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4dn:phase1:working_groups:joint_4d_nucleome_analysis [2020/09/03 01:57] yanzm [JA presentations in 2020:] |
4dn:phase1:working_groups:joint_4d_nucleome_analysis [2025/04/22 16:21] (current) |
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| * [[https://docs.google.com/spreadsheets/d/1ONfcbvM1iP30vhStJuOemho039hMA0juFvjEU92zse4/edit#gid=0|Data generation plan (Google sheets)]] | * [[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 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>** | * 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>** | ||
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| **If you want to share your slides, please sent them to Zhangming (Frank) email: <yanzm@ucsd.edu>** | **If you want to share your slides, please sent them to Zhangming (Frank) email: <yanzm@ucsd.edu>** | ||
| - | ==== ==== | ||
| ==== JA presentations in 2020: ==== | ==== JA presentations in 2020: ==== | ||
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| ~~CKG_TABLE_NBSP~~ | ~~CKG_TABLE_NBSP~~ | ||
| - | [[https://drive.google.com/file/d/15167FEBhT0OJ5XM_BIsjVR0uVDysE4HP/view?usp=sharing|Link to recording]] | + | [[https://drive.google.com/file/d/15167FEBhT0OJ5XM_BIsjVR0uVDysE4HP/view?usp=sharing|Link to meeting recording 08/06/2020]] |
| - | + | ||
| - | [[https://drive.google.com/file/d/15167FEBhT0OJ5XM_BIsjVR0uVDysE4HP/view?usp=sharing|08/06/2020]] | + | |
| </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| Line 203: | Line 199: | ||
| </WRAP>~~TABLE_CELL_WRAP_STOP~~| ~~TABLE_CELL_WRAP_START~~<WRAP> | </WRAP>~~TABLE_CELL_WRAP_STOP~~| ~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| - | [[https://drive.google.com/file/d/1B8QH_0o3Zhb-aR_4LO1rkiGbVNfsDOs1/view?usp=sharing|Link to recording]] | + | ~~CKG_TABLE_NBSP~~ |
| - | [[https://drive.google.com/file/d/1B8QH_0o3Zhb-aR_4LO1rkiGbVNfsDOs1/view?usp=sharing|08/20/2020]] | + | [[https://drive.google.com/file/d/1B8QH_0o3Zhb-aR_4LO1rkiGbVNfsDOs1/view?usp=sharing|Link to meeting recording 08/20/2020]] |
| </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| Line 213: | Line 209: | ||
| </WRAP>~~TABLE_CELL_WRAP_STOP~~|:::|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | </WRAP>~~TABLE_CELL_WRAP_STOP~~|:::|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| + | |09/03/2020|Daofeng Li|Wang Lab|~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | Updates on WashU Epigenome Browser: Supporting 4DN and beyond | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | [[https://drive.google.com/file/d/1BKEMikg_2nlw_HU0vfNSjUEdhB8kNWMD/view?usp=sharing|Link]] | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~| ~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | [[https://drive.google.com/file/d/1BKjITdBei4WfDndat5uGD4cdVEp9LHpX/view?usp=sharing|Link to meeting recording 09/03/2020]] | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| + | |09/17/2020|Minji Kim|Ruan Lab|Cohesin-mediated chromatin folding dynamics and transcriptional interactions|~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | [[https://drive.google.com/file/d/1BaysaDcaSa4GeVGoRY0c1Y6x86WTU5Bs/view?usp=sharing|Link]] | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~| ~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | [[https://drive.google.com/file/d/1C113IpTq9AqRBgfoDmiZVYYwxdtvSgv2/view?usp=sharing|Link to recording]] | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| + | |09/17/2020|Xingzhao Wen|Zhong Lab|Genome-wide RNA-chromatin interaction reveals RNA localization specificity along the nucleus radial axis|~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| + | |||
| + | [[https://drive.google.com/file/d/1BpIUz-nb-jTAAPCF9AlA_W8GoRirXDrt/view?usp=sharing|Link]] | ||
| + | |||
| + | </WRAP>~~TABLE_CELL_WRAP_STOP~~| ~~CKG_TABLE_NBSP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| + | |10/01/2020|Andrew Belmont|Belmont Lab|Integrative genome-wide analysis of nuclear compartmentalization in human cells|~~CKG_TABLE_NBSP~~| ~~CKG_TABLE_NBSP~~ |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| | ||
| + | |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|~~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~~| | ||
| === Older JA presentation archives === | === Older JA presentation archives === | ||
| - | * [[:4dn:working_groups:ja_presentations|Older JA presentation archives (2018 - 2019)]] | + | * [[:4dn:phase1:working_groups:ja_presentations|Older JA presentation archives (2018 - 2019)]] |
| ===== Meeting Archives ===== | ===== 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: | ||
| + | * Presentation by Dr. Daofeng Li (Wang Lab): Update on the WashU Epigenome Browser — Supporting 4DN and Beyond | ||
| + | * August 20, 2020 | ||
| + | * 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 | ||
| * August 6, 2020 | * August 6, 2020 | ||
| * Meeting Agenda: | * Meeting Agenda: | ||
| Line 263: | Line 328: | ||
| ===== Older Meeting Archives ===== | ===== Older Meeting Archives ===== | ||
| - | * [[:4dn:working_groups:jawg_meeting_archive|Older Meeting Archives (2017 - 2019)]] | + | * [[4dn:phase1:working_groups:jawg_meeting_archive|Older Meeting Archives (2017 - 2019)]] |
4dn/phase1/working_groups/joint_4d_nucleome_analysis.1599123425.txt.gz · Last modified: 2025/04/22 16:21 (external edit)