Related papers: GOLEM: distribution of Gene regulatOry eLEMents wi…
The discovery of motifs underlying gene expression is a challenging one. Some of these motifs are known transcription factors, but sequence inspection often provides valuable clues, even discovery of novel motifs with uncharacterized…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
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…
BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets…
Our aim is to predict how often genic and non-genic promoters fire within a cell. We first review a parsimonious pan-genomic model for genome organization and gene regulation, where transcription rate is determined by proximity in 3D space…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
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…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
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…
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium ${\it Escherichia coli}$, for $\approx$ 65$\%$ of the promoters we remain completely ignorant of…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
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,…
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…
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…
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…