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Meeting Archives: 2019
December 19, 2019
Meeting Agenda:
Discussion of 4DN JAWG Marker Paper Outline: https://docs.google.com/document/d/1TNk17MMvh1iuMugyuU1QImmOYDwojt85f02XdJYw47M/edit
We have created a Slack workspace for 4DN Joint Analysis. We will have more discussion on the marker paper there. You are welcome to join in using the invitation link: https://join.slack.com/t/4dnjawg/shared_invite/enQtODcyNzMwOTg4MDUyLWIxNmQwZjZmMDFkM2RjZmQ4ZjEyMzg4ZTEzZThkOWZkYmY0NmQ1MzJhMmMzYzkxZWFiMjY4OTYyOGIxZTM4M2Y
Meeting recording
December 12, 2019
Meeting Agenda:
Presentation by Xiaotao Wang (Yue Lab) and Andy Schroeder (DCIC): Sharing analysis products within the JAWG via the DCIC
November 21, 2019
Meeting Agenda:
Presentation by Ruan Lab: Brief updates on 1) methods comparison; 2) human ChIA-Drop data
Presentation by Dekker Lab: Hi-C protocol parameter sweep
November 14, 2019
Meeting Agenda:
Presentation by Christoph Thieme / Teresa Szczepinska (Pombo, Plewczynski, Nicodemi Labs): GAM versus Hi-C comparisons mESC and H1 hESC
Presentation by Jian Ma: Update on recent progress
November 7, 2019
Meeting Agenda:
Discussion on manuscript coordination
October 31, 2019
Meeting Agenda:
Presentation by Frank Alber: Comparative genome structure analysis (H1/HFF/GM12878)
Annual meeting planning (agenda) https://docs.google.com/document/d/1dGMfu7VUUoMifpCQ19hCom5aVVe7UqWGXJ0i4YRPSFE/edit?ts=5db7287d#heading=h.oplwmnls7v3
Go over planned data sets (listed here and here). https://docs.google.com/spreadsheets/d/1ONfcbvM1iP30vhStJuOemho039hMA0juFvjEU92zse4/edit#gid=0
Google Doc for sharing analysis results. https://docs.google.com/document/d/1-0oWZsmXhEaD20WJNgIt6cgwIi-rhZVCiBDYqxVXQXE/edit?usp=sharing
Minutes:
Perhaps have a plenary session for JAWG, visualization and imaging.
The imaging demo may be open the entire time, not just during the breakout.
Action items:
[Burak] Contact David Grunewald to find out more.
[Feng] Continue scheduling discussion via email.
[Bill] Email to find out what data is on the way. Put a deadline.
[Bill] Schedule presentations for the next three meetings. Frank, Job, Feng (cross-platform comparisons), Jian. Make sure we get important discussions about manuscripts into the agenda for upcoming calls.
October 3, 2019
Meeting Agenda:
1. Presentation by Jennifer E. Phillips-Cremins
2. Discussion of Jie Liu's associate member application (https://drive.google.com/file/d/0B1Uh14Y8H75dVUN4YS1XOU1BaVR5Q0syN3JvMlB2THdDMmJV/view)
3. Outreach session (chaired by Peter Fraser)
September 26, 2019
Meeting Agenda:
Presentation by Dr. Jie Liu for 4DN association member application: Computational methods for high resolution chromatin organization (https://drive.google.com/file/d/1VYwFZ-QQ8fHpOo7Iqv5mZCMEm_nb-eLL/view)
September 5, 2019
Meeting Agenda:
Presentation by Kyle Xiong (Ma Lab): SNIPER - call subcompartments by imputing inter-chromosomal chromatin interactions
Discussion of authorship and data release policy
Discussion of publication of individual datasets by data producers and the use of individual datasets generated by others in the group in publications.
August 15, 2019
Meeting Agenda:
Presentation by Tarik Salameh (Yue Lab): A supervised learning framework for chromatin loop detection in genome-wide contact maps
Outreach discussion (Sheng Zhong)
Updates of recent outreach activities.
July 25, 2019
Meeting Agenda:
Presentation by Daniel Capurso (Ruan Lab): Comparative analysis of methods for protein-enriched chromatin interactions
July 11, 2019
Meeting Agenda:
Presentation by Liguo Zhang (Belmont Lab): Development and Application of TSA-Seq 2.0 to Measuring 3D Genome Organization Relative to Nuclear Compartments
Outreach discussion (Lucie Hebert):
Discuss the 4DN promotional material and the next conferences related to 4DN
Jun 20, 2019
Meeting Agenda:
Discussion on how to perform the joint analysis as a group.
Proposal to assemble an analysis team with members from interested centers and labs.
