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Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data.
TLDR
We developed chromoR, an R package to analyse chromosomal interaction data using statistical bioinformatics, offering a new and comprehensive solution to this task. Expand
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An integrated suite of fast docking algorithms
TLDR
The CAPRI experiment (Critical Assessment of Predicted Interactions) simulates realistic and diverse docking challenges, each case having specific properties that may be exploited by docking algorithms. Expand
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FisHiCal: an R package for iterative FISH-based calibration of Hi-C data
TLDR
We present FisHiCal, an R package for an iterative FISH-based Hi-C calibration that exploits in full the information coming from these methods. Expand
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Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration
TLDR
We present chromoHBM, an algorithm that compresses high-throughput 3C (HiT-3C) data into topological features that are efficiently summarized with an HBM representation. Expand
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Automated Synthesis and Analysis of Switching Gene Regulatory Networks
TLDR
We introduce the concept of a Switching Gene Regulatory Network (SGRN), which is a modelling language and framework for the analysis and synthesis of reconfiguring GRNs. Expand
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Introduction to Camera Pose Estimation with Deep Learning
Over the last two decades, deep learning has transformed the field of computer vision. Deep convolutional networks were successfully applied to learn different vision tasks such as imageExpand
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CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks
TLDR
We present CytoHiC, a plugin for the Cytoscape platform, which allow users to view and compare spatial maps of genomic landmarks, based on normalized Hi-C datasets. Expand
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How computer science can help in understanding the 3D genome architecture
TLDR
We describe the critical issues of this new branch of bioinformatics, oriented at the comprehension of the three-dimensional genome architecture, which we call 'Nucleome Bioinformatrics', looking beyond the currently available tools and methods, and highlight yet unaddressed challenges and the potential approaches that could be applied for tackling them. Expand
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Switching Gene Regulatory Networks
TLDR
We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior. Expand
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Combining wavelet change point and Bayes Factor for analysing chromosomal interactions data
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