====== Joint 4D Nucleome Analysis ======

===== Objective =====

A growing number of OMICS- and imaging-based methods have been developed to characterize the chromatin architecture in mammalian cells. Individually, each method provides a snapshot of the chromatin organization but falls short in depicting the full picture. To gain a better understanding of the chromatin structure, a collaborative research project is conceived by members of the Nuclear Organization and Function Interdisciplinary Consortium (NOFIC). The overarching goal of this project is to study the chromatin organization of a panel of common genetic loci in a heterogeneous set of common cell lines using a diverse array of OMICS- and imaging-based technologies. Systematic comparisons of the different assays will be carried out to reveal the strengths and weaknesses of each method, to generate appropriate data standards, and to learn how different chromatin architectural features such as loops and TADs present themselves when examined using different methodologies. Results from this collaborative project are expected to greatly improve our understanding of the nuclear organization and its dynamics in mammalian cells, and provide important guidelines for expanding such studies to additional cell types and biological contexts.

===== Plans and Documents =====

  * [[https://docs.google.com/document/d/14GrmHI2UOcTRVGIex2WGwDT3waZYZxrhkDyj6_5gJWg/edit?usp=sharing|Agendas and minutes from phone calls]]

  * [[https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0|Signup for presentations]]

  * [[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: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>**
  * 2019 January: [[https://docs.google.com/document/d/1Riv1WeOyHWDAkZn874h87ykHqz0ogotNuaC-cryLtDU/edit|Joint Analysis paper plan]]
  * 2018 July: [[https://docs.google.com/document/d/1xxv44RGLqVz_nqXUw9Oa972JIV-TOoQ6dp2xr2dJ9AE/edit|Draft analysis design for the integrative analysis]].
  * 2017 September: [[https://docs.google.com/document/d/1d-s3NOxNbRAL0mZvVbTddohVwV1XqCKaypJBFOszvgU/edit|Joint Analysis discussion points during annual meeting]]
  * 2017 August: [[https://docs.google.com/document/d/1aTgN9rjxGgfvRkCjab6-lxK0i1unITNDINRVVQn2BtI/edit|Discussion on biological questions for 4DN joint analysis]]
  * <font inherit/inherit;;inherit;;#ffff66>2017 April:</font><font inherit/inherit;;inherit;;#ffff66>[[https://docs.google.com/document/d/1n4QPYp47CDINj2Rci2vl6xaxf-ihDxEoQMvyhwq_buA/edit|Joint Analysis Project Design]]</font><font inherit/inherit;;inherit;;#ffff66>(initated by NOFIC)</font>
  * [[https://www.google.com/url?q=https://data.4dnucleome.org/joint-analysis&sa=D&sntz=1&usg=AFQjCNH0Yih3G3T92YEACgPH_TqMrD63iw|Joint Analysis Data @ the 4DN Data Portal]]
  * More info on [[https://docs.google.com/spreadsheets/d/1sT6dHJb5T3xOIH_vJguQav-rZM4PePASfrylT5lO7RE/edit#gid=0|Available Derived Results]]
  * (Outdated) [[https://docs.google.com/spreadsheets/d/1GuuD8OiPK-b3E4AjyU3BVN31eRDhie6Ue57IWHLamAY/edit?usp=sharing|Groups, assays, cell line information]]
  * (Outdated) [[https://docs.google.com/spreadsheets/d/1kOW2m_DSKQJaupXnANqImwqJ3BmjUaPYhR8rxG3pgxM/edit?usp=sharing|Selected genetic loci]]
  *


===== Related Projects =====

  * [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/imaging-data-standards-wg/microscope-calibration-project|Microscope Calibration Project]]

===== Co-chairs =====

Job Dekker, <Job.Dekker@umassmed.edu>

Feng Yue, <yuefeng.psu@gmail.com>

===== Meeting Information (4DN JAWG/DAWG Meeting) =====

From March 1, 2018, the meetings of JAWG and DAWG merge together to the weekly 4DN JAWG/DAWG Meeting. From Oct 3, 2019, the JAWG/DAWG meeting becomes a biweekly meeting.