Jun 6, 2019
Meeting Agenda:
Presentation by Dr. Thomas C. Bishop (Louisiana Tech University): G-Dash: A Genome Dashboard Integrating Modeling and Informatics
Recording:
May 30, 2019
Meeting Agenda:
Presentation by Nils Krietenstein (Rando, Mirny, Dekker Labs): Micro-C vs Hi-C
Recording:
May 23, 2019
Meeting Agenda:
Presentation by DCIC: Pipelines, visualization, sites supporting joint papers
Recording:
May 2, 2019
Meeting Agenda:
Discussion on handling co-authorships across JAWG papers
Recording:
Apr 18, 2019
Meeting Agenda:
Presentation by Xiaotao Wang (Yue Lab): cross-platform comparisonsOutreach
Recording:
Apr 4, 2019
Meeting Agenda:
Presentation by Sheng Zhong: Brief update on analysis of inter-chromosomal interactions
Outreach
Feedback of the Keystone meeting of 2 weeks ago
Kate Rivera (4DN Program Coordinator) has drafted a version of a 4DN brochure. Please have a look, we will go over it and discuss suggestions/modifications.
Retrospective of the last meeting's actions items and their implementation. (minutes of last outreach discussion)
Recording:
Mar 28, 2019
Meeting Agenda:
Presentation by Alber/Ma Labs: Structural models vs SPIN
Presentation by Bill/Erez Labs: ENCODE to present their 4D Nucleome related work
Recording:
Mar 14, 2019
Meeting Agenda:
Presentation by Xiaotao Wang (Yue Lab): a short update on the cross-platform comparison.
Presentation by Peiyao Zhao (Gilbert Lab): High Res Repli-seq (H1, H9, HCT116, F121-9 ESC and NPC)
Mar 7, 2019
Meeting Agenda:
Presentation by Tarik Salameh (Yue Lab): PIKACHU: A supervised machine learning method to identify chromatin loops from genome-wide interaction data
Outreach Discussion (Peter Fraser):
Plans for intensifying Outreach activities: https://docs.google.com/document/d/174APgE9ppCWaR0H9OLUjuX7Z0gwx9dL3dsCKzRnaMRQ/edit
Present the Outreach activities google sheet: https://docs.google.com/spreadsheets/d/1b_QkvoI86FSakGteLjYC81Q0hQ92RR_uI8jYN6Rx6mU/edit#gid=1386834576
Feb 28, 2019
Meeting Agenda:
Presentation by Rando/Mirny/Dekker labs: Micro-C vs Hi-C - long presentation
Feb 21, 2019
Meeting Agenda:
Presentation by Ruan/Aiden/Dekker/Ren/Ma labs: pull-down vs non-pulldown 3C methods comparisons
Presentation by Guttman lab: ligation vs non-ligation assays (HiC vs SPRITE/GAM)
Recording:
Feb 14, 2019
Meeting Agenda:
Presentation by Zhong/Ren labs: RNA-chromatin interactions
Presentation by Pombo/Nicodemi/Ren/Hu labs: Allelic GAM/Hi-C/PLAC-seq + other data (cell line F123)
Feb 7, 2019
Meeting Agenda:
Presentation by Alber / Data producing labs: Structural modeling
Presentation by Ren/Hu.Pombo/Nicodemi: PLAC-seq - Hi-C - GAM
Recording: https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=9f659cc9563efe122e5ed34b0ccfb263
Notes:
Burak: No JAWG DCIC data update. Encouraged upcoming JAWG presentations to start with a slide on data availability
Sheng: Gave an outreach activities update. Encouraged conference organizers/attendees to update the worksheet ‘4DN workshops and posters
David Gilbert: Gave an anecdote about a scientific meeting that discouraged a 4DN-specific talk. But urged everyone to do their best to put 4DN affiliation in presentation/posters.
Jan 31, 2019
Meeting Agenda:
Updates of nuclear speckle project: Belmont/Zhong/Guttman
Updates of SPIN states project: Ma/Belmont/van Steensel/Gilbert
Jan 24, 2019
Meeting Agenda:
DCIC/Burak Alver to give an update on processed data available for JA for the various groups to use ChIP status
Discussion of the planned presentation schedule: https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0
Jan 17, 2019
Meeting Agenda:
Continue discussion of plans for papers. Discussion on how to coordinate and report updates of ongoing analyses towards these papers to the JAWG/DAWG groups
Update on ENCODE data being generated by ENCODE for 4DN Tier 1 cells (Job and Feng).
Coordination between JAWG/DAWG with the larger outreach strategy discussed at this weeks 4DN Steering Committee call.
Jan 10, 2019
Meeting Agenda:
Planning of manuscripts. Feng has created a google doc for listing proposed manuscripts. Please add your planned manuscript before the call on Jan 10. We will discuss it at the meeting. Here is the link to the google doc: https://docs.google.com/document/d/1Riv1WeOyHWDAkZn874h87ykHqz0ogotNuaC-cryLtDU/edit
Jan 3, 2019
Meeting Agenda:
Feedback and discussion of the annual meeting
Discussion of next steps
RFI from groups about publication plans on Joint Analysis projects
Meeting Archives: 2017 - 2018
- May 4, 2017 - Monthly Call 1
- May 18, 2017 - Monthly Call 2
- June 1, 2017 - Monthly Call 1
- June 15, 2017 - Monthly Call 2
- July 6, 2017 - Monthly Call 1
- Meeting Agenda: Discussion of data generation plan
- Minutes: Link
- Document: data generation plan
- July 20, 2017 - Monthly Call 2
- August 3, 2017 - Monthly Call 1
- Minutes: Link
- August 17, 2017 - Monthly Call 2
- Minutes: Presentations from Jian Ma and Frank Alber
- September 1, 2017 - Additional call for strategic discussion
- October 5, 2017 - Monthly Call 1
- Meeting Agenda: Link
- October 19, 2017 - Monthly Call 2
- Meeting Agenda:
- 1. Discussion of the Omics data freeze
- November 16, 2017
- Meeting Agenda:
- 1. DCIC updates
- December 21, 2017
- Meeting Agenda:
- 1. Summary report from each lab that promised Omics data generation by the January data freeze.
- February 1, 2018
- Meeting Agenda:
- Update from DCIC: data freeze progress - Burak Alver
- Discussion of data analysis plans - Job and Feng
- A report from the imaging WG and their plans for benchmarking technologies - Imaging WG
- Update from microscope calibration efforts - David Grunwald
- Scheduling JAWG scientific presentations - Feng and Job
- February 15, 2018
- Meeting Agenda:
- 1. Data submission status update
- 2. Discussion of data analysis plan
- 3. Scheduling JAWG scientific presentations
- 4. Discussion of the monthly joint call plan for DAWG and JAWG
- Meeting Notes: [Link to meeting nots]
- March 8, 2018
- Meeting Agenda:
- 1. Presentation by DCIC: Data Processing Pipeline
- 2. Update and Discussion of ENCODE data generation for 4DN cell lines HFFc6 and Endoderm.
- March 15, 2018
- Meeting Agenda:
- 1. Presentation by Wouter de Laat: Multi-contact 4C
- 2. Microscope calibration project updates (David Grunwald)
- March 22, 2018
- Meeting Agenda:
- 1. Presentation by Kami Ahmad: CUT&RUN for chromatin structure
- March 29, 2018
- Meeting Agenda:
- 1. Presentation by Karla Neugebauer: The Cell Nucleus under Stress
- April 5, 2018
- Meeting Agenda：
- 1. Presentation by Sheng Zhong: Global mapping of RNA-genome interactions
- 2. Discussion of “Craig’s list for collaborative projects”. https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/collaboration-plaza
- April 12, 2018
- Meeting Agenda:
- 1. Presentation by Jian Ma: Computational methods for probing nuclear compartmentalization
- 2. Discussion of “Craig’s list for collaborative projects”. https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/collaboration-plaza
- April 19, 2018
- Meeting Agenda:
- 1. Presentation by Jie Liu (Noble Lab): Unsupervised Embedding of Single-cell Hi-C Data
- 2. Discussion of associate member application from Dr. Maxwell Libbrecht. https://drive.google.com/file/d/1D3GAZcfJ4Czz_wkLGKckqDb1T4qV2_un/view
- April 26, 2018
- Meeting Agenda:
- 1. Presentation by Alexander Kukalev and Warren Winick-Ng (Pombo Lab): Update on H1 hESC GAM data production and QC
- May 3, 2018
- Meeting Agenda:
- 1. Discussion of the 4DN network feedback about the associate member application from Dr. Maxwell Libbrecht.
- May 10, 2018
- Meeting Agenda:
- 1. Presentation by Nicola Neretti: Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data
- May 17, 2018
- Meeting Agenda:
- 1. Discussion of draft analysis design for the integrative analysis. Please add comments to the draft plan in suggesting mode. Link to the google doc.
- May 24, 2018
- Meeting Agenda:
- 1. Presentation by Maxwell Libbrecht for 4DN associate member application from Maxwell Libbrecht & Michael Hoffman: Understanding large-scale genome regulation through joint analysis of chromatin state and chromatin conformation
- May 31, 2018
- Meeting Agenda:
- 1. Discussion of the associate member application by Drs. Maxwell Libbrecht & Michael Hoffman. https://drive.google.com/file/d/1D3GAZcfJ4Czz_wkLGKckqDb1T4qV2_un/view
- 2. Discussion of the new associate member application by Dr. Kai Tan. https://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view
- June 14, 2018
- Meeting Agenda:
- 1. Presentation by Dr. Dave Gilbert: 16 fraction repliseq
- 2. Discussion of associate membership application Drs. Libbrecht and Hoffman
- 3. Discussion of associate member application by Dr. Kai Tan. https://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view
- June 28, 2018
- Meeting Agenda:
- 1. Presentation by Dr. Kai Tan for 4DN associate member application (https://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view)
- 2. Planning of next data freeze: endoderm data
- July 5, 2018
- Meeting Agenda:
- 1. Discussion about associate member application by Dr. Kai Tan. Here is the application letter: https://[[http://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view|drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view]]
- 2. Scheduling of the first round data analyses
- 3. Discuss proposals on how to do the integrative analysis: form groups that analyze specific features of the data using multiple approaches.
- 4. Please read the new associate member application submitted by Dr. Peter Yingxiao Wang. We will discuss it on July 12. Here is the application letter: https://drive.google.com/file/d/1LKhwC0_GHnKwTcb0AT-lHLZthxyZm4Ki/view
- