相关论文: Exploring 3D community inconsistency in human chro…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
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…
Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of…
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…
Chromosome capture techniques like Hi-C have expanded our understanding of mammalian genome 3D architecture and how it influences gene activity. To analyze Hi-C data sets, researchers increasingly treat them as DNA-contact networks and use…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
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…
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…
Community detection plays a pivotal role in uncovering closely connected subgraphs, aiding various real-world applications such as recommendation systems and anomaly detection. With the surge of rich information available for entities in…
Complex data in social and natural sciences find effective representation through networks, wherein quantitative and categorical information can be associated with nodes and connecting edges. The internal structure of networks can be…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
Finding meaningful communities - subnetworks of interest within a large scale network - is a problem with a variety of applications. Most existing work towards community detection focuses on a single network. However, many real-life…
The detection of community structure is probably one of the hottest trends in complex network research as it reveals the internal organization of people, molecules or processes behind social, biological or computer networks\dots The issue…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
We consider a community finding problem called Co-located Community Detection (CCD) over geo-social networks, which retrieves communities that satisfy both high structural tightness and spatial closeness constraints. To provide a solution…
The spatial transcriptomics (ST) data produced by recent biotechnologies, such as CosMx and Xenium, contain huge amount of information about cancer tissue samples, which has great potential for cancer research via detection of community: a…
Community detection is a cornerstone problem in social network analysis (SNA), aimed at identifying cohesive communities with minimal external links. However, the rise of generative AI and Metaverse introduce complexities by creating hybrid…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
High-resolution point clouds~(HRPCD) anomaly detection~(AD) plays a critical role in precision machining and high-end equipment manufacturing. Despite considerable 3D-AD methods that have been proposed recently, they still cannot meet the…