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--- 4dn:phase2:scientific_webinar [2022/10/21 07:01]
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+++ 4dn:phase2:scientific_webinar [2025/08/22 08:04] (current)
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@@ Line 5: / Line 5: @@
 **<font inherit/inherit;;#c0392b;;inherit>Scientific Webinar Calendar:</font> **  [[https://4dnucleome-org.zoom.us/meeting/tJEsc-ytrDksEtWNHy00h-5RmkNx7equ3Nca/ics?icsToken=98tyKuCtrz8vH9aXthGGRowMBY-gZ-_zpnpdj7dqsjf8U3BbL1bEO-lsKuV6Ac2D|click here]] to add all the Scientific Webinar events to your personal calendar
-<font inherit/inherit;;#c0392b;;inherit>**Scientific Webinar Assignments (2021-2024):**</font> [[http://docs.google.com/spreadsheets/d/122eouLgJtMoCJNKmNhygufdU1qqEy-dDomxqqyQ1TxM/edit?usp=sharing|docs.google.com/spreadsheets/d/122eouLgJtMoCJNKmNhygufdU1qqEy-dDomxqqyQ1TxM/edit?usp=sharing]]
+<font inherit/inherit;;#c0392b;;inherit>**Scientific Webinar Assignments (2021-2025):**</font> [[http://docs.google.com/spreadsheets/d/122eouLgJtMoCJNKmNhygufdU1qqEy-dDomxqqyQ1TxM/edit?usp=sharing|docs.google.com/spreadsheets/d/122eouLgJtMoCJNKmNhygufdU1qqEy-dDomxqqyQ1TxM/edit?usp=sharing]]
 ===== Mission =====
@@ Line 19: / Line 19: @@
 The Webinar organization committee has discussed and come up with a schedule for presentations after February 2021. See the schedule here: [[https://docs.google.com/spreadsheets/d/122eouLgJtMoCJNKmNhygufdU1qqEy-dDomxqqyQ1TxM/edit?usp=sharing|Scientific Webinar Assignment 2021-2024]].
-The schedule is ranked by funded project and the corresponding PI's last name. While the corresponding PI is put in the presentation slot, it is up to the corresponding PI to decide who in their team is to give the talk. It is encouraged that trainees are given the chance to present. If the corresponding PI wants to switch with someone else on the list in a mutual agreement, then she/he has the responsibility to arrange it and let the Webinar organization committee know.
+**The schedule is ranked by funded project and the corresponding PI's last name. While the corresponding PI is put in the presentation slot, it is up to the corresponding PI to decide who in their team is to give the talk. It is encouraged that trainees are given the chance to present. If the corresponding PI wants to switch with someone else on the list in a mutual agreement, then she/he has the responsibility to arrange it and let the Webinar organization committee know.**
 **Scientific Webinar Committee: **Ana Pombo, Golnaz Vahedi, Sheng Zhong, Ting Wang, Wenbo Li, Sui Huang, Yin Shen, Taekjip Ha
@@ Line 25: / Line 25: @@
 ===== Scientific Webinar Series slides presentations =====
-**October 28, 2022**
+**August 22, 2025**
-**Moderator: Ana Pombo**
+**Zoom recording link**
-**Presenter: Yang Zhang** (CMU - Swedlow Team) - //"Multimodal Visualization for 4DN data using Nucleome Browser and OME”// ([[https://drive.google.com/file/d/1Ya9ZpqGyNI_7E9aAPotqmfZPal3xdUto/view?usp=sharing|Link to presenter slides]])
+**Moderator: Yuan Liu**
+**Presenter: Jodi Lee **//(University of California, San Francisco) //**-** //**"Predictive modeling to assess the role of 3D genome folding in human congenital heart disease"**//  ([[https://drive.google.com/file/d/11mB2tB0l9egVjxAfJckfR3CKb3hy0qxe/view?usp=sharing|Link to presenter slides]])
+**Presenter: Yanyu Zhu** //(Stanford University) //- **//“High-resolution Dynamic Imaging of Chromatin DNA Communication using Oligo-LiveFISH”//**  ([[https://docs.google.com/presentation/d/1o9bXE1ZnWB0bxaXBYzDf1GE14dgzolUx/edit?usp=drive_link&ouid=105768913603538088409&rtpof=true&sd=true|Link to presenter slides]])
   * Scientific Webinar presentations (Phase 1) can be found [[https://wiki.4dnucleome.org/4dn:phase1:scientific_webinar_series:scientific_webinar_presentation_archive|here]].
