4d nucleome data portal

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Last Updated: 19 Mar, 2022
  • 4D Nucleome Data Portal
    • 4D Nucleome Data Portal
    • https://mastertest.4dnucleome.org/
    • The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear ...
  • About Us – 4DN Data Portal - 4D Nucleome
    • About Us – 4DN Data Portal - 4D Nucleome
    • http://dcic.4dnucleome.org/
    • More information about the 4D Nucleome program can be obtained at the 4DN portal and the NIH program website, which also lists the funded research centers. The 4DN data portal is developed and managed by the 4D Nucleome Data Coordination and Integration Center (DCIC) .
  • 4D Nucleome Web Portal
    • 4D Nucleome Web Portal
    • https://www.4dnucleome.org/centers-and-teams.html
    • The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization.
  • 4D Nucleome Center
    • 4D Nucleome Center
    • https://4d.nucleome.center/
    • The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. Nucleome Browser The Nucleome Browser is a multimodal, interactive data visualization and exploration platform to integrate genomic, imaging, and 3D genome structure data.
  • 4D Nucleome - NIH Common Fund
    • 4D Nucleome - NIH Common Fund
    • https://commonfund.nih.gov/4Dnucleome
    • 4D Nucleome Portal Visit the 4D Nucleome Portal to find information about the data, protocols, reagents, resources, and methods that are currently being developed by 4DN Network investigators. 4DN Program Announces Associate Membership
  • 4Dn Web - 4D Nucleome Web Portal
    • 4Dn Web - 4D Nucleome Web Portal
    • https://portalslocate.com/4dn-web/
    • The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data ...
  • Add 4D Nucleome Data Portal preprint · Issue #310 · hms ...
  • MULTISCALE ANALYSES OF 4D NUCLEOME STRUCTURE AND ...
    • MULTISCALE ANALYSES OF 4D NUCLEOME STRUCTURE AND ...
    • https://data.4dnucleome.org/awards/1UM1HG011593-01/
    • Our navigable reference maps will be publicly accessible through an analysis platform that provides interactive visualization of multiple data types, thus enabling investigators with diverse expertise to simultaneously explore their own data and related datasets/tools and promoting collaborations that will open new horizons into the role of the 4D nucleome in human health and disease.
  • Data integration and visualization at the 4D nucleome data ...
    • Data integration and visualization at the 4D nucleome data ...
    • https://f1000research.com/posters/8-440
    • Data integration and visualization at the 4D nucleome data portal. Burak Alver, Alexander Balashov, Shannon Ehmsen, Koray Kirli, Soohyun Lee, Luisa Mercado, Sarah Reiff, Andrew Schroeder, Chad Serrant, Carl Vitzthum, Nils Gehlenborg 1 ...
  • 4D Nucleome Data Coordination and Integration Center · GitHub
    • 4D Nucleome Data Coordination and Integration Center · GitHub
    • https://github.com/4dn-dcic
    • Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell ...
  • Reference Files – 4DN Data Portal
    • Reference Files – 4DN Data Portal
    • http://staging.4dnucleome.org/resources/data-analysis/reference-files
    • The 4DN Data Portal currently hosts the genome references of 5 species - human, mouse, chicken, fruit fly and zebrafish, in various formats. The reference genomes of human and mouse are identical to those used by the ENCODE consortium. ... 4D Nucleome Data Coordination and Integration Center.
  • Data Collections – 4DN Data Portal
    • Data Collections – 4DN Data Portal
    • http://staging.4dnucleome.org/resources/data-collections
    • Hi-C Data Sets and Studies on the 4DN Portal. High-Resolution Hi-C Datasets. Inflammation/Stress Datasets. Previous Section Data Analysis. 4D Nucleome Data Coordination and Integration Center. Harvard University | Massachusetts Institute of Technology ...
  • start [4D Nucleome Network Wiki]
    • start [4D Nucleome Network Wiki]
    • https://wiki.4dnucleome.org/
    • 4DN Members, please follow the instruction page to log in to the new 4DN Wiki with the quot;Sign in with Googlequot; button using your previous credentials. Please use ...
  • 4D Nucleome - Funded Research | NIH Common Fund
    • 4D Nucleome - Funded Research | NIH Common Fund
    • https://commonfund.nih.gov/4dnucleome/fundedresearch
    • 4D Nucleome Network Organizational Hub (U01) RFA-RM-14-010; PI Name Institution Name Title; ZHONG, SHENG (contact) CHIEN, SHU REN, BING SUBRAMANIAM, SHANKAR: UNIVERSITY OF CALIFORNIA SAN DIEGO: The Organizational Hub and Web Portal for the 4D Nucleome Network
