Related papers: Kerfuffle: a web tool for multi-species gene coloc…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
It is widely accepted that traditional modular structures suffer from the dominant decomposition problem. Therefore, to improve current modularity views, it is important to investigate the impact of design decisions concerning modularity in…
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
To understand complex biological systems, the research community has produced huge corpus of gene expression data. A large number of clustering approaches have been proposed for the analysis of gene expression data. However, extracting…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
We introduce CoHiRF (Consensus Hierarchical Random Features), a hierarchical consensus framework that enables existing clustering methods to operate beyond their usual computational and memory limits. CoHiRF is a meta-algorithm that…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
Species complexes are groups of closely related populations exchanging genes through dispersal. We study the dynamics of the structure of species complexes in a class of metapopulation models where demes can exchange genetic material…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
Literature analysis is a key step in obtaining background information in biomedical research. However, it is difficult for researchers to obtain knowledge of their interests in an efficient manner because of the massive amount of the…
Background: Mining gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. In this work, we explore the plausibility of detecting gene modules by…
Clustering is one of the main tasks in exploratory data analysis and descriptive statistics where the main objective is partitioning observations in groups. Clustering has a broad range of application in varied domains like climate,…
A general method to obtain a representation of the structural landscape of nanoparticles in terms of a limited number of variables is proposed. The method is applied to a large dataset of parallel tempering molecular dynamics simulations of…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential…
Inaccuracies in conventional dependency-tracking methods frequently undermine the security and integrity of modern software supply chains. This paper introduces a kernel-level framework leveraging extended Berkeley Packet Filter (eBPF) to…