The 4DN JAWG/DAWG Meeting is <font inherit/inherit;;#e74c3c;;inherit>**once every two weeks, on****Thursday at 1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time)**</font>

You can use email address <meeting-4dn-dj@4dnucleome.org> to send emails to all the JAWG/DAWG meeting members.

**Joint Analysis presentations: **

  - Everyone is welcome to give a presentation at the meetings, and in particular, we are interested in work relevant to the JA effort, for example, algorithms or effort related to data modeling or integration. Please sign up in the linked [[https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0|Google sheet]].
  - Scheduled report of data generation and analysis group: [[https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0|Google sheet]]

<font 20px/inherit;;inherit;;inherit>**WebEx Meeting Information**</font>

**Biweekly Call - 4DN JAWG/DAWG Meeting**

**Once every two weeks, on Thursday（from Oct 3, 2019)**

**1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time) **

<font 20px/inherit;;inherit;;inherit>**[[https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m8ea943b4f866758ce61e412a002a8a95&sa=D&sntz=1&usg=AFQjCNF6uGcS20RnYEw3eNQCt5LdpcpmcQ|Click here to Join WebEx meeting]]**</font>

Meeting number: 805 283 801

Meeting password: uJe93m63

Host key: 347076

**Join by phone**

+1-415-655-0002 US Toll

Access code: 805 283 801

<font 10px/inherit;;inherit;;inherit><font inherit/inherit;;rgb(41, 128, 185);;inherit>WEBEX EMERGENCY CONTACT INFORMATION:\\ KATE RIVERA\\ 858-822-1626 (OFFICE)</font></font>

**Meeting Chairs**

  * Job Dekker, Job.Dekker@umassmed.edu
  * Feng Yue, yuefeng.psu@gmail.com
  * William Noble, wnoble@uw.edu
  * Peter Kharchenko, peter_kharchenko@hms.harvard.edu


===== Joint Analysis Presentations =====

We encourage to share your slides. All the slides are only shared within the 4DN network. They are stored in 4DN Google Drive. You need to use your 4DN associated google account to view the slides.

**If you want to share your slides, please sent them to Zhangming (Frank) email: <yanzm@ucsd.edu>**


==== JA presentations in 2020: ====

^  Date  ^  Presenter  ^  PI/Lab  ^  Title  ^  Slides  ^  Recordings  ^  Data accession  ^  Other info  ^  Other info  |
|02/06/2020|Ana Pombo|Pombo Lab|Selection of H1 hESC genomic features and genomic window classification for joint analysis 3D-1D integration|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|02/20/2020|Luca Fiorillo and Francesco Musella|Nicodemi Lab|Comparison of the Hi-C, GAM and SPRITE by use of polymer models of chromatin|~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|02/20/2020|Xingzhao Wen|Zhong Lab|Joint analysis of global RNA-DNA interaction data (iMARGI) and other 4DN omics data|~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|04/16/2020|Luca Fiorillo and Francesco Musella|Nicodemi’s Lab|Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin|~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|05/14/2020|Jian Ma|Ma Lab|Integrative analysis of nuclear compartmentalization in human cell|~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|05/14/2020|Frank~~CKG_TABLE_NBSP~~Alber|Alber Lab|Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling|~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|06/25/2020|Jian Ma|Ma Lab|Nucleome Browser: A multimodal, interactive data exploration platform for the 4D Nucleome~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1NqPIGPA8r5fdOIHto6wLHduTGOb5ecZm/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