  • Past Work - GitHub Pages
    • Past Work - GitHub Pages
    • https://alexkb0009.github.io/
    • 4D Nucleome Data Portal. Data coordination portal for the 4D Nucleome (4DN) project built in Harvard Medical School’s Department of Biomedical Informatics (HMS DBMI). Leading front-end development. A single-page application (SPA) built on React.js... 2016-Present
  • RFA-RM-14-011: 4D Nucleome Network Data Coordination and ...
    • RFA-RM-14-011: 4D Nucleome Network Data Coordination and ...
    • https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-011.html
    • The 4DN Data Portal will provide user-friendly submission of and access to 4DN data (both raw data and derived datasets), metadata, and analysis and visualization tools. The web-interface should provide controlled-access to both 4DN Network members and the broader scientific community.
  • 4DNucleome Data Portal | BiŌkeanós
    • 4DNucleome Data Portal | BiŌkeanós
    • https://biokeanos.com/source/4DNucleome%20Data%20Portal
    • The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.
  • FAIRsharing: biodbcore-001270: 4DN
    • FAIRsharing: biodbcore-001270: 4DN
    • https://fairsharing.org/FAIRsharing.CugtbQ
    • The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.
  • The 4D nucleome project | Nature
    • The 4D nucleome project | Nature
    • https://www.nature.com/articles/nature23884
    • The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights ...
  • Resources and challenges for integrative analysis of ...
    • Resources and challenges for integrative analysis of ...
    • https://www.sciencedirect.com/science/article/pii/S0959437X20301738
    • When the user finds a Hi-C dataset in the 4D Nucleome Data Portal, for instance, the interaction map is already in place, ready to be browsed. The challenge in visualization of the matrix is its sheer size at high resolution: at 10 kb resolution, the matrix is 300 k bins by 300 k bins (3 billion bases in the genome divided by 10k), containing ...
  • The Organizational Hub and Web Portal for the 4D Nucleome ...
    • The Organizational Hub and Web Portal for the 4D Nucleome ...
    • https://grantome.com/grant/NIH/U01-CA200147-05
    • Large cohorts of data are being generated to investigate the impact of the temporal changes of nuclear organization (the 4D nucleome) to normal development and disease processes. The primary goal of this proposal is the creation of an effective organizational hub and web portal for the 4D nucleome.
  • RFA-RM-14-010: 4D Nucleome Network Organizational Hub (U01)
    • RFA-RM-14-010: 4D Nucleome Network Organizational Hub (U01)
    • https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-010.html
    • RFA-RM-14-011 4D Nucleome Network – Data Coordination amp; Integration Center (U01) ... (4DN-VRR) to be developed by 4DN-OH, as well as an interface with the data portal that will be developed and maintained by the 4DN-DCIC, in order to allow investigators within and outside of the 4DN Network access to all data, tools, and reagents generated by ...
  • Clinical Genomic Analysis Platform - GitHub Pages
    • Clinical Genomic Analysis Platform - GitHub Pages
    • https://alexkb0009.github.io/cgap-portal
    • 4D Nucleome Data Portal. Data coordination portal for the 4D Nucleome (4DN) project built in Harvard Medical School’s Department of Biomedical Informatics (HMS DBMI)....
  • Data | Guttman Lab at Caltech
    • Data | Guttman Lab at Caltech
    • https://guttmanlab.caltech.edu/lab-resources/data/
    • 4D Nucleome Data Portal . Single Cell SPRITE Downloads. Data from GEO . SARS-CoV-2 Downloads. SARS-CoV-2 protein-RNA interactions SARS-CoV-2 Nascent and total RNA-Seq data. Guttman Lab. California Institute of Technology 1200 E California Blvd MC 140-18 Pasadena, CA 91125 Quick Links. Research: Protocols: Publications: Software: Technologies: Data:
  • Zhong lab software - systemsbio.ucsd.edu
    • Zhong lab software - systemsbio.ucsd.edu
    • https://systemsbio.ucsd.edu/softwarelist.html
    • 4D Nucleome web portal. This web portal is the first entry point for biomedical researchers and scientists to the 4D Nucleome (4DN) network. 4DN resources, data, and protocols can be retrieved through this web portal. GeNemo search engine. A web-based search engine for functional genomic data.
  • Welcome to Zhong Lab of Systems Biology
    • Welcome to Zhong Lab of Systems Biology
    • https://systemsbio.ucsd.edu/index.html
    • Mapping personal functional data to personal genomes. Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong. Bioinformatics, 2011, 27(24):3427-3429. Text. Software; ... 4D Nucleome web portal. 4D Nucleome Portal. Entry to NIH 4D Nucleome network. COURSES. BENG100: Probability for Bioengineering
  • Research Resources | Center for Strategic Scientific ...
    • Research Resources | Center for Strategic Scientific ...
    • https://cssi.cancer.gov/research-resources
    • 4D Nucleome Data Portal. A platform to search, visualize, and download nucleomics data. Bioinformatics Tools. Tools from the ITCR program that support the analysis of -omics, imaging, and clinical data, as well as network biology and data standards ...
  • 4D Retinal Nucleome Initiative - PeCan | St. Jude Cloud
    • 4D Retinal Nucleome Initiative - PeCan | St. Jude Cloud
    • https://pecan.stjude.cloud/retinalnucleome
    • a variant found only in a tumor sample. a variant that arose in recurrence tumor. The Audacious Goals Initiative (AGI) is an effort by the National Eye Institute to push the boundaries of vision science. By facilitating cross-disciplinary research, the AGI is tackling the most devastating and difficult-to ...
  • The 4D Nucleome Data Portal: a resource for searching and ...
  • Schema for Hi-C and Micro-C - Comparison of Micro-C and In ...
    • Schema for Hi-C and Micro-C - Comparison of Micro-C and In ...
    • https://genome-euro.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=regulation&hgta_track=hicAndMicroC&hgta_table=h1hescMicroC&hgta_doSchema=describe+table+schema
    • Data Access The data for this track can be explored interactively with the Table Browser in the interact format. Direct access to the raw data files in .hic format can be obtained from the 4D Nucleome Data Portal at the URL provided in the Methods section or from our own download server.
  • NIH Establishes 4D Nucleome Research Centers and ...
    • NIH Establishes 4D Nucleome Research Centers and ...
    • https://health.ucsd.edu/news/releases/Pages/2015-10-05-NIH-4D-nucleome-hub.aspx
    • In collaboration with another one of the six program initiatives, the Data Coordination and Integration Center, the organizational hub will create a web portal and serve as a community-wide resource and point of access for all data, protocols, reagents, resources and methods developed by 4D Nucleome Program investigators nationally and globally.
  • December Report – Appendix A – 4D Nucleome Deep Dive ...
    • December Report – Appendix A – 4D Nucleome Deep Dive ...
    • https://www.nih-cfde.org/resource/december-report-appendix-a-4d-nucleome-deep-dive/
    • 4D Nucleome Site Visit 4D Nucleome Overview Program Lifestage Data Platform Harmonization and Metadata Sustainability Training FAIR Cross-pollination SSO (Single Sign-on) Outcomes Agenda. 4D Nucleome Site Visit. Location: Harvard Medical School. 302 ...
  • 4D Nucleome Network Data Coordination and Integration ...
  • Capturing cell type-specific chromatin structural patterns ...
    • Capturing cell type-specific chromatin structural patterns ...
    • https://www.biorxiv.org/content/10.1101/534800v1.full.pdf
    • Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data Hyeon-Jin Kim 1, Galip Gurkan Yardımcı#168; , Giancarlo Bonora , Vijay Ramani1,2, Jie Liu 1, Ruolan Qiu , Choli Lee1, Jennifer Hesson3,5, Carol B. Ware3,5, Jay Shendure1, Zhijun Duan 4,5, and William Stafford Noble 1,6 1Department of Genome Sciences, University of Washington
  • Alexander Balashov - Lead Front-End Developer - Harvard ...
  • Director's Report-Related Documents: February 2021
    • Director's Report-Related Documents: February 2021
    • https://www.genome.gov/event-calendar/92nd-Meeting-of-National-Advisory-Council-for-Human-Genome-Research/Directors-Report
    • 4D Nucleome (4DN) 4D Nucleome Data Portal 4D Nucleome Home Page 4D Nucleome Common Fund Program Page 4D Nucleome Common Fund Awards What is the 4D Nucleome Program? Video Nature - The 4D Nucleome Project: 30: All of Us Research Program All of Us Research Program Website All of Us News, Events, and Media page
  • NIH Awards UC San Diego Researchers $14.3 Million to ...
    • NIH Awards UC San Diego Researchers $14.3 Million to ...
    • https://health.ucsd.edu/news/releases/Pages/2020-10-13-nih-awards-uc-san-diego-researchers-14-milion-to-continue-4d-nucleome-research.aspx
    • 4D Nucleome Network Organizational Hub at UC San Diego. Funding for a second phase of the 4D Nucleome Program organizational hub was awarded to UC San Diego’s Sheng Zhong, PhD, professor of bioengineering, with Shu Chien, MD, PhD, professor of bioengineering and medicine and Ren as co-investigators.
  • Clara Bakker | Department of Biomedical Informatics
    • Clara Bakker | Department of Biomedical Informatics
    • https://dbmi.hms.harvard.edu/people/clara-bakker
    • Clara Bakker is a Junior Scientific Programmer at the 4D Nucleome Data Coordination and Integration Center, where she focuses on reproducible analysis of genomic data. Bakker is a graduate of Columbia University, where she received a B.A. in Computer Science and Mathematics.
  • Sarah Reiff - Senior Data Curator - Harvard Medical School ...
  • OMEGA | Open Microscopy Environment inteGrated Analysis
    • OMEGA | Open Microscopy Environment inteGrated Analysis
    • http://big.umassmed.edu/omegaweb/news/
    • In October 2018, Caterina became an associate member of the 4D Nucleome initiative with a project aimed at developing microscopy metadata and particle tracking standards to aide in the reproducibility of shared 4DN imaging datasets.. For more details about the aims of the 4DN project take a look here –gt;
  • People | Park Lab | Computational Genomics | Harvard
    • People | Park Lab | Computational Genomics | Harvard
    • https://compbio.hms.harvard.edu/people
    • 4DN Data Portal. [email protected] Clara Bakker. Jr. Scientific Programmer, 4D Nucleome DCIC. Clara Bakker is a Junior Scientific Programmer with the 4D Nucleome Data Coordination and Integration Center. She is a graduate of Columbia University in... Read more about Clara Bakker.
  • Postdoctoral Fellow - Genomics and Imaging Data ...
    • Postdoctoral Fellow - Genomics and Imaging Data ...
    • http://gehlenborglab.org/team/positions/postdoctoral-fellow-nucleomics-visualization/
    • We are hiring multiple postdoctoral fellows to develop novel visualization methods and tools for data generated by the NIH 4D Nucleome Consortium.This project is highly interdisciplinary and being conducted in close cooperation with computational and experimental domain experts, providing an excellent opportunity for collaborative research.
  • Genome Function Circa 2016: Updates from ENCODE and ...
    • Genome Function Circa 2016: Updates from ENCODE and ...
    • https://www.genome.gov/Multimedia/Slides/ENCODE2015/06-07_Pazin_Gilchrist.pdf
    • 4D Nucleome •Goals are to understand: • the principles of nuclear organization • the role of nuclear organization in cellular function, development, and disease ... • Data Portal (https://tcga-data.nci.nih.gov/tcga/), CGHub (https://cghub.ucsc.edu/) 22
  • July Report – Appendix B – Overview of all DCCs – Common ...
    • July Report – Appendix B – Overview of all DCCs – Common ...
    • https://www.nih-cfde.org/resource/july-report-appendix-b-overview-of-all-dccs/
    • Table of Contents: Kids First GTEx HMP/iHMP LINCS 4D Nucleome Metabolomics MoTrPAC SPARC HuBMAP. Kids First. General description Integrates genomic and clinical data from different disease types to accelerate discovery using cloudbased analyses systems.. Cohorts / supported data sources Approximately 20 data contributors generating whole genome sequence data and, in some cases, ...
  • 4d data [KFX3J2]
    • 4d data [KFX3J2]
    • https://makeishi.rifugi.piemonte.it/data_4d.html
    • Search: data 4d. If you are looking for data 4d, simply look out our links below :

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4d nucleome data portal FAQ

Why is the 4D nucleome important to the common fund?

The Common Fund’s 4D Nucleome program aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.

What is the name of the 4D nucleome integration center?

Data Coordination and Integration Center (4DN-DCIC): 4DN-DCIC tracks, stores, and displays all data generated by 4D Nucleome investigators.

How many datasets are available in the 4DN portal?

Program deliverables currently available through the public 4DN Portal include nearly 2000 datasets from hundreds of experiments, 52 software packages and 23 protocols and reagents for researchers to use.

Is there a web portal for 4D nucleome?

Launch Data Portal The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization.