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The combination of modelling and experimental advances can provide deep insights for understanding chromatin 3D organization and ultimately its underlying mechanisms. In particular, models of polymer physics can help comprehend the complexity of genomic contact maps, as those emerging from technologies such as Hi-C, GAM or SPRITE. Here we discuss a method to reconstruct 3D structures from Genome Architecture Mapping (GAM) data, based on PRISMR, a computational approach introduced to find the minimal polymer model best describing Hi-C input data from only polymer physics. After recapitulating the PRISMR procedure, we describe how we extended it for treating GAM data. We successfully test the method on a 6Mb region around the Sox9 gene and, at a lower resolution, on the whole chromosome 7 in mouse embryonic stem cells. The PRISMR derived 3D structures from GAM co-segregation data are finally validated against independent Hi-C contact maps. The method results to be versatile and robust, hinting that it can be similarly applied to different experimental data, such as SPRITE or microscopy distance data.
This article was published in the following journal.
Name: Methods (San Diego, Calif.)
The problem of three-dimensional (3D) chromosome structure inference from Hi-C data sets is important and challenging. While bulk Hi-C data sets contain contact information derived from millions of ce...
In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that c...
HLA*LA implements a new graph alignment model for HLA type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99%...
There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid-state N...
We report the results of a study that examines the effects of trivalent Yb impurities occupying different sites in cubic Gd2O3 on the latter's structure and vibrational spectrum. The shell model is em...
Office hysteroscopy is the gold standard technique in the diagnosis of the intrauterine pathologies. Some interventions may also be carried out through the hysteroscopy. No-touch hysterosc...
Computational simulation will be performed to represent motion of knees with a dislocating kneecap. Common surgical treatment methods will be simulated and anatomical parameters commonly a...
Recent adolescent-based research shows that inference making improves across grades 6-12, uniquely accounts for variance in sentence- and passage-level comprehension, and that individual d...
Our vision, that of the researchers at the University of Texas Health Science Center at San Antonio, is that every person with a chromosome 18 abnormality will have an autonomous and healt...
In this study, 20 COPD patients will undergo a high-resolution/multi slice CT scan and lung function tests to obtain patient specific geometries of the central and peripheral small airways...
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories applicable to MOLECULAR BIOLOGY and areas of computer-based techniques for solving biological problems including manipulation of models and datasets.
Protective measures against unauthorized access to or interference with computer operating systems, telecommunications, or data structures, especially the modification, deletion, destruction, or release of data in computers. It includes methods of forestalling interference by computer viruses or so-called computer hackers aiming to compromise stored data.
Structures which are contained in or part of CHROMOSOMES.
The study of the characteristics, behavior, and internal structures of the atomic nucleus and its interactions with other nuclei. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Clinical conditions caused by an abnormal sex chromosome constitution (SEX CHROMOSOME ABERRATIONS) in which there is extra or missing sex chromosome material (either a whole chromosome or a chromosome segment).
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
Track and monitor developments in stem cell research and commercial development. Follow the tabs above to read the latest global news, research, clinical trials on stem cells and follow companies active in the stem cell industry. BioPort...