Related papers: Spectral-based detection of chromatin loops in mul…
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…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
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…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated…
Spectral clustering is a popular method for community detection in network graphs: starting from a matrix representation of the graph, the nodes are clustered on a low dimensional projection obtained from a truncated spectral decomposition…
Autonomous synthesis and characterization of inorganic materials requires the automatic and accurate analysis of X-ray diffraction spectra. For this task, we designed a probabilistic deep learning algorithm to identify complex multi-phase…
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…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
Cognitive radio is a potential solution to meet the upcoming spectrum crunch issue. In a cognitive radio, spectrum holes can be identified using spectrum sensing techniques. A high resolution spectrum hole detection can ensure even the…
We investigate numerically the time evolution of velocity and magnetic field fluctuations in a coronal loop, focusing on the dynamics due to both phase mixing and turbulent cascade. The intensity, doppler velocity and non-thermal broadening…
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,…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Numerous networked systems feature a structure of nontrivial communities, which often correspond to their functional modules. Such communities have been detected in real-world biological, social and technological systems, as well as in…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Several items on the diagnostics and interpretation of coronal loop observations are under debate. In this work, we analyze a well-defined loop system detected in a time-resolved observation in several spectral bands. The dataset includes…
The determination of chemical mixture components is vital to a multitude of scientific fields. Oftentimes spectroscopic methods are employed to decipher the composition of these mixtures. However, the sheer density of spectral features…