Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization

2021 ◽  
pp. 1-15
Author(s):  
Cyril Matthey-Doret ◽  
Lyam Baudry ◽  
Shogofa Mortaza ◽  
Pierrick Moreau ◽  
Romain Koszul ◽  
...  
Keyword(s):  
Contact Maps ◽  
Matrix Balancing

scholarly journals Erythrocytes 3D genome organization in vertebrates

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anastasia Ryzhkova ◽  
Alena Taskina ◽  
Anna Khabarova ◽  
Veniamin Fishman ◽  
Nariman Battulin
Keyword(s):  
Blood Cells ◽  
Genome Organization ◽  
Large Scale ◽  
Chromatin Condensation ◽  
Erythroid Differentiation ◽  
Interaction Patterns ◽  
3D Interaction ◽  
Interphase Chromosome ◽  
3D Genome ◽  
Contact Maps

AbstractGeneration of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.

scholarly journals On the Reconstruction of Three-dimensional Protein Structures from Contact Maps

Algorithms ◽  
2009 ◽  
Vol 2 (1) ◽  
pp. 76-92 ◽  
Author(s):  
Pietro Di Lena ◽  
Marco Vassura ◽  
Luciano Margara ◽  
Piero Fariselli ◽  
Rita Casadio
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Contact Maps

Predicting helix pair structure from fuzzy contact maps

2014 ◽  
Vol 14 ◽  
pp. 357-362 ◽  
Author(s):  
Tony C.Y. Kuo ◽  
Janice Glasgow
Keyword(s):  
Contact Maps

scholarly journals Automated method to differentiate between native and mirror protein models obtained from contact maps

PLoS ONE ◽  
2018 ◽  
Vol 13 (5) ◽  
pp. e0196993
Author(s):  
Monika Kurczynska ◽  
Malgorzata Kotulska
Keyword(s):  
Contact Maps ◽  
Automated Method ◽  
Protein Models

scholarly journals Fast Feature-Preserving Approach to Carpal Bone Surface Denoising

Sensors ◽  
2018 ◽  
Vol 18 (7) ◽  
pp. 2379
Author(s):  
Ibrahim Salim ◽  
A. Hamza
Keyword(s):  
Objective Function ◽  
Linear Equations ◽  
Noise Model ◽  
Carpal Bone ◽  
Geometric Framework ◽  
Sparse System ◽  
Adaptive Kernel ◽  
Feature Preserving ◽  
Data Adaptive ◽  
Matrix Balancing

We present a geometric framework for surface denoising using graph signal processing, which is an emerging field that aims to develop new tools for processing and analyzing graph-structured data. The proposed approach is formulated as a constrained optimization problem whose objective function consists of a fidelity term specified by a noise model and a regularization term associated with prior data. Both terms are weighted by a normalized mesh Laplacian, which is defined in terms of a data-adaptive kernel similarity matrix in conjunction with matrix balancing. Minimizing the objective function reduces it to iteratively solve a sparse system of linear equations via the conjugate gradient method. Extensive experiments on noisy carpal bone surfaces demonstrate the effectiveness of our approach in comparison with existing methods. We perform both qualitative and quantitative comparisons using various evaluation metrics.

scholarly journals Prediction of contact maps with neural networks and correlated mutations

2001 ◽  
Vol 14 (11) ◽  
pp. 835-843 ◽  
Author(s):  
Piero Fariselli ◽  
Osvaldo Olmea ◽  
Alfonso Valencia ◽  
Rita Casadio
Keyword(s):  
Neural Networks ◽  
Contact Maps ◽  
Correlated Mutations
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