Related papers: Minimum error correction-based haplotype assembly:…
The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their…
Microscopy images contain rich information about how cells respond to perturbations, making them essential to applications like drug screening. To quantify images, researchers often use representation extraction methods, and recent years…
The goal of the trace reconstruction problem is to recover a string $x\in\{0,1\}^n$ given many independent {\em traces} of $x$, where a trace is a subsequence obtained from deleting bits of $x$ independently with some given probability…
This paper introduces Multi-population Ensemble Genetic Programming (MEGP), a computational intelligence framework that integrates cooperative coevolution and the multiview learning paradigm to address classification challenges in…
We explore the application of concepts developed in High Energy Physics (HEP) for advanced medical data analysis. Our study case is a problem with high social impact: clinically-feasible Magnetic Resonance Fingerprinting (MRF). MRF is a…
Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the…
Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome…
Semantic segmentation of electron microscopy (EM) images of biological samples remains a challenge in the life sciences. EM data captures details of biological structures, sometimes with such complexity that even human observers can find it…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
Understanding the applicability and limitations of electronic-structure methods needs careful and efficient comparison with accurate reference data. Knowledge of the quality and errors of electronic-structure calculations is crucial to…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
A deterministic mutation-selection model in the sequence space approach is investigated. Genotypes are identified with two-letter sequences. Mutation is modelled as a Markov process, fitness functions are of Hopfield type, where the fitness…
Biometric data is often highly sensitive, and a leak of this data can lead to serious privacy breaches. Some of the most sensitive of this type of data relates to the usage of DNA data on individuals. A leak of this type of data without…
We propose a new sparse estimation method, termed MIC (Minimum approximated Information Criterion), for generalized linear models (GLM) in fixed dimensions. What is essentially involved in MIC is the approximation of the $\ell_0$-norm with…
Precise measurements of $b\to c\tau\bar\nu$ decays require large resource-intensive Monte Carlo (MC) samples, which incorporate detailed simulations of detector responses and physics backgrounds. Extracted parameters may be highly sensitive…
Binary measurements arise naturally in a variety of statistical and engineering applications. They may be inherent to the problem---e.g., in determining the relationship between genetics and the presence or absence of a disease---or they…
Region-based methods have proven necessary for improving segmentation accuracy of neuronal structures in electron microscopy (EM) images. Most region-based segmentation methods use a scoring function to determine region merging. Such…
With the aim to propose a non parametric hypothesis test, this paper carries out a study on the Matching Error (ME), a comparison index of two partitions obtained from the same data set, using for example two clustering methods. This index…