Related papers: Inferring evolutionary histories of pathway regula…

Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…

It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…

Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…

Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…

Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…

Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…

Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…

Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation…

Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…

The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses…

Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…

Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…

We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…

It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…

For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to…

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…

The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…