic permutation is fundamental to privacy-preserving computations based on batch-encoding homomorphic encryption. It underpins nearly all homomorphic matrix operations and predominantly influences their complexity. Permutation…
We propose a homotopy sampling procedure, loosely based on importance sampling. Starting from a known probability distribution, the homotopy procedure generates the unknown normalization of a target distribution. In the context of…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
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…
Genome Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. GWAS typically use a p-value threshold of 5 x 10-8 to identify highly ranked single nucleotide polymorphisms…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…
We describe a new method (HOP) for identifying groups of particles in N-body simulations. Having assigned to every particle an estimate of its local density, we associate each particle with the densest of the N_hop particles nearest to it.…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Quadratic Assignment Problem (QAP) is an NP-hard combinatorial optimization problem, therefore, solving the QAP requires applying one or more of the meta-heuristic algorithms. This paper presents a comparative study between Meta-heuristic…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
The Partitioning Min-Max Weighted Matching (PMMWM) problem, being a practical NP-hard problem, integrates the task of partitioning the vertices of a bipartite graph into disjoint sets of limited size with the classical Maximum-Weight…
Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges.…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…