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Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Tactile sensing remains far less understood in neuroscience and less effective in artificial systems compared to more mature modalities such as vision and language. We bridge these gaps by introducing a novel Encoder-Attender-Decoder (EAD)…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Equiatomic TaNbHfZr and TaNbHfZrTi high-entropy alloys (HEAs) have been investigated for their phase stability, short-range clustering (SRC) type chemical ordering, other structural phenomena and and the effects on strengthening. Ab-initio…
Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome. Results: We compiled…
Graph neural networks (GNNs) have been widely used in deep learning on graphs. They can learn effective node representations that achieve superior performances in graph analysis tasks such as node classification and node clustering.…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Using radio data at 1.4 GHz from the ATCA we identify five head-tail (HT) galaxies in the central region of the Horologium-Reticulum Supercluster (HRS). Physical parameters of the HT galaxies were determined along with substructure in the…
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants, and provided clear evidence of recent rapid…
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are…
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be…
Graph embeddings play a critical role in graph representation learning, allowing machine learning models to explore and interpret graph-structured data. However, existing methods often rely on opaque, high-dimensional embeddings, limiting…
Synchrotron radiation images from runaway electrons (REs) in an ASDEX Upgrade discharge disrupted by argon injection are analyzed using the synchrotron diagnostic tool SOFT and coupled fluid-kinetic simulations. We show that the evolution…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Numerous diseases, particularly autoimmune disorders, are associated with the human leukocyte antigen (HLA), a small genomic region located on human chromosome 6. Adequate characterization of linkage disequilibrium (LD) in the HLA across…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…