Related papers: Modelling the evolution of transcription factor bi…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting,…
We consider integrative modeling of multiple gene networks and diverse genomic data, including protein-DNA binding, gene expression and DNA sequence data, to accurately identify the regulatory target genes of a transcription factor (TF).…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…
Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
We developed a method for estimating the positional distribution of transcription fac-tor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs; OCT4, SOX2, NANOG, HNF1A,…
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The…
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…
The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…
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…
We discuss two new approaches to extract relevant biological information on the Transcription Factors (and in particular to identify their binding sequences) from the statistical distribution of oligonucleotides in the upstream region of…
The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…