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--- 4dn:phase2:scientific_webinar [2022/09/23 09:32]
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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 =====
-**September 23, 2022**
+**August 22, 2025**
-**Moderator: Wenbo Li**
+**Zoom recording link**
-**Presenter: Andrew Schroeder** (4DN-DCIC) - //"////The 4DN Data Portal - Data, Resources and Tools to help elucidate nuclear organization in space and time" // ([[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>**September 23, 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 #1 ([[https://drive.google.com/file/d/1Loh2MC-8f1cs5TcAAXLzQCGK6ksWse71/view?usp=sharing|Announcement in PDF format]])**
+**Jodi Lee**
-//**“The 4DN Data Portal - Data, Resources and Tools to help elucidate nuclear organization in space and time” ** //
+**Grad Student**
-**Presenter: Andrew Schroeder, Senior Data Curator **
+[[jodi.lee@gladstone.ucsf.edu|]]
-Andrew Schroeder is currently working as part of the 4D Nucleome Data Coordination and Integration Center, assisting with project management and focusing on data management. Andrew received his PhD in Molecular and Cellular Biology from UMass, Amherst, followed by postdoctoral research at Tufts Medical School on circadian rhythms and neurobiology in Drosophila. Andrew then joined FlyBase, a database of Drosophila Genes and Genomes as a data curator and software developer at Harvard University, shifting from wet lab research to computational biology before joining the Park lab and the 4DN-DCIC.
+**Title: //“Predictive modeling to assess the role of 3D genome folding in human congenital heart disease”// **
-**4DN - DCIC**
+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.
-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 organization affect normal development as well as various diseases. To that end, the 4DN data portal hosts a variety of data generated from sequencing and imaging based assays, with an emphasis on data from chromatin conformation capture (CCC) techniques and more recently multiplexed FISH imaging experiments.
+<font 14px/inherit;;inherit;;inherit>**8:30-9:00 am Pacific Time (20 minute presentation, 10 minute QA)**</font>
-This tutorial will introduce:
+**Yanyu Zhu**
-  * How to navigate the metadata to find those data that are of interest.
+**Postdoctoral Researcher**
-  * 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.
-===== HOW TO Join the Webinar =====
+[[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.**
-**Join Zoom Meeting**\\ [[https://4dnucleome-org.zoom.us/j/89394518110?pwd=Z01JN3VxNlZXYkoxdW1PYWNZTzdaQT09|https://4dnucleome-org.zoom.us/j/89394518110?pwd=Z01JN3VxNlZXYkoxdW1PYWNZTzdaQT09]]
+**4DN OH is inviting you to a scheduled Zoom meeting.**
-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]]
+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]]
+**Join Zoom Meeting**\\ [[https://4dnucleome-org.zoom.us/j/89394518110?pwd=Z01JN3VxNlZXYkoxdW1PYWNZTzdaQT09|https://4dnucleome-org.zoom.us/j/89394518110?pwd=Z01JN3VxNlZXYkoxdW1PYWNZTzdaQT09]]
 Meeting ID: 893 9451 8110\\ Passcode: 049455\\ One tap mobile\\ +16694449171,,89394518110#,,,,*049455# US\\ +16699006833,,89394518110#,,,,*049455# US (San Jose)
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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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