[[https://drive.google.com/file/d/1OV0yWfU_T1aaPvSi49Ei6gKFdAhxu8Fj/view?usp=sharing|Link to Meeting Recording 06/25/2020]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|06/25/2020|Naoki Kubo|Ren Lab|Active role of CTCF in enhancer-promoter contacts and gene expression|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1OCRwN14pe6lxhpI5eTjURfYbkgbsTEGe/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|:::|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|06/25/2020|Hui Huang|Ren Lab|CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1NlZj8onTncwbGg_L6pycesPJu47423eA/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|:::|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|07/09/2020|Ruochi Zhang|Ma Lab|Exploiting single cell Hi-C data using Higashi|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1-C6KsTv_58HggiCoqY-FuCwvVKIisG-f/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1-ln9lg1JqwzsqFzRQfRXjv41JtPePqjw/view?usp=sharing|Link to recording]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|07/09/2020|Warren Winick-Ng|Pombo Lab|Cell-type specialization in the brain is encoded by specific long-range chromatin topologies|  NO  |  NO  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|07/09/2020|Riccardo Calandrelli|Zhong Lab|Dynamic Changes in RNA-Chromatin Interactome Promote Endothelial Dysfunction|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1-2Xb6FUFQkCyXKlNpV2hU_qruUwEYTxg/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1-sQWxgSwy1nmtQ0969And8A6hTc_Ufd3/view?usp=sharing|Link to recording]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|07/23/2020|Jie Liu|Liu Lab|Connecting high-resolution 3D chromatin organization with epigenomics|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1-srR-h_ul2aZt73HQOzkQqMXZDHX9jue/view|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1056iXMp0n7GxAJ9SfTOd1Mijeq-B-44x/view?usp=sharing|Link to recording]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |  ~~CKG_TABLE_NBSP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|07/23/2020|Caterina Strambio De Castillia|Strambio De Castillia Lab|Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/10xHfDesuIZHqSiCHiKk91uSHoQaAmJ4R/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/10GO3jkPkboL4CPszrLpaeUYASb_d7G2e/view?usp=sharing|Link to recording]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|08/06/2020|Frank Alber|Alber Lab|Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1B0MOVFkEWsu8NJMVZwaDItDuczdbpsXN/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

[[https://drive.google.com/file/d/15167FEBhT0OJ5XM_BIsjVR0uVDysE4HP/view?usp=sharing|Link to meeting recording 08/06/2020]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~  |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|08/06/2020|Betul Akgol Oksuz|Dekker Lab|Comprehensive evaluation of 3C parameters identifies optimal methods for compartment or loop detection|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1B2LmsCsAH6tPjP5iiG5lEfF5fFDgA2IS/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|:::|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
|08/20/2020|Derek Janssens|Henikoff Lab|High-Throughput Chromatin Profiling Identifies Pathological Chromatin Signatures in Pediatric Acute Leukemia|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1AvTaJ2UsiUR7HkDf8LqKCIYofrfe5ueg/view?usp=sharing|Link]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|  ~~TABLE_CELL_WRAP_START~~<WRAP>

~~CKG_TABLE_NBSP~~

[[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~~|
|08/20/2020|Burak Alver|DCIC|4DN Data Portal and JAWG Data|~~TABLE_CELL_WRAP_START~~<WRAP>

[[https://drive.google.com/file/d/1B0AyMFUyWbgFzL4qMOQKcIk_-Z3AhtZ8/view?usp=sharing|Link]]

</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 ===

  * [[:4dn:phase1:working_groups:ja_presentations|Older JA presentation archives (2018 - 2019)]]


===== 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
    * 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
  * July 23, 2020
    * 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
  * July 9, 2020
    * 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 Riccardo Calandrelli (Zhong Lab): Dynamic Changes in RNA-Chromatin Interactome Promote Endothelial Dysfunction
  * June 25, 2020
    * 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. 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
  * May 14, 2020
    * 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
  * April 16, 2020
    * 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
  * April 2, 2020
    * Meeting Agenda:
      * Planning the set of 4DN papers, the marker paper, and the Mol Cell review.
  * February 20, 2020
    * 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
  * February 6, 2020
    * Meeting Agenda:
      * 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:
      * Updates by every group on current ongoing analyses
      * Discussion of coordination of paper submission

===== Older Meeting Archives =====

  * [[4dn:phase1:working_groups:jawg_meeting_archive|Older Meeting Archives (2017 - 2019)]]


