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--- 4dn:phase1:working_groups:joint_4d_nucleome_analysis [2020/11/12 13:22]
yanzm [Meeting Archives]
+++ 4dn:phase1:working_groups:joint_4d_nucleome_analysis [2025/04/22 16:21] (current)
@@ Line 13: / Line 13: @@
   * [[https://docs.google.com/spreadsheets/d/1ONfcbvM1iP30vhStJuOemho039hMA0juFvjEU92zse4/edit#gid=0|Data generation plan (Google sheets)]]
-  * **<font inherit/inherit;;#2980b9;;inherit><font inherit/inherit;;inherit;;#ffff33>[[https://wiki.4dnucleome.org/4dn:working_groups:jawg_sandbox|Data analysis sandbox, with links to analysis products]]</font></font>**
+  * **<font inherit/inherit;;#2980b9;;inherit><font inherit/inherit;;inherit;;#ffff33>[[https://wiki.4dnucleome.org/4dn:phase2:working_groups:jawg_sandbox?s[]=sandbox|Data analysis sandbox, with links to analysis products]]</font></font>**
   * 2019 Dec:**<font inherit/inherit;;inherit;;#ffff33><font inherit/inherit;;#e74c3c;;inherit>[[https://docs.google.com/document/d/1TNk17MMvh1iuMugyuU1QImmOYDwojt85f02XdJYw47M/edit|Joint Analysis Marker Paper Outline]]</font></font>**
   * 2019 May: **<font inherit/inherit;;inherit;;#ffff33><font inherit/inherit;;#e74c3c;;inherit>[[https://docs.google.com/spreadsheets/d/1HqXeIBTcOnb-dVgqgRzpQcdi9A9bf3jITx2K5vwvUTg/edit#gid=0|Joint Analysis paper plan tracking table]]</font></font>**
@@ Line 240: / Line 239: @@
 |10/15/2020|Kai Sandvold Beckwith|Ellenberg Lab|A method to resolve the nanoscale fold of chromosomal DNA below five kilobase resolution in single human cells under near-native conditions|~~CKG_TABLE_NBSP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |10/29/2020|Andrew D Stephens|Stephens Lab|HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics|~~TABLE_CELL_WRAP_START~~<WRAP>
 [[https://drive.google.com/file/d/1ZyrbGxJaC5I7LAO6lc4urU6DQx-qQ_x1/view?usp=sharing|Link]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |10/29/2020|Jennifer E. Phillips-Cremins|Phillips-Cremins Lab|Dissecting the genome’s structure function-relationship during replication|~~CKG_TABLE_NBSP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
-|11/12/2020|Caterina Strambio De Castillia|Strambio De Castillia Lab|Micro-Meta App, an interactive tool for the collection of microscopy metadata based on the 4DN-OME tiered system of guidelines|~~CKG_TABLE_NBSP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
+|11/12/2020|Caterina Strambio De Castillia|Strambio De Castillia Lab|Micro-Meta App, an interactive tool for the collection of microscopy metadata based on the 4DN-OME tiered system of guidelines|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[https://drive.google.com/file/d/1_iOqrOImFZIIZ7zGrUTqp2m4gzAWQRGh/view?usp=sharing|Link]]
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>
+[[https://drive.google.com/file/d/1_f3N3oYryKPtgSLWgUmTKf8ZZ17bg-07/view?usp=sharing|Link to recording]]
+</WRAP>~~TABLE_CELL_WRAP_STOP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |11/12/2020|Kaustav Sengupta and~~CKG_TABLE_NBSP~~Dariusz Plewczynski|Plewczynski Lab|Phase condensation by percolation model with the single chromatin loop resolution|~~CKG_TABLE_NBSP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
@@ Line 254: / Line 259: @@
 ===== Meeting Archives =====
+  * November 12, 2020
+    * Meeting Agenda:
+      * Presentation by Dr. Caterina Strambio De Castillia: Micro-Meta App, an interactive tool for the collection of microscopy metadata based on the 4DN-OME tiered system of guidelines
+      * Presentation by Drs. Kaustav Sengupta and Dariusz Plewczynski: Phase condensation by percolation model with the single chromatin loop resolution
+  * October 29, 2020
+    * Meeting Agenda:
+      * Presentation by Dr. Andrew D Stephens: HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
+      * Presentation by Dr. Jennifer E. Phillips-Cremins: Dissecting the genome’s structure function-relationship during replication
+  * October 15, 2020
+    * Meeting Agenda:
+      * Presentation by Dr. Kai Sandvold Beckwith (Ellenberg Lab): A method to resolve the nanoscale fold of chromosomal DNA below five kilobase resolution in single human cells under near-native conditions
+  * October 1, 2020
+    * Meeting Agenda:
+      * Presentation by Dr. Andrew Belmont: Integrative genome-wide analysis of nuclear compartmentalization in human cells
+      * Presentation by Dr. David Grunwald: Meta-max: an easy-to-use calibration tool to maximize the value of fluorescence microscopy data
+  * September 17, 2020
+    * Meeting Agenda:
+      * Presentation by Dr. Minji Kim (Ruan Lab): Cohesin-mediated chromatin folding dynamics and transcriptional interactions
+      * Presentation by Xingzhao Wen (Zhong Lab): Genome-wide RNA-chromatin interaction reveals RNA localization specificity along the nucleus radial axis
   * September 3, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Dr. Daofeng Li (Wang Lab): Update on the WashU Epigenome Browser — Supporting 4DN and Beyond
-        * Presentation by Dr. Daofeng Li (Wang Lab): Update on the WashU Epigenome Browser — Supporting 4DN and Beyond
   * August 20, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Dr. Burak Alver: 4DN Data Portal and JAWG Data
+      * Presentation by Dr. Derek Janssens: High-Throughput Chromatin Profiling Identifies Pathological Chromatin Signatures in Pediatric Acute Leukemia
-        * Presentation by Dr. Burak Alver: 4DN Data Portal and JAWG Data