@@ Line 36: / Line 40: @@
 ===== 4DN Scientific Webinar Series =====
-<font 16px/inherit;;inherit;;inherit>**October 28, 2022**</font>
+<font 16px/inherit;;inherit;;inherit>**August 22, 2025**</font>
-<font 14px/inherit;;inherit;;inherit>**8:00-9:00 am Pacific Time,**</font>
+<font 14px/inherit;;inherit;;inherit>**8:00-8:30 am Pacific Time (20 minute presentation, 10 minute QA)**</font>
-**4DN Tutorial Series #2 ([[https://drive.google.com/file/d/1Loh2MC-8f1cs5TcAAXLzQCGK6ksWse71/view?usp=sharing|Announcement in PDF format]])**“Multimodal Visualization for 4DN data using Nucleome Browser and OME”
+**Jodi Lee**
-**Presenter: Yang Zhang, (Project Scientist, CMU, Swedlow Team)**
+**Grad Student**
-The 4D Nucleome (4DN) project has been generating a large collection of multimodal datasets including genomic data, imaging data, structure modeling and other analysis results with an important goal to provide navigable reference maps of the 4D Nucleome for a diverse set of human cells. However, how to make effective comparisons, coherent integration, and user-friendly visualization of such multimodal data remains a challenge. In this tutorial, we will introduce the recently developed Nucleome Browser ([[http://vis.nucleome.org|http://vis.nucleome.org]]), a multimodal, interactive data visualization and exploration platform for 4DN data. In particular, for the imaging-omics integration, the Nucleome Browser team works with OME team to develop a unique web application to perform integrative data exploration between data hosted on the Nucleome Browser and imaging data hosted on the Image Data Resources (IDR).
+[[jodi.lee@gladstone.ucsf.edu|]]
-Tutorial schedules:
+**Title: //“Predictive modeling to assess the role of 3D genome folding in human congenital heart disease”// **
-  * Overview the different data types for probing 3D genome organization, including sequencing-based, imaging-based methods, and integrative modeling and analysis results.
+Jodi is a 4th year graduate student studying genetics in Dr. Katherine Pollard’s Lab at the University of California, San Francisco. Jodi’s research focuses on creating and working with deep learning models to study the complex DNA sequence grammar regulating the genome. Currently, she is leveraging Cardiac-Akita, a DNA sequence to 3D genome folding deep learning model, to predict how genetic variants associated with congenital heart defects disrupt 3D genome contacts.
-  * 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
-===== HOW TO Join the Webinar =====
+<font 14px/inherit;;inherit;;inherit>**8:30-9:00 am Pacific Time (20 minute presentation, 10 minute QA)**</font>
+**Yanyu Zhu**
+**Postdoctoral Researcher**
+[[yanyuzhu@stanford.edu|]]
+**Title: //“High-resolution Dynamic Imaging of Chromatin DNA Communication using Oligo-LiveFISH”// **
+Yanyu Zhu is a postdoctoral researcher in Prof. Stanley Qi’s Lab in the Department of Bioengineering at Stanford University. He obtained his B.S. in Chemistry from Peking University and his Ph.D. in Chemistry from the University of Wisconsin–Madison. In collaboration with Prof. W. E. Moerner’s lab, he developed and applied a high-resolution, reagent-based DNA imaging platform, Oligo-LiveFISH, to investigate 3D chromatin dynamics in live cells. His current research focuses on applying Oligo-LiveFISH to study various biological questions such as the relationship between the 3D genome and gene regulation in real time, as well as investigating the dynamic process of DNA repair.
 The Webinar Series will be on the **4th Friday of each month from 8am-9am Pacific Time, 11am-12pm Eastern Time.**
-DN OH is inviting you to a scheduled Zoom meeting.
+**4DN OH is inviting you to a scheduled Zoom meeting.**
 Topic: 4DN Scientific Webinar\\ Please download and import the following iCalendar (.ics) files to your calendar system.\\ Monthly: [[https://4dnucleome-org.zoom.us/meeting/tZ0ufu2trzMrG9SNYBoxiO0YxjK3-LEvoHWL/ics?icsToken=98tyKuGhrTIuH9WdsRiHRpx5A4r4LO_zmFxcjfpusibHDDhaTVPPLuhpYf9TNc7f|https://4dnucleome-org.zoom.us/meeting/tZ0ufu2trzMrG9SNYBoxiO0YxjK3-LEvoHWL/ics?icsToken=98tyKuGhrTIuH9WdsRiHRpx5A4r4LO_zmFxcjfpusibHDDhaTVPPLuhpYf9TNc7f]]
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 <font 16px/inherit;;inherit;;inherit>**Next Scientific Webinar Presentation**</font>
-**When: October 28, 2022**
-**Moderator: Ana Pombo**
-  * **4DN Tutorial Series # 2****Jason Swedlow/OME Team joint with Jian Ma/Nucleome Browser team**

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