Related papers: Pervasive variation of transcription factor orthol…
Chromosomal inversions are structural mutations resulting in the reversal of the gene order along the corresponding genomic region. Due to their influence on recombination patterns, they can have a major influence on genetic variation and…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
Ciliopathies are a class of human diseases marked by dysfunction of the cellular organelle, cilia. While many of the molecular components that make up cilia have been identified and studied, comparatively little is understood about the…
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower…
We have performed a statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. The analysis reveals that operons that regulate each other and operons that are coregulated tend…
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
Gene regulatory networks present a wide variety of dynamical responses to intrinsic and extrinsic perturbations. Arguably, one of the most important of such coordinated responses is the one of amplification cascades, in which activation of…
Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria…
Cancer drug response varies widely across tumors due to multi-layer molecular heterogeneity, motivating computational decision support for precision oncology. Despite recent progress in deep CDR models, robust alignment between…
We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
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…
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…
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…
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…