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High Resolution Modeling of Chromatin Interactions [chapter]

Christopher Reeder, David Gifford
2013 Lecture Notes in Computer Science  
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

Yan Zhang, Lin An, Jie Xu, Bo Zhang, W. Jim Zheng, Ming Hu, Jijun Tang, Feng Yue
2018 Nature Communications  
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]

Ron Schwessinger, Matthew Gosden, Damien Downes, Richard Brown, Jelena Telenius, Yee Whye Teh, Gerton Lunter, Jim R. Hughes
2019 bioRxiv   pre-print
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

Anthony D. Schmitt, Ming Hu, Bing Ren
2016 Nature reviews. Molecular cell biology  
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

Zhilan Li, Zhiming Dai
2020 Frontiers in Genetics  
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]

Wenran Li, Wing Hung Wong, Rui Jiang
2018 bioRxiv   pre-print
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

Qiu Sun, Alan Perez-Rathke, Daniel M. Czajkowsky, Zhifeng Shao, Jie Liang
2021 Nature Communications  
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]

Hao Hong, Shuai Jiang, Hao Li, Cheng Quan, Chenghui Zhao, Ruijiang Li, Wanying Li, Guifang Du, Xiaoyao Yin, Yangchen Huang, Cheng Li, Hebing Chen (+1 others)
2019 bioRxiv   pre-print
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

Stephen E. Farr, Esmae J. Woods, Jerelle A. Joseph, Adiran Garaizar, Rosana Collepardo-Guevara
2021 Nature Communications  
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

Yangyang Hu, Wenxiu Ma
2021 Bioinformatics  
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

Hao Hong, Shuai Jiang, Hao Li, Guifang Du, Yu Sun, Huan Tao, Cheng Quan, Chenghui Zhao, Ruijiang Li, Wanying Li, Xiaoyao Yin, Yangchen Huang (+4 others)
2020 PLoS Computational Biology  
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

Shaun Mahony, B. Franklin Pugh
2015 Critical reviews in biochemistry and molecular biology  
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

Sergei A. Grigoryev
2018 Biophysical Journal  
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

Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi, Michael Q. Zhang
2016 Quantitative Biology  
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]

Fan Feng, Yuan Yao, Xue Qing David Wang, Xiaotian Zhang, Jie Liu
2020 bioRxiv   pre-print
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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