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High Resolution Modeling of Chromatin Interactions
[chapter]
2013
Lecture Notes in Computer Science
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Sprout is a novel generative model for ChIA-PET data that characterizes physical chromatin interactions and points of contact at high spatial resolution. ...
pairs to anchors which allows for the identification of high confidence interactions. ...
The second is to accurately assign read pairs to chromatin interaction anchors or to a background noise model. ...
doi:10.1007/978-3-642-37195-0_16
fatcat:rilfidmhcvd35ek6hjdyzdueii
Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus
2018
Nature Communications
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Our work not only provides a computational framework to enhance Hi-C data resolution but also reveals features underlying the formation of 3D chromatin interactions. ...
Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. ...
of meaningful chromatin interactions. ...
doi:10.1038/s41467-018-03113-2
pmid:29467363
pmcid:PMC5821732
fatcat:kauepvparfgwla6skllongl5su
DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning
[article]
2019
bioRxiv
pre-print
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The model generalizes well to unseen chromosomes and works across cell types, Hi-C data resolutions and a range of sequencing depths. ...
Computational models sophisticated enough to grasp the determinants of chromatin folding provide a unique window into the functional determinants of 3D genome structure as well as the effects of genome ...
It is of particularly interested to resolve high levels of Hi-C interactions at high resolution and only a low percentage of chromatin interactions is expected to yield strong interactions at larger distances ...
doi:10.1101/724005
fatcat:ia5wpstqarenzibwmtl6wnyl7u
Genome-wide mapping and analysis of chromosome architecture
2016
Nature reviews. Molecular cell biology
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However, the mechanisms by which chromatin interactions are formed and maintained during development remain to be elucidated. ...
The chromosome conformation capture (3C) method and its studying chromatin interactions in eukaryotic cells [22] [23] [24] [25] [26] [27] (TABLE 1) . ...
Acknowledgments The authors dedicate this manuscript in loving memory of Joseph Schmitt. They would like to give special thanks to members of the Ren laboratory for their suggestions. ...
doi:10.1038/nrm.2016.104
pmid:27580841
pmcid:PMC5763923
fatcat:2eyv2yjh2rcc5nbzpmvtv5bv2a
SRHiC: A Deep Learning Model to Enhance the Resolution of Hi-C Data
2020
Frontiers in Genetics
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Hi-C data is important for studying chromatin three-dimensional structure. However, the resolution of most existing Hi-C data is generally coarse due to sequencing cost. ...
Therefore, it will be helpful if we can predict high-resolution Hi-C data from low-coverage sequencing data. ...
For each method, we calculated the overlap of its identified chromatin interactions with those identified from real high-resolution Hi-C data. ...
doi:10.3389/fgene.2020.00353
pmid:32322265
pmcid:PMC7156553
fatcat:3c3yw2r64ngpthit76jp5bfxma
DeepTACT: predicting high-resolution chromatin contacts via bootstrapping deep learning
[article]
2018
bioRxiv
pre-print
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High-resolution interactions among regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanism. ...
of GWAS data and high-resolution contacts inferred by DeepTACT. ...
The success of previous applications of deep neural networks in biological fields inspires us to design a deep learning model to detect high-resolution chromatin contacts among regulatory elements, utilizing ...
doi:10.1101/353284
fatcat:62jih7mqqbb33dhbiqome3u4qm
High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis
2021
Nature Communications
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Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization ...
However, balancing high-resolution and genome wide-coverage remains challenging. ...
In Fig. 2
Code availability Source code for null model chromatin folding by fractal Monte Carlo is available via git repository at https://bitbucket.org/aperezrathke/chr-folder. ...
doi:10.1038/s41467-020-20490-9
pmid:33420075
fatcat:lgsbftc6hrb2jiez3oqvjcdchy
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
[article]
2019
bioRxiv
pre-print
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We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. ...
However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. ...
Acknowledgement We thank the Aiden Lab, the Wei Xie lab, and ENCODE Consortium for high-quality data. ...
doi:10.1101/718148
fatcat:3wziq7ttlja2hcb6dvd4rvoh4a
Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
2021
Nature Communications
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To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. ...
Here, we develop an advanced multiscale chromatin model—integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model—to resolve individual nucleosomes within sub-Mb ...
Code availability The authors are delighted to share the computational implementation of their models with the community. ...
doi:10.1038/s41467-021-23090-3
pmid:34001913
fatcat:g4wgl7jvdnew5hvprbmlaibzsq
EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework
2021
Bioinformatics
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Moreover, EnHiC-predicted high-resolution matrices facilitated the accurate detection of topologically associated domains and fine-scale chromatin interactions. ...
Motivation The high-throughput chromosome conformation capture (Hi-C) technique has enabled genome-wide mapping of chromatin interactions. ...
The method performance tests of this study were performed in the High-Performance Computing Center at UC Riverside.
Funding This work was supported by the U.S. ...
doi:10.1093/bioinformatics/btab272
pmid:34252966
fatcat:gkjdr5mqlvfyhhjqhx2eextani
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
2020
PLoS Computational Biology
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We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. ...
However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. ...
Acknowledgments We thank the Aiden Lab, the Wei Xie lab, and ENCODE Consortium for high-quality data.
Author Contributions Conceptualization: Cheng Li, Hebing Chen, Xiaochen Bo. ...
doi:10.1371/journal.pcbi.1007287
pmid:32084131
pmcid:PMC7055922
fatcat:6cn3phnuxjbhnbyit2jegxlq6a
Protein–DNA binding in high-resolution
2015
Critical reviews in biochemistry and molecular biology
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We also discuss the opportunities and challenges associated with building integrative models of regulatory organization from collections of high-resolution data types. ...
Current models of regulatory organization are hampered by the relatively low spatial resolution of current regulatory genomics assays. ...
No existing assay yet enables high-resolution characterization of protein-DNA binding events alongside their associated chromatin interactions. ...
doi:10.3109/10409238.2015.1051505
pmid:26038153
pmcid:PMC4580520
fatcat:qygnojyg55ekfnej2nxsfvnkni
Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles
2018
Biophysical Journal
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Strikingly, many recent studies, including genome-wide nucleosome interaction mapping and chromatin imaging, show an excellent agreement with the results of three-dimensional computational modeling based ...
The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to ...
An important approach for understanding the specific roles of LH and other linker-DNA-interacting architectural factors in chromatin folding would be accurate and high-resolution measurements of their ...
doi:10.1016/j.bpj.2018.03.009
pmid:29628212
pmcid:PMC6129572
fatcat:lbllwz6vlzbfdnllptul3evrmm
Developing bioimaging and quantitative methods to study 3D genome
2016
Quantitative Biology
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We also reviewed the progress of quantitative and visualization tools to evaluate and visualize chromatin interactions in 3D genome derived from Hi-C data. ...
Here we at first introduce briefly genome organization at chromosome, domain and sub-domain level, respectively; then we provide a short introduction to various super-resolution microscopy techniques which ...
ACKNOWLEDGEMENTS Due to the space constraints, we regret that we are unable to address the importance of all work in the field. ...
doi:10.1007/s40484-016-0065-2
fatcat:r6o5za2uwfbepenoyqmb6hhmwy
Connecting high-resolution 3D chromatin organization with epigenomics
[article]
2020
bioRxiv
pre-print
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regulation with 3D chromatin organization at high resolution. ...
The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization ...
the trained model to impute high-resolution chromatin contact maps for other human tissues and cell lines. ...
doi:10.1101/2020.10.13.338004
fatcat:nuiytokx7rc6jc4rtuoddmmycm
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