scholarly journals Computer vision for pattern detection in chromosome contact maps

2020 ◽  
Author(s):  
Cyril Matthey-Doret ◽  
Lyam Baudry ◽  
Axel Breuer ◽  
Rémi Montagne ◽  
Nadège Guiglielmoni ◽  
...  
Keyword(s):  
Computer Vision ◽  
Higher Order ◽  
Pattern Detection ◽  
Biological Functions ◽  
Contact Maps ◽  
Link Type ◽  
Organizational Features

AbstractChromosomes of all species studied so far display a variety of higher order organizational features such as domains or loops often associated to biological functions and visible on Hi-C contact maps. We developed Chromosight, an algorithm inspired from computer vision that can detect patterns in Hi-C maps. Chromosight has greater sensitivity than existing methods, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Code and documentation: https://github.com/koszullab/chromosight

scholarly journals Computer vision for pattern detection in chromosome contact maps

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Cyril Matthey-Doret ◽  
Lyam Baudry ◽  
Axel Breuer ◽  
Rémi Montagne ◽  
Nadège Guiglielmoni ◽  
...  
Keyword(s):  
Computer Vision ◽  
Simulated Data ◽  
Pattern Detection ◽  
Training Dataset ◽  
Biological Functions ◽  
Prior Training ◽  
Chromosome Conformation ◽  
Contact Maps ◽  
Genome Wide ◽  
Wide Contact

AbstractChromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.

scholarly journals May the four be with you: novel IR-subtraction methods to tackle NNLO calculations

2021 ◽  
Vol 81 (3) ◽  
Author(s):  
W. J. Torres Bobadilla ◽  
G. F. R. Sborlini ◽  
P. Banerjee ◽  
S. Catani ◽  
A. L. Cherchiglia ◽  
...  
Keyword(s):  
High Energy Physics ◽  
High Energy ◽  
Higher Order ◽  
Field Theories ◽  
Quantum Field Theories ◽  
Quantum Field ◽  
Link Type ◽  
Mathematical Properties ◽  
Energy Physics ◽  
The Way

AbstractIn this manuscript, we report the outcome of the topical workshop: paving the way to alternative NNLO strategies (https://indico.ific.uv.es/e/WorkStop-ThinkStart_3.0), by presenting a discussion about different frameworks to perform precise higher-order computations for high-energy physics. These approaches implement novel strategies to deal with infrared and ultraviolet singularities in quantum field theories. A special emphasis is devoted to the local cancellation of these singularities, which can enhance the efficiency of computations and lead to discover novel mathematical properties in quantum field theories.

scholarly journals ZDOG: zooming in on dominating genes with mutations in cancer pathways

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rudi Alberts ◽  
Jinyu Chen ◽  
Louxin Zhang
Keyword(s):  
Somatic Mutations ◽  
Positional Information ◽  
Signalling Pathways ◽  
Biological Functions ◽  
Tree Model ◽  
Master Regulators ◽  
Cancer Pathways ◽  
Link Type ◽  
Dominating Tree ◽  
User Friendly

Abstract Background Inference of cancer-causing genes and their biological functions are crucial but challenging due to the heterogeneity of somatic mutations. The heterogeneity of somatic mutations reveals that only a handful of oncogenes mutate frequently and a number of cancer-causing genes mutate rarely. Results We develop a Cytoscape app, named ZDOG, for visualization of the extent to which mutated genes may affect cancer pathways using the dominating tree model. The dominator tree model allows us to examine conveniently the positional importance of a gene in cancer signalling pathways. This tool facilitates the identification of mutated “master” regulators even with low mutation frequency in deregulated signalling pathways. Conclusions We have presented a model for facilitating the examination of the extent to which mutation in a gene may affect downstream components in a signalling pathway through its positional information. The model is implemented in a user-friendly Cytoscape app which will be freely available upon publication. Availability Together with a user manual, the ZDOG app is freely available at GitHub (https://github.com/rudi2013/ZDOG). It is also available in the Cytoscape app store (http://apps.cytoscape.org/apps/ZDOG) and users can easily install it using the Cytoscape App Manager.

Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material

2012 ◽  
Vol 14 (11) ◽  
pp. 1148-1158 ◽  
Author(s):  
Steffen Lawo ◽  
Monica Hasegan ◽  
Gagan D. Gupta ◽  
Laurence Pelletier
Keyword(s):  
Higher Order ◽  
Pericentriolar Material ◽  
Organizational Features

scholarly journals MetQy – an R package to query metabolic functions of genes and genomes

2017 ◽  
Author(s):  
Andrea Martinez–Vernon ◽  
Frederick Farrell ◽  
Orkun S. Soyer
Keyword(s):  
Metabolic Engineering ◽  
R Package ◽  
Biological Functions ◽  
Sequencing Data ◽  
Kegg Database ◽  
Flat File ◽  
Link Type ◽  
Metabolic Functions ◽  
Rapid Accumulation ◽  
Available Information

AbstractSummaryWith the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open–source R package designed for query–based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Furthermore, MetQy contains visualization and analysis tools and facilitates KEGG’s flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user–specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.Availability and ImplementationThe MetQy R package is freely available and can be downloaded from our group’s website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy)[email protected]

scholarly journals CRISPR-Cas9 multiplex genome editing of the hydroxyproline-O-galactosyltransferase gene family alters arabinogalactan-protein glycosylation and function in Arabidopsis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuan Zhang ◽  
Michael A. Held ◽  
Dasmeet Kaur ◽  
Allan M. Showalter
Keyword(s):  
Gene Family ◽  
Female Gametophyte ◽  
Gene Editing ◽  
Seed Set ◽  
Higher Order ◽  
Protein Glycosylation ◽  
Arabinogalactan Protein ◽  
Composition Analysis ◽  
Biological Functions ◽  
Knockout Mutants

Abstract Background Arabinogalactan-proteins (AGPs) are a class of hydroxyproline-rich proteins (HRGPs) that are heavily glycosylated (> 90%) with type II arabinogalactans (AGs). AGPs are implicated in various plant growth and development processes including cell expansion, somatic embryogenesis, root and stem growth, salt tolerance, hormone signaling, male and female gametophyte development, and defense. To date, eight Hyp-O-galactosyltransferases (GALT2–6, HPGT1–3) have been identified; these enzymes are responsible for adding the first sugar, galactose, onto AGPs. Due to gene redundancy among the GALTs, single or double galt genetic knockout mutants are often not sufficient to fully reveal their biological functions. Results Here, we report the successful application of CRISPR-Cas9 gene editing/multiplexing technology to generate higher-order knockout mutants of five members of the GALT gene family (GALT2–6). AGPs analysis of higher-order galt mutants (galt2 galt5, galt3 galt4 galt6, and galt2 galt3 galt4 galt5 gal6) demonstrated significantly less glycosylated AGPs in rosette leaves, stems, and siliques compared to the corresponding wild-type organs. Monosaccharide composition analysis of AGPs isolated from rosette leaves revealed significant decreases in arabinose and galactose in all the higher-order galt mutants. Phenotypic analyses revealed that mutation of two or more GALT genes was able to overcome the growth inhibitory effect of β-D-Gal-Yariv reagent, which specifically binds to β-1,3-galactan backbones on AGPs. In addition, the galt2 galt3 galt4 galt5 gal6 mutant exhibited reduced overall growth, impaired root growth, abnormal pollen, shorter siliques, and reduced seed set. Reciprocal crossing experiments demonstrated that galt2 galt3 galt4 galt5 gal6 mutants had defects in the female gametophyte which were responsible for reduced seed set. Conclusions Our CRISPR/Cas9 gene editing/multiplexing approach provides a simpler and faster way to generate higher-order mutants for functional characterization compared to conventional genetic crossing of T-DNA mutant lines. Higher-order galt mutants produced and characterized in this study provide insight into the relationship between sugar decorations and the various biological functions attributed to AGPs in plants.

