The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1093/nar/gkaa818 http://hdl.handle.net/11449/205441 |
Resumo: | We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu. |
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Repositório Institucional da UNESP |
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spelling |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genomeWe introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.Welch FoundationNational Science FoundationCenter for Theoretical Biological Physics Rice UniversityBrazilian Biorenewables National Laboratory-LNBR Brazilian Center for Research in Energy and Materials-CNPEMDepartment of Physics São Paulo State University (UNESP) Institute of Biosciences Humanities and Exact SciencesDepartment of Computer Science University of HoustonTheoretical and Computational Physics Laboratory University of Costa RicaChemical Engineering Department Military Institute of EngineeringThe Center for Genome Architecture Department of Molecular and Human Genetics Baylor College of MedicineDepartment of Physics and Astronomy Rice UniversityDepartment of Chemistry Rice UniversityDepartment of Biosciences Rice UniversityDepartment of Physics Northeastern UniversityDepartment of Physics São Paulo State University (UNESP) Institute of Biosciences Humanities and Exact SciencesWelch Foundation: C-0016Welch Foundation: C-1792National Science Foundation: CHE-1614101National Science Foundation: PHY-2019745Rice UniversityBrazilian Center for Research in Energy and Materials-CNPEMUniversidade Estadual Paulista (Unesp)University of HoustonUniversity of Costa RicaMilitary Institute of EngineeringBaylor College of MedicineNortheastern UniversityContessoto, Vinícius G. [UNESP]Cheng, Ryan R.Hajitaheri, AryaDodero-Rojas, EstebanMello, Matheus F.Lieberman-Aiden, ErezWolynes, Peter G.Di Pierro, MicheleOnuchic, José N.2021-06-25T10:15:21Z2021-06-25T10:15:21Z2021-01-08info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleD172-D182http://dx.doi.org/10.1093/nar/gkaa818Nucleic Acids Research, v. 49, n. D1, p. D172-D182, 2021.1362-49620305-1048http://hdl.handle.net/11449/20544110.1093/nar/gkaa8182-s2.0-85095707350Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengNucleic Acids Researchinfo:eu-repo/semantics/openAccess2021-10-23T14:27:07Zoai:repositorio.unesp.br:11449/205441Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T14:27:07Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
title |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
spellingShingle |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome Contessoto, Vinícius G. [UNESP] |
title_short |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
title_full |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
title_fullStr |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
title_full_unstemmed |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
title_sort |
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-dimensional genome |
author |
Contessoto, Vinícius G. [UNESP] |
author_facet |
Contessoto, Vinícius G. [UNESP] Cheng, Ryan R. Hajitaheri, Arya Dodero-Rojas, Esteban Mello, Matheus F. Lieberman-Aiden, Erez Wolynes, Peter G. Di Pierro, Michele Onuchic, José N. |
author_role |
author |
author2 |
Cheng, Ryan R. Hajitaheri, Arya Dodero-Rojas, Esteban Mello, Matheus F. Lieberman-Aiden, Erez Wolynes, Peter G. Di Pierro, Michele Onuchic, José N. |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Rice University Brazilian Center for Research in Energy and Materials-CNPEM Universidade Estadual Paulista (Unesp) University of Houston University of Costa Rica Military Institute of Engineering Baylor College of Medicine Northeastern University |
dc.contributor.author.fl_str_mv |
Contessoto, Vinícius G. [UNESP] Cheng, Ryan R. Hajitaheri, Arya Dodero-Rojas, Esteban Mello, Matheus F. Lieberman-Aiden, Erez Wolynes, Peter G. Di Pierro, Michele Onuchic, José N. |
description |
We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T10:15:21Z 2021-06-25T10:15:21Z 2021-01-08 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1093/nar/gkaa818 Nucleic Acids Research, v. 49, n. D1, p. D172-D182, 2021. 1362-4962 0305-1048 http://hdl.handle.net/11449/205441 10.1093/nar/gkaa818 2-s2.0-85095707350 |
url |
http://dx.doi.org/10.1093/nar/gkaa818 http://hdl.handle.net/11449/205441 |
identifier_str_mv |
Nucleic Acids Research, v. 49, n. D1, p. D172-D182, 2021. 1362-4962 0305-1048 10.1093/nar/gkaa818 2-s2.0-85095707350 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Nucleic Acids Research |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
D172-D182 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803045932108873728 |