Related papers: Computational modeling of RNA-protein binding inte…

Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…

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…

RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…

Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…

We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…

CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…

Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. RNA-binding antiterminators are particularly important regulatory…

The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…

Physiological changes which result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Since the availability of RNA polymerase (RNAP) in cells is dependent on the…

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data,…

The intrinsic stochasticity of gene expression can lead to large variability in protein levels for genetically identical cells. Such variability in protein levels can arise from infrequent synthesis of mRNAs which in turn give rise to…

We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…

This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…

Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…

The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…

We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…

We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…

In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…