scholarly journals Meningioma Detection in MR Images Using Convolutional Neural Network and Computer Vision Methods

2020 ◽  
pp. 030301
Author(s):  
Yulia D. Agafonova ◽  
Andrey V. Gaidel ◽  
Evgeniy N. Surovtsev ◽  
Aleksandr V. Kapishnikov
Keyword(s):  
Neural Network ◽  
Computer Vision ◽  
Convolutional Neural Network ◽  
Pattern Detection ◽  
Diffusion Weighted Mri ◽  
Mr Images ◽  
Post Contrast ◽  
Novel Approach ◽  
Medical University ◽  
Real Patients

The article discusses research efficacy of different architectures of convolutional neural network and methods of computer vision. This paper presents a novel approach to pattern detection of meningioma of the human brain in MR images. MRI images of real patients were made with a help of Samara State Medical University. The result of the research is the automatic procedure of meningioma detection. As a result, post-contrast T1 weighted MRI sequence was the most appropriate for the method based on the baseline statistical segmentation and the diffusion weighted MRI sequence was the most appropriate for the method based on the convolutional neural network.

scholarly journals Unsupervised deep learning on biomedical data with BoltzmannMachines.jl

2019 ◽  
Author(s):  
Stefan Lenz ◽  
Moritz Hess ◽  
Harald Binder
Keyword(s):  
Input Data ◽  
Genomic Data ◽  
Small Sample ◽  
Pattern Detection ◽  
Biomedical Data ◽  
Data Types ◽  
Boltzmann Machines ◽  
Link Type ◽  
Unsupervised Deep Learning ◽  
Small Sample Sizes

AbstractDeep Boltzmann machines (DBMs) are models for unsupervised learning in the field of artificial intelligence, promising to be useful for dimensionality reduction and pattern detection in clinical and genomic data. Multimodal and partitioned DBMs alleviate the problem of small sample sizes and make it possible to combine different input data types in one DBM model. We present the package “BoltzmannMachines” for the Julia programming language, which makes this model class available for practical use in working with biomedical data.AvailabilityNotebook with example data: http://github.com/stefan-m-lenz/BMs4BInf2019 Julia package: http://github.com/stefan-m-lenz/BoltzmannMachines.jl

scholarly journals The role of the nucleosome acidic patch in modulating higher order chromatin structure

2013 ◽  
Vol 10 (82) ◽  
pp. 20121022 ◽  
Author(s):  
Anna A. Kalashnikova ◽  
Mary E. Porter-Goff ◽  
Uma M. Muthurajan ◽  
Karolin Luger ◽  
Jeffrey C. Hansen
Keyword(s):  
Higher Order ◽  
Folding Pathway ◽  
Computational Studies ◽  
Biological Functions ◽  
Histone H4 ◽  
Chromatin Fibre ◽  
Chromatin Folding ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Higher order folding of chromatin fibre is mediated by interactions of the histone H4 N-terminal tail domains with neighbouring nucleosomes. Mechanistically, the H4 tails of one nucleosome bind to the acidic patch region on the surface of adjacent nucleosomes, causing fibre compaction. The functionality of the chromatin fibre can be modified by proteins that interact with the nucleosome. The co-structures of five different proteins with the nucleosome (LANA, IL-33, RCC1, Sir3 and HMGN2) recently have been examined by experimental and computational studies. Interestingly, each of these proteins displays steric, ionic and hydrogen bond complementarity with the acidic patch, and therefore will compete with each other for binding to the nucleosome. We first review the molecular details of each interface, focusing on the key non-covalent interactions that stabilize the protein–acidic patch interactions. We then propose a model in which binding of proteins to the nucleosome disrupts interaction of the H4 tail domains with the acidic patch, preventing the intrinsic chromatin folding pathway and leading to assembly of alternative higher order chromatin structures with unique biological functions.

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

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