Related papers: Superimposed Hi-C: A Solution Proposed for Identif…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
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…
Motivation: Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C…
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,…
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…
Hyperspectral image (HI) analysis approaches have recently become increasingly complex and sophisticated. Recently, the combination of spectral-spatial information and superpixel techniques have addressed some hyperspectral data issues,…
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…
Photonic biosensors that use optical resonances to amplify signals from refractive index changes offer high-sensitivity, real-time readout, and scalable, low-cost fabrication. However, when used with classic affinity assays they struggle…
Chromosome recognition is an essential task in karyotyping, which plays a vital role in birth defect diagnosis and biomedical research. However, existing classification methods face significant challenges due to the inter-class similarity…
The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features…
Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF and STAT1, identifies non-random…
Motivation: Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin…
The goal of this paper is Human-object Interaction (HO-I) detection. HO-I detection aims to find interacting human-objects regions and classify their interaction from an image. Researchers obtain significant improvement in recent years by…
Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH…
Drug repositioning offers an effective solution to drug discovery, saving both time and resources by finding new indications for existing drugs. Typically, a drug takes effect via its protein targets in the cell. As a result, it is…
Cell recognition is a fundamental task in digital histopathology image analysis. Point-based cell recognition (PCR) methods normally require a vast number of annotations, which is extremely costly, time-consuming and labor-intensive.…
Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is…
We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
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…