-        * Presentation by Dr. Derek Janssens: High-Throughput Chromatin Profiling Identifies Pathological Chromatin Signatures in Pediatric Acute Leukemia
   * August 6, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Dr. Frank Alber: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
+      * Presentation by Dr. Betul Akgol Oksuz: Comprehensive evaluation of 3C parameters identifies optimal methods for compartment or loop detection
-        * Presentation by Dr. Frank Alber: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
-        * Presentation by Dr. Betul Akgol Oksuz: Comprehensive evaluation of 3C parameters identifies optimal methods for compartment or loop detection
   * July 23, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Dr. Jie Liu: Connecting high-resolution 3D chromatin organization with epigenomics
+      * Presentation by Dr. Caterina Strambio De Castillia: Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
-        * Presentation by Dr. Jie Liu: Connecting high-resolution 3D chromatin organization with epigenomics
-        * Presentation by Dr. Caterina Strambio De Castillia: Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
   * July 9, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Ruochi Zhang (Ma Lab): Exploiting single cell Hi-C data using Higashi
+      * Presentation by Dr. Warren Winick-Ng (Pombo Lab): Cell-type specialization in the brain is encoded by specific long-range chromatin topologies
-        * Presentation by Ruochi Zhang (Ma Lab): Exploiting single cell Hi-C data using Higashi
+      * Presentation by Riccardo Calandrelli (Zhong Lab): Dynamic Changes in RNA-Chromatin Interactome Promote Endothelial Dysfunction
-        * Presentation by Dr. Warren Winick-Ng (Pombo Lab): Cell-type specialization in the brain is encoded by specific long-range chromatin topologies
-        * Presentation by Riccardo Calandrelli (Zhong Lab): Dynamic Changes in RNA-Chromatin Interactome Promote Endothelial Dysfunction
   * June 25, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Dr. Jian Ma: Nucleome Browser: A multimodal, interactive data exploration platform for the 4D Nucleome (15+5 mins)
+      * Presentation by Dr. Naoki Kubo (Ren Lab): Active role of CTCF in enhancer-promoter contacts and gene expression (15+5 mins)
-        * Presentation by Dr. Jian Ma: Nucleome Browser: A multimodal, interactive data exploration platform for the 4D Nucleome (15+5 mins)
+      * Presentation by Dr. Hui Huang (Ren Lab): CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains (15+5 mins)
+    * Recordings: https://drive.google.com/file/d/1OV0yWfU_T1aaPvSi49Ei6gKFdAhxu8Fj/view
-        * Presentation by Dr. Naoki Kubo (Ren Lab): Active role of CTCF in enhancer-promoter contacts and gene expression (15+5 mins)
-        * Presentation by Dr. Hui Huang (Ren Lab): CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains (15+5 mins)
-      * Recordings: [[https://drive.google.com/file/d/1OV0yWfU_T1aaPvSi49Ei6gKFdAhxu8Fj/view|https://drive.google.com/file/d/1OV0yWfU_T1aaPvSi49Ei6gKFdAhxu8Fj/view]]
   * May 14, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Jian Ma: Integrative analysis of nuclear compartmentalization in human cell
+      * Presentation by Alber Lab: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
-        * Presentation by Jian Ma: Integrative analysis of nuclear compartmentalization in human cell
-        * Presentation by Alber Lab: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
   * April 16, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Luca Fiorillo and Francesco Musella (Nicodemi’s Lab): Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin
-        * Presentation by Luca Fiorillo and Francesco Musella (Nicodemi’s Lab): Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin
   * April 2, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Planning the set of 4DN papers, the marker paper, and the Mol Cell review.
-        * Planning the set of 4DN papers, the marker paper, and the Mol Cell review.
   * February 20, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Luca Fiorillo and Francesco Musella (Nicodemi Lab): Comparison of the Hi-C, GAM and SPRITE by use of polymer models of chromatin
+      * Presentation by Xingzhao Wen (Zhong Lab): Joint analysis of global RNA-DNA interaction data (iMARGI) and other 4DN omics data
-        * Presentation by Luca Fiorillo and Francesco Musella (Nicodemi Lab): Comparison of the Hi-C, GAM and SPRITE by use of polymer models of chromatin
-        * Presentation by Xingzhao Wen (Zhong Lab): Joint analysis of global RNA-DNA interaction data (iMARGI) and other 4DN omics data
   * February 6, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Presentation by Pombo Lab: Selection of H1 hESC genomic features and genomic window classification for joint analysis 3D-1D integration
-        * Presentation by Pombo Lab: Selection of H1 hESC genomic features and genomic window classification for joint analysis 3D-1D integration
   * January 9, 2020
+    * Meeting Agenda:
-      * Meeting Agenda:
+      * Updates by every group on current ongoing analyses
+      * Discussion of coordination of paper submission
-        * Updates by every group on current ongoing analyses
-        * Discussion of coordination of paper submission
 ===== Older Meeting Archives =====

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