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--- 4dn:phase2:scientific_webinar [2023/03/22 16:59]
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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 =====
-**March 24, 2023**
+**August 22, 2025**
-**Moderator: Sui Huang**
+**Zoom recording link**
-**Presenter: Meng Xu **// (Carnegie Mellon University)// - //"TERRA-LSD1 condensates promote R-loop formation for telomere maintenance in ALT cancer cells////”// ([[https://docs.google.com/presentation/d/1ViC3BBr_LlEhrvjbk7HH7WGQXFh7dH17/edit?usp=share_link&ouid=105768913603538088409&rtpof=true&sd=true|Link to presenter slides]])
+**Moderator: Yuan Liu**
-**Presenter: Yarui Diao** (//Duke University//) - //"Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells”// (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]].
+**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]].
   * Scientific Webinar presentations (Phase 2) can be found [[https://wiki.4dnucleome.org/4dn:phase2:scientific_webinar_archive|here]].
 ===== 4DN Scientific Webinar Series =====
-<font 16px/inherit;;inherit;;inherit>**March 24, 2023**</font>
+<font 16px/inherit;;inherit;;inherit>**August 22, 2025**</font>
 <font 14px/inherit;;inherit;;inherit>**8:00-8:30 am Pacific Time (20 minute presentation, 10 minute QA)**</font>
-{{:4dn:phase2:meng-xu.jpg?nolink&250x200|meng-xu.jpg}}
+**Jodi Lee**
-**Meng XU**
+**Grad Student**
-**Postdoctoral Fellow**
+[[jodi.lee@gladstone.ucsf.edu|]]
-[[mengx@andrew.cmu.edu|]]
+**Title: //“Predictive modeling to assess the role of 3D genome folding in human congenital heart disease”// **
-**Title: "TERRA-LSD1 condensates promote R-loop formation for telomere maintenance in ALT cancer cells"**
+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.
-Dr. Meng Xu earned his Ph.D. degree from the Institute of Genetics and Developmental Biology (IGDB), Chinese Academy of Sciences (CAS) in 2016. Currently, he is working as a postdoctoral fellow in Prof. Huaiying Zhang's lab at Carnegie Mellon University. His current research focuses on the formation of protein-protein or protein-RNA condensates by phase transition and their biological roles in physiological and pathological conditions.
 <font 14px/inherit;;inherit;;inherit>**8:30-9:00 am Pacific Time (20 minute presentation, 10 minute QA)**</font>
-{{:4dn:phase2:yaruidiao.png?nolink&250x200}}
+**Yanyu Zhu**
-**Yarui Diao**
+**Postdoctoral Researcher**
-Assistant Professor
+[[yanyuzhu@stanford.edu|]]
-**[[yarui.diao@duke.edu|]]**
+**Title: //“High-resolution Dynamic Imaging of Chromatin DNA Communication using Oligo-LiveFISH”// **
-**Title: "****Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells"**
+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.
-<font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit>Yarui earned his PhD in Biochemistry under the guidance of Dr. Zhenguo Wu in 2011 from the Hong Kong University of Science and Technology. During his graduate studies, he focused primarily on the transcription and epigenetic regulation of skeletal muscle regeneration. Following his PhD, Yarui pursued postdoctoral training in gene regulation under the mentorship of Dr. Bing Ren at UC San Diego as a Human Frontier Science Program (HFSP) fellow. During this time, he expanded his knowledge of gene regulation and developed a strong interest in genomics. In 2018, Yarui established his independent research program, "Regeneration Genomics," at Duke Cell Biology, where he investigates gene regulation of tissue regeneration in injury and diseases. His lab is dedicated to developing innovative genomics tools and applying genomics technologies to study stem cell biology tissue regeneration in health and disease.</font></font></font></font>
-===== HOW TO Join the Webinar =====
 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]]
@@ Line 95: / Line 91: @@
 <font 16px/inherit;;inherit;;inherit>**Next Scientific Webinar Presentation**</font>
-**When: April 28, 2023**
-**Moderator: Yin Shen**
-  * Presenter from **Sheng Zhong****'s**  team
-  * Presenter from **Jennifer Phillips-Cremins (contact), Gerd Blobel, Lei Stanley Qi, Arjun Raj****'s team **

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