Related papers: Weak transcription factor clustering at binding si…

Deciphering how genes interpret information from the concentration of transcription factors (TFs) within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have unveiled the heterogeneous distribution of…

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…

A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…

We examine the binding of transcription factors to DNA in terms of an information transfer problem. The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA…

Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random…

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…

The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…

Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…

Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is…

Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…

Many membrane-bound molecules in cells form small clusters. It has been hypothesized that these clusters convert an analog extracellular signal into a digital intracellular signal and that this conversion increases signaling fidelity.…

We propose a novel classification model for weak signal data, building upon a recent model for Bayesian multi-view learning, Group Factor Analysis (GFA). Instead of assuming all data to come from a single GFA model, we allow latent…

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…

The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features…

Currently, data-driven discovery in biological sciences resides in finding segmentation strategies in multivariate data that produce sensible descriptions of the data. Clustering is but one of several approaches and sometimes falls short…

We propose a change-point detection method for large scale multiple testing problems with data having clustered signals. Unlike the classic change-point setup, the signals can vary in size within a cluster. The clustering structure on the…

It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…

Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…

In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…

Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription…