Education & Outreach

Past and up-coming conferences and tutorial material advertising 4DN progress with workshops and scientific talks.

Tutorial for 4DN new members

Welcome to 4DN! Watch this video on YouTube to learn how to use 4DN tools and services!

Tutorial Materials

This is a list of past and up-coming conferences and tutorial material advertising 4DN progress with workshops
and scientific talks. If you have any suggestion please contact us sending an email to oh@4dnucleome.org

4DN Investigator Featured on 'Science Happens!'
In Episode 5 of 'Science Happens,' named: 'Everything you thought you knew about the shape of DNA is wrong'. Watch Dr. Job Dekker describe how the folding of DNA strands holds cues to human health here.
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Conversations: A Guide to Packing Your DNA
Genetic material is not randomly organized within the nucleus of a cell. How this organization occurs and why it matters are questions that Cell editor Marta Koch posed to Mitchell Guttman, Job Dekker, and Stavros Lomvardas. The 4D Nucleome grantees Drs. Job Dekker, Mitchell Guttman, and Stavros Lomvardas discuss the organization of genetic material in the nucleus, how it occurs, and why it matters.
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A quick guide to 4DN visualization software
Plot a course through the genome: inspired by Google Maps, a suite of tools is allowing researchers to chart the complex conformations of chromosomes.
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Hi-C Data Analysis Bootcamp
A tutorial on measuring, analyzing, and visualizing the 3D genome with Hi-C provided by Harvard, MIT, and UMassMed (Burak Alver, Nils Gehlenborg and Peter Park).
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Reporting and Reproducibility in Microscopy

The Nature Methods FOCUS issue on Reporting and reproducibility in microscopy features a series of papers that emerged from the work of the 4D Nucleome Imaging Working group in collaboration with BioImaging North America, QUAREP-LiMi, and Global Bioimaging, offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use. Following up on this work, Nature Methods featured two editorials describing the importance of Imaging standards to ease reproducibility and the everyday and The making microscope camera standards by bringing together the imaging community with microscope camera manufacturers.
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TechBlog: HiPiler simplifies chromatin structure analysis

A blog post about the software HiPiler from Nils Gehlenborg Lab published on Nature.
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4DN Perspectives

A Conundrum in 3D Genome Organization and Expression?

Author: Thoru Pederson

Institution: Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School

To read the paper click here.

4DN Tutorial #1 - The 4DN Data Portal - Data, Resources and Tools to help elucidate nuclear organization in space and time

When: September 23, 2022
Where: Virtual on Zoom

Presenter: Andrew Schroeder, Senior Data Curator (4DN-DCIC)

YouTube recording: Go to the video

 

This tutorial introduces:

– How to navigate the metadata to find those data that are of interest.

– How to download data files.

– How CCC and other genomic data can be visualized in the portal with HiGlass.

– How to find information and software used on the portal for standardized bioinformatics analyses.

– Highlighted data collections and resources.

– A hosted Jupyterhub for preliminary data exploration on the cloud.

4DN Tutorial #2 - Multimodal Visualization for 4DN data using Nucleome Browser and OME

When: October 28, 2022. 8AM-9AM PST.
Where: Virtual on Zoom

Presenter: Yang Zhang, Project Scientist (CMU – Swedlow Team)

YouTube recording: Go to the video

 

This tutorial introduces:

– Overview the different data types for probing 3D genome organization, including sequencing-based, imaging-based methods, and integrative modeling and analysis results.

– How to search and navigate genomic data.
– How to perform integrative visualization on multimodal datasets.
– How to host private data to perform integrative analysis on the Nucleome Browser using resources from 4DN and other consortia for 3D epigenomics analysis.
– Demonstration on imaging-omics integrative exploration using Nucleome Browser and IDR.

4D YouTube Channel

Click below to visit the official 4D Nucleome YouTube channel. You can
watch webinars, workshops and other 4DN-related videos are posted. Subscribe to the channel!

4DN YouTube Channel

Upcoming Workshops & Conferences

Third Annual Meeting on Advances in Nuclear Topology and 3D Chromatin Architecture in Cancer

When: November 8, 2022
Where: FREE Virtual Symposium on Zoom

Registration: https://nyulangone.zoom.us/webinar/register/WN_gAxtTi0GTsaElot1qMBZaw

Past Workshops & Conferences

CytoData Symposium 2022

Keystone Symposia: Higher-Order Chromatin Architecture in Time and Space

When: November 15-17, 2021. 10AM EST.
Where: Virtual Meeting
Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas

Higher-Order Chromatin Architecture in Time and Space

The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.

When: March 15 – 19, 2020
Where: Whistler Conference Centre, Whistler, BC, Canada
Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas

2019 4DN-ASCB Satellite Meeting

Bridging the 4D Genome with Cell Biology
When: December 5-6, 2019
Where: Capital Hilton, Washington, D.C.
Meeting Committee Chairs: Jennifer Phillips-Cremins, Bing Ren, Sheng Zhong

2019 Gordon Research Conference

Genome Architecture in Cell Fate and Disease: The Eukaryotic Genome in 4 Dimensions: Integrative Approaches to Bridging Genotype and Phenotype
When: August 4-9, 2019
Where: The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
Organizers: Dave Gilbert, Yijun Ruan, Victor Corces and Danny Leung

François Jacob Conference

Evolution, Structure and Function of Chromosomes High Order Structure
When: June 4-7, 2019
Where: Institute Pasteur, Paris, France

Second Annual Meeting on Advances on Nuclear Topology and 3D Chromatin Architecture in Cancer

When: September 24, 2021
Where: Virtual on Zoom
Scientific Organizers: Jane Skok, Iannis Aifantis, Ari Melnick

The Four-Dimensional Genome

This symposium brought together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.

Where: EMBL Heidelberg, Germany
Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.

Long-Read Sequencing Workshop

When: September 17-20, 2019
Where: The Jackson Laboratory for Genomic Medicine, Farmington, CT
Organizers: Chia-Lin Wei, Rachel Goldfeder

2020 FASEB meeting on Nuclear Bodies

When: July 26-31, 2019
Where: Oak island Resort and Conference Center, Nova Scotia, Canada
Organizers: Paul Kaufman, Karla Neugebauer, Thoru Pederson

Southwestern Bioinformatics Conference

When: May 31, 2019
Where: Sanford Consortium, San Diego, CA

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