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Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome…
Many real-world heterogeneous graphs exhibit pronounced heterophily, where connected nodes often have dissimilar labels or play different semantic roles. In such settings, standard heterogeneous graph neural networks that aggregate messages…
Hickson Compact Groups (HCGs) are dense configurations of 4 to 10 galaxies, whose HI (neutral gas) morphology appears to follow an evolutionary sequence of three phases, with gas initially confined to galaxies, then significant amounts…
Tumor growth is constrained by spatial, mechanical, and metabolic factors whose alignment progressively breaks down across cellular, mesoscopic, and tissue scales as tumors expand. We hypothesize that this misalignment drives tumors toward…
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
There has been an increasing focus in learning interpretable feature representations, particularly in applications such as medical image analysis that require explainability, whilst relying less on annotated data (since annotations can be…
In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones…
Evolutionary Reinforcement Learning (ERL), training the Reinforcement Learning (RL) policies with Evolutionary Algorithms (EAs), have demonstrated enhanced exploration capabilities and greater robustness than using traditional policy…
Recent discovery of high-temperature superconductivity (Tc = 190 K) in sulfur hydrides at megabar pressures breaks the traditional belief on the Tc limit of 40 K for conventional superconductors, and open up the doors in searching new…
A morphogenic protein known as Dorsal patterns the embryonic dorsoventral body axis of Drosophila by binding to transcriptional enhancers across the genome. Each such enhancer activates a neighboring gene at a unique threshold concentration…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
Graph Representation Learning (GRL) is an influential methodology, enabling a more profound understanding of graph-structured data and aiding graph clustering, a critical task across various domains. The recent incursion of attention…
The relative strength of different proximity spin-orbit couplings in graphene on transition metal dichalcogenides (TMDC) can be tuned via the metal composition in the TMDC layer. While Gr/MoSe$_2$, has a normal gap, proximity to WSe$_2$…
Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…
A quantitative phase analysis of substrate-free single-component and binary clusters of the Ar-Kr system obtained by adiabatic expansion of gas into vacuum through a supersonic nozzle was performed. The studies were carried out in-situ…
Attributed graph clustering, which aims to group the nodes of an attributed graph into disjoint clusters, has made promising advancements in recent years. However, most existing methods face challenges when applied to large graphs due to…
A time-resolved synchrotron X-ray total scattering study sheds light on the evolution of the different structural length scales involved during the intercalation of the layered iron-selenide host by organic molecular donors, aiming at the…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
Metallic transition metal dichalcogenides (TMDs), consisting of H-NbSe$_2$, H-NbS$_2$, H-TaSe$_2$ and H-TaS$_2$, remain superconducting down to a thickness of a single layer. In these materials, thickness affects a variety of properties,…