===== Documents =====

  * **Working Protocol**
      * [[https://docs.google.com/spreadsheets/d/1-B8wjWfB-dlAdmLur-Nik7oWDfUI4RWrEsUmRl_bXks/edit?usp=sharing|Draft version]]
  * **Questionnaire of locus engineering efforts in 4DN**
      * [[https://docs.google.com/forms/d/e/1FAIpQLScLdW1toOFcJnE8YHM69LGuH_x53gC5f6jVGB6SDUUZ6nYYuA/viewform|Questionnaire Form]]
      * [[https://docs.google.com/spreadsheets/d/15JHMz3KlMbcIaSx2rW-erwmmFTKG9T6B_H8kZokE32g/edit#gid=836156226|Result Table]]
  * **Data generation plan**
      * [[https://docs.google.com/spreadsheets/d/1ONfcbvM1iP30vhStJuOemho039hMA0juFvjEU92zse4/edit#gid=0|Table]]
  * **Discussion on biological questions for 4DN joint analysis (July 2017)**
      * [[https://docs.google.com/document/d/1aTgN9rjxGgfvRkCjab6-lxK0i1unITNDINRVVQn2BtI/edit|Google Doc]]
  * **Joint Analysis Discussion during Annual Meeting (Sept 2017)**
      * [[https://docs.google.com/document/d/1d-s3NOxNbRAL0mZvVbTddohVwV1XqCKaypJBFOszvgU/edit?usp=sharing|Google Doc]]
  * **Defining durable goods (Sept 2017)**
      * [[https://docs.google.com/document/d/18TGAHjntscflCFG_WQGWeSy_3vLyq8mvfN9UkjD8NSU/edit|Google Doc]]

===== Members =====

Please use <joint-4dn-analysis@4dnucleome.org> to send an email to the JAWG mailing group.

As currently JAWG and DAWG are working together, so we have another JAWG/DAWG joint mailing group, which includes all the JAWG and DAWG people: <meeting-4dn-dj@4dnucleome.org>

^Name^Role (Student, Postdoc, staff, PI)^PI of Group^contact (email)|
|Bing Ren|PI|Bing Ren/Murre|biren@ucsd.edu|
|Job Dekker|PI|Dekker/Mirny|job.dekker@umassmed.edu|
|Johan Gibcus|Instructor|Dekker/Mirny|johan.gibcus@umassmed.edu|
|Zhijun Duan|Research Associate Professor|Shendure/Noble|zjduan@uw.edu|
|Giancarlo Bonora|Postdoc|Shendure/Noble|gbonora@uw.edu|
|Burak Alver|Scientific project manager|Park (DCIC)|burak_alver@hms.harvard.edu|
|David Gorkin|Staff|Bing Ren/Murre|dgorkin@ucsd.edu|
|Leonid Mirny|PI|Dekker/Mirny|leonid@mit.edu|
|Ana Pombo|PI|Bing Ren/Murre|ana.pombo@mdc-berlin.de|
|Alexander Kukalev|Postdoc - Pombo lab|Bing Ren/Murre|alexander.kukalev@mdc-berlin.de|
|Christoph Thieme|Postdoc - Pombo lab|Bing Ren/Murre|christoph.thieme@mdc-berlin.de|
|Rieke Kempfer|PhD student - Pombo lab|Bing Ren/Murre|rieke.kempfer@mdc-berlin.de|
|Feng Yue|PI|Wang (DCIC)|yuefeng.psu@gmail.com|
|Soo Lee|Senior Bioinformatics Scientist|Park (DCIC)|duplexa@gmail.com|
|Hakan Ozadam|Senior Bioinformatics Scientist|Dekker/Mirny|hakan.Ozadam@umassmed.edu|
|Frank Alber|PI|Alber/Chen|alber@usc.edu|
|Larry Gerace|PD/PI|Larry Gerace|lgerace@scripps.edu|
|Nan Hua|PhD student|Alber/Chen|nhua@usc.edu|
|Guido Polles|Postdoc|Alber/Chen|polles@usc.edu|
|Lin Chen|PI|Alber/Chen|linchen@usc.edu|
|Yi Kou|Postdoc|Alber/Chen|yik109@hotmail.com|
|Jiang Xu|Postdoc|Alber/Chen|foxjuly@gmail.com|
|Yijun Ruan|PI|Ruan|yijun.ruan@jax.org|
|Sheng Li|PI|Ruan|sheng.li@jax.org|
|Dave Gilbert|PI|Belmont|gilbert@bio.fsu.edu|
|Zhonghui Tang|Postdoc|Ruan|zhonghui.tang@jax.org|
|Peter Park|PI|Park (DCIC)|peter_park@hms.harvard.edu|
|Nils Gehlenborg|PI|Park (DCIC)|nils@hms.harvard.edu|
|Tim Hu|Postdoc|Park (DCIC)|tim_hu@hms.harvard.edu|
|Peter Kerpedijev|Postdoc|Park (DCIC)|pkerp@hms.harvard.edu|
|Andrew Belmont|PI|Belmont|asbel@illinois.edu|
|Chia-Lin Wei|PI|Ruan|Chia-lin.Wei@jax.org|
|Harianto Tjong|Staff|Ruan|Harianto.Tjong@jax.org|
|Jian Ma|PI|Belmont|jianma@cs.cmu.edu|
|Miao Yu|Postdoc|Ren|miy059@ucsd.edu|
|David Grunwald|PI|Grunwald|David.Grunwald@umassmed.edu|
|Jie Xu|PhD student|Wang/Yue|jiexu@hmc.psu.edu|
|Fan Song|PhD student|Wang/Yue|fxs26@psu.edu|
|Mayank NK Choudhary|PhD student|Wang/Yue|mayank-choudhary@wustl.edu|
|Daofeng Li|Postdoc|Wang/Yue|dli@genetics.wustl.edu|
|Joan Ritland|PI|Groudine|jritland@fredhutch.org|
|Clodagh O'Shea|PI|~~CKG_TABLE_NBSP~~|oshea@salk.edu|
|Jan Liphardt|PI|~~CKG_TABLE_NBSP~~|jan.liphardt@stanford.edu|
|Zhangming Yan|Postdoc|Sheng Zhong (OH)|yanzm@eng.ucsd.edu|
|Xavier Darzacq|PI|~~CKG_TABLE_NBSP~~|darzacq@berkeley.edu|
|Paul Kaufman|PI|Kaufman|Paul.Kaufman1@umassmed.edu|
|David Gorkin|PI|Bing Ren/Murre|dgorkin@ucsd.edu|
|Erez Lieberman Aiden|PI|~~CKG_TABLE_NBSP~~|erez@erez.com|
|David Scalzo|Senior Research Technician|Mark Groudine|scalzod@fhcrc.org|
|Ivan Bochkov|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|ibochkov33@gmail.com|
|Neva Cherniavsky|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
[[neva@broadinstitute.org|]]
</WRAP>~~TABLE_CELL_WRAP_STOP~~|
|Jesse Turner|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|jturner@bio.fsu.edu|
|Sheng Zhong|PI|Sheng Zhong (OH)|szhong@eng.ucsd.edu|
|Bill Noble|PI|Shendure/Noble|wnoble@uw.edu|
|Jie Liu|~~CKG_TABLE_NBSP~~|Noble|liu6@uw.edu|
|Dariusz Plewczynski|PI|Ruan|dariuszplewczynski@gmail.com|
|William S Noble|PI|~~CKG_TABLE_NBSP~~|wnoble@uw.edu|
|Kate Cook|Postdoc|William S Noble|katecook@uw.edu|
|Dejun Lin|Postdoc|William S Noble|dejunlin@uw.edu|
|Warren Winick-Ng|Postdoc - Pombo lab|Bing Ren/Murre|warren.winick-ng@mdc-berlin.de|
|Mike Pazin|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
[[pazinm@mail.nih.gov|]]
</WRAP>~~TABLE_CELL_WRAP_STOP~~|
|Mario Nicodemi|co-PI|Bing Ren|nicodem@na.infn.it|
|Sofi Quinodoz|Graduate Student|Mitchell Guttman|squinodo@lncrna.caltech.edu|
|Gurkan Yardimci|Postdoc|William S Noble|gurkan@uw.edu|
|Daniel Vera|Research Scientist|Gilbert/Belmont|vera@genomics.fsu.edu|
|Daniel Capurso|scientist|Yijun Ruan|Daniel.Capurso@jax.org|
|Peiyao Zhao|PhD student|David Gilbert|pzhao@bio.fsu.edu|
|Sarah Reiff|Data Curator|Peter Park|sarah_reiff@hms.harvard.edu|
|Izabela Harabula|PhD student - Pombo lab|Bing Ren/Murre|izabela.harabula@mdc-berlin.de|
|Tom Sparks|PhD student - Pombo lab|Bing Ren/Murre|Thomas.Sparks@mdc-berlin.de|
|Gesa Loof|PhD student - Pombo lab|Bing Ren/Murre|gesa.loof@mdc-berlin.de|
|Ehsan Irani|Postdoc - Pombo lab|Bing Ren/Murre|ehsan.irani@mdc-berlin.de|
|Nicola Neretti|PI|~~CKG_TABLE_NBSP~~|nicola_neretti@brown.edu|
|Xianghong J. Zhou|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|xjzhou@mednet.ucla.edu|
|Ibai Irastorza|Postdoc - Pombo lab|Bing Ren/Murre|Ibai.IrastorzaAzcarate@mdc-berlin.de|
|Hu Jin|Grad Student|Peter Park|Hu_Jin@hms.harvard.edu|
|Ritambhara Singh|Lab Associate: Graduate Student/Student/Trainee/Administrator/Manager/Project Coordinator|William Noble|89.ritambhara@gmail.com|
|Gesine Cauer|Lab Associate: Graduate Student/Student/Trainee/Administrator/Manager/Project Coordinator|William Noble|gesine@uw.edu|
|Shirley Lam|Lab Associate: Graduate Student/Student/Trainee/Administrator/Manager/Project Coordinator|William Noble|sklam@uw.edu|
|Kai Tan|Associate Members|Kai Tan|tank1@email.chop.edu|
|Maxwell Libbrecht|Associate Members|Maxwell Libbrecht|maxwl@sfu.ca|
|Michael Hoffman|Associate Members|Michael Hoffman|michael.hoffman@utoronto.ca|
|Omid Gholamalamdari|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|omid.alamdari@GMAIL.COM|
|Luisa Mercado|Lab Associate: Graduate Student/Student/Trainee/Administrator/Manager/Project Coordinator|Peter Park|luisa_mercado@hms.harvard.edu|
|Ian Fingerman|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|ian.fingerman@nih.gov|
|Judy Mietz|NIH Officer|~~CKG_TABLE_NBSP~~|mietzj@mail.nih.gov|
|Caterina Strambio de Castillia|Associate Member|Caterina Strambio de Castilla|caterina.strambio@umassmed.edu|
|Changya Chen|Lab Associate: Postdoctoral Researcher|Kai Tan|CHENC6@EMAIL.CHOP.EDU|
|Wenbao Yu|~~CKG_TABLE_NBSP~~|Kai Tan|YUW1@EMAIL.CHOP.EDU|
|Sergey Venev|Bioinformatics Specialist I|Job Dekker|SergeyV.Venev@umassmed.edu|
|Peter Yingxiao Wang|Associate Member|Peter Wang|yiw015@eng.ucsd.edu|
|Dhawal Jain|Grad Student|Peter Park|dhawal.sjain@gmail.com|
|Luna Zea Redondo|PhD student Pombo lab|Ren/Murre|Luna.ZeaRedondo@mdc-berlin.de|
|Teresa Szczepinska|Joint Postdoc Pombo/Plewczynski|Ren/Murre and Juan|t.szczepinska@cent.uw.edu.pl|
|Lucie Hebert|Postdoc|Sheng Zhong|luhebert@eng.ucsd.edu|
|Susanne Rafelski|Associate Member|Susanne Rafelski|susanner@alleninstitute.org|
|Ru Gunawardane|Associate Member|Susanne Rafelski|rug@alleninstitute.org|
|Lorenzo Boninsegna|Postdoc|Frank Alber|bonimba@g.ucla.edu|
|Riccardo Calandrelli|Research Associate|Sheng Zhong|rcalandrelli@eng.ucsd.edu|

===== Calendar =====

{{url>https://calendar.google.com/calendar/embed?src=4dnucleome.org_m6gfod7tp0da3drmls7i7kbfro%40group.calendar.google.com&ctz=America%2FLos_Angeles 800,400 noborder|4DN OMICS WG Calendar}}

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