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Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele…

Despite significant progress in dissecting the genetic architecture of complex diseases by genome-wide association studies (GWAS), the signals identified by association analysis may not have specific pathological relevance to diseases so…

Commonly-used clustering algorithms usually find ellipsoidal, spherical or other regular-structured clusters, but are more challenged when the underlying groups lack formal structure or definition. Syncytial clustering is the name that we…

Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…

Semantic similarity measures (SSMs) refer to a set of algorithms used to quantify the similarity of two or more terms belonging to the same ontology. Ontology terms may be associated to concepts, for instance in computational biology gene…

Acquiring, processing, and visualizing geospatial data requires significant computing resources, especially for large spatio-temporal domains. This challenge hinders the rapid discovery of predictive features, which is essential for…

In the last decade the broad scope of complex networks has led to a rapid progress. In this area a particular interest has the study of community structures. The analysis of this type of structure requires the formalization of the intuitive…

Convolutional Neural Networks (CNNs) have gained a remarkable success on many image classification tasks in recent years. However, the performance of CNNs highly relies upon their architectures. For most state-of-the-art CNNs, their…

Unsupervised clustering, also known as natural clustering, stands for the classification of data according to their similarities. Here we study this problem from the perspective of complex networks. Mapping the description of data…

Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…

Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…

Traditional clustering methods are limited when dealing with huge and heterogeneous groups of gene expression data, which motivates the development of bi-clustering methods. Bi-clustering methods are used to mine bi-clusters whose subsets…

High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…

Studying the effects of groups of Single Nucleotide Polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases, above that which can be gleaned from studying SNPs individually. Common…

Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…

Taking advantages of high-throughput genotyping technology of single nucleotide polymorphism (SNP), large genome-wide association studies (GWASs) have been considered as the promise to unravel the complex relationships between genotypes and…

The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the…

Because of the high cost of commercial genotyping chip technologies, many investigations have used a two-stage design for genome-wide association studies, using part of the sample for an initial discovery of ``promising'' SNPs at a less…

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe…