Related papers: Characteristics of transposable element exonizatio…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
It has been recently argued that the depletion attraction may play an important role in different aspects of the cellular organization, ranging from the organization of transcriptional activity in transcription factories to the formation of…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Tungsten (W) is widely considered as the most promising plasma facing material (PFM), which will be used in nuclear fusion devices. Due to the transmutation reaction caused by the fusion neutron irradiation, transmutation elements (such as…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
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…
Deep learning has proven to successfully learn variations in tissue and cell morphology. Training of such models typically relies on expensive manual annotations. Here we conjecture that spatially resolved gene expression, e.i., the…
Impurities play an important role during recombination processes in semiconductors. Their important role is sharpened in atomically-thin transition-metal dichalcogenides whose two-dimensional character renders electrons and holes highly…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Transposons are small, self-replicating DNA sequences found in every branch of life. Often, one transposon will parasitize another, forming a tiny intracellular ecosystem. In some species these ecosystems thrive, while in others they go…
RNA editing by members of the double-stranded RNA-specific ADAR family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential…
A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and…
This article studies the solutions of time-dependent differential inclusions which is motivated by their utility in the modeling of certain physical systems. The differential inclusion is described by a time-dependent set-valued mapping…
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single…
This work examines the presence of modularity in pre-trained Transformers, a feature commonly found in human brains and thought to be vital for general intelligence. In analogy to human brains, we consider two main characteristics of…
Recently, different works proposed a new way to mine patterns in databases with pathological size. For example, experiments in genome biology usually provide databases with thousands of attributes (genes) but only tens of objects…
In this article, I put forward the idea that the neoplastic process (NP) has deep evolutionary roots and make specific predictions about the connection between cancer and the formation of the first embryo, which allowed for the evolutionary…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…