Related papers: Adaptive evolution of transcription factor binding…
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…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
Evolutionary trajectories and phenotypic states available to cell populations are ultimately dictated by intermolecular interactions between DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in…
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…
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…
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…
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…
We develop revised theoretical ideas on the mechanism by which the transcription factor proteins locate their specific binding sites on DNA faster than the three-dimensional (3D) diffusion controlled rate limit. We demonstrate that the…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…
Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is…
Somatic mutations in cancer cells affect various genomic elements disrupting important cell functions. In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and expression…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
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 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…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
We present a simple and efficient method for prediction of transcription factor binding sites from DNA sequence. Our method computes a random approximation of a convolutional kernel feature map from DNA sequence and then learns a linear…