Related papers: DNA methylation heterogeneity induced by collabora…
DNA-based biodiversity surveys involve collecting physical samples from survey sites and assaying the contents in the laboratory to detect species via their diagnostic DNA sequences. DNA-based surveys are increasingly being adopted for…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
The ability to significantly enhance energy transfer processes at the nanoscale requires the simultaneous optimization of molecular-scale orientation and macroscopic photonic enhancement between multiple quantum emitters. However, achieving…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
Measuring natural selection on genomic elements involved in the cis-regulation of gene expression -- such as transcriptional enhancers and promoters -- is critical for understanding the evolution of genomes, yet it remains a major…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
DNA samples crime cases analysed in forensic genetics, frequently contain DNA from multiple contributors. These occur as convolutions of the DNA profiles of the individual contributors to the DNA sample. Thus, in cases where one or more of…
Bulk tissue RNA sequencing of heterogeneous samples provides averaged gene expression profiles, obscuring cell type-specific dynamics. To address this, we present a probabilistic hierarchical Bayesian model that deconvolves bulk RNA-seq…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
When simulating metabolite productions with genome-scale constraint-based metabolic models, gene deletion strategies are necessary to achieve growth-coupled production, which means cell growth and target metabolite production occur…
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53…