相关论文: Multiscale Identification of Topological Domains i…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
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…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…
Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. One specific feature of the 3D organization is known as topologically associating domains (TADs), which are…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
A connected component labeling algorithm is developed for implicitly-defined domains specified by multivariate polynomials. The algorithm operates by recursively subdividing the constraint domain into hyperrectangular subcells until the…
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is…
Over the years, web content has evolved from simple text and static images hosted on a single server to a complex, interactive and multimedia-rich content hosted on different servers. As a result, a modern website during its loading time…
Unsupervised domain adaptation algorithms aim to transfer the knowledge learned from one domain to another (e.g., synthetic to real images). The adapted representations often do not capture pixel-level domain shifts that are crucial for…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
In numerous functional materials, such as steels, ferroelectrics and magnets, new functionalities can be achieved through the engineering of the domain structures, which are associated with the ordering of certain parameters within the…
Top-tier parallel computing clusters continue to accumulate more and more computational power with more and better CPUs and Networks. This allows, especially for environmental simulations, computations with larger domain sizes and better…
Spatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form \textit{spatial domains}. Specialized ST clustering algorithms have been developed…
The intricate interplay of structural, charge and spin orders in layered cuprates leads to emergent phenomena, most notably high-temperature superconductivity. However, there is growing awareness that both the structure and electronic…
Topology is a powerful tool for categorizing magnetization textures by defining a topological index in both two-dimensional (2D) systems, such as thin films or curved surfaces, and in 3D bulk systems. In the emerging field of 3D…