scholarly journals Boost-HiC : Computational enhancement of long-range contacts in chromosomal contact maps

2018 ◽  
Author(s):  
L. Carron ◽  
J.B. Morlot ◽  
Matthys V. ◽  
A. Lesne ◽  
J. Mozziconacci
Keyword(s):  
Long Range ◽  
Short Range ◽  
Missing Information ◽  
High Confidence ◽  
Contact Maps ◽  
Link Type ◽  
Genome Wide ◽  
Contact Frequency ◽  
Algorithmic Procedure

AbstractGenome-wide chromosomal contact maps are widely used to uncover the 3D organisation of genomes. They rely on the collection of millions of contacting pairs of genomic loci. Contact frequencies at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts.We propose to use the sparse information contained in raw contact maps to determine high-confidence contact frequency between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library. Boost-HiC can also be used to compare contact maps at an improved resolution.Boost-HiC is available at https://github.com/LeopoldC/Boost-HiC

scholarly journals Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps

2019 ◽  
Vol 35 (16) ◽  
pp. 2724-2729 ◽  
Author(s):  
L Carron ◽  
J B Morlot ◽  
V Matthys ◽  
A Lesne ◽  
J Mozziconacci
Keyword(s):  
Long Range ◽  
Short Range ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Missing Information ◽  
High Confidence ◽  
Contact Maps ◽  
Genome Wide ◽  
Algorithmic Procedure

Abstract Motivation Genome-wide chromosomal contact maps are widely used to uncover the 3D organization of genomes. They rely on collecting millions of contacting pairs of genomic loci. Contacts at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts. Results We propose to use the sparse information contained in raw contact maps to infer high-confidence contact counts between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library. Boost-HiC can also be used to compare contact maps at an improved resolution. Availability and implementation Boost-HiC is available at https://github.com/LeopoldC/Boost-HiC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

2016 ◽  
Author(s):  
Koon-Kiu Yan ◽  
Galip Guürkan Yardimci ◽  
William S. Noble ◽  
Mark Gerstein
Keyword(s):  
Spectral Analysis ◽  
Data Structures ◽  
Spectral Decomposition ◽  
Source Code ◽  
Cell Types ◽  
Proximity Ligation ◽  
Contact Maps ◽  
Link Type ◽  
Genome Wide ◽  
Different Cell Types

AbstractSummaryGenome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition. The metric successfully separates contact maps mapped from Hi-C data coming from biological replicates, pseudo-replicates and different cell types.AvailabilitySource code in Julia and the documentation of HiC-spector can be freely obtained athttps://github.com/gersteinlab/[email protected]

scholarly journals Structural basis of long-range to short-range synaptic transition in NHEJ

Nature ◽  
2021 ◽  
Author(s):  
Siyu Chen ◽  
Linda Lee ◽  
Tasmin Naila ◽  
Susan Fishbain ◽  
Annie Wang ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Basis

scholarly journals Comparison of short-range order in irradiated dysprosium titanates

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Roman Sherrod ◽  
Eric C. O’Quinn ◽  
Igor M. Gussev ◽  
Cale Overstreet ◽  
Joerg Neuefeind ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Model ◽  
Ion Irradiation ◽  
Function Analysis ◽  
Ion Beam ◽  
Structural Response ◽  
Heavy Ion ◽  
Range Order ◽  
Radiation Resistant

AbstractThe structural response of Dy2TiO5 oxide under swift heavy ion irradiation (2.2 GeV Au ions) was studied over a range of structural length scales utilizing neutron total scattering experiments. Refinement of diffraction data confirms that the long-range orthorhombic structure is susceptible to ion beam-induced amorphization with limited crystalline fraction remaining after irradiation to 8 × 1012 ions/cm2. In contrast, the local atomic arrangement, examined through pair distribution function analysis, shows only subtle changes after irradiation and is still described best by the original orthorhombic structural model. A comparison to Dy2Ti2O7 pyrochlore oxide under the same irradiation conditions reveals a different behavior: while the dysprosium titanate pyrochlore is more radiation resistant over the long-range with smaller degree of amorphization as compared to Dy2TiO5, the former involves more local atomic rearrangements, best described by a pyrochlore-to-weberite-type transformation. These results highlight the importance of short-range and medium-range order analysis for a comprehensive description of radiation behavior.

scholarly journals The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ilona E. Grabowicz ◽  
Bartek Wilczyński ◽  
Bożena Kamińska ◽  
Adria-Jaume Roura ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Genetic Alterations ◽  
Chromatin Organization ◽  
Open Chromatin ◽  
Low Grade ◽  
Strong Impact ◽  
Cell Matrix ◽  
Topologically Associating Domains ◽  
Genome Wide

AbstractGenome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell–matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.

SHORT-RANGE AND LONG-RANGE ORDER OF TITANIUM IN Ti1+xS2

1977 ◽  
Vol 38 (C7) ◽  
pp. C7-202-C7-206 ◽  
Author(s):  
R. MORET ◽  
M. HUBER ◽  
R. COMÈS
Keyword(s):  
Long Range ◽  
Short Range ◽  
Range Order ◽  
Long Range Order

scholarly journals Short range smectic order driving long range nematic order: example of cuprates

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
R. S. Markiewicz ◽  
J. Lorenzana ◽  
G. Seibold ◽  
A. Bansil
Keyword(s):  
Long Range ◽  
Short Range ◽  
Nematic Order

ANDERSON LOCALIZATION FOR A MULTIDIMENSIONAL MODEL INCLUDING LONG RANGE POTENTIALS AND DISPLACEMENTS

2002 ◽  
Vol 14 (03) ◽  
pp. 273-302 ◽  
Author(s):  
HERIBERT ZENK
Keyword(s):  
Long Range ◽  
Anderson Model ◽  
Anderson Localization ◽  
Short Range ◽  
Energy Interval ◽  
Multidimensional Model ◽  
Short Summary

We give a short summary on how to combine and extend results of Combes and Hislop [2] (short range Anderson model with additional displacements), Kirsch, Stollmann and Stolz [13] and [14] (long range Anderson model without displacements) to get localization in an energy interval above the infimum of the almost sure spectrum for a continuous multidimensional Anderson model including long range potentials and displacements.

Study on the relationships of mechanical performance with the short-range and long-range structure of 500–900℃ carbonized fiber

2014 ◽  
Vol 45 (1) ◽  
pp. 33-47 ◽  
Author(s):  
Xue Lin ◽  
Chengguo Wang ◽  
Meijie Yu ◽  
Zhitao Lin ◽  
Yuzhen Liu
Keyword(s):  
Long Range ◽  
Short Range ◽  
Mechanical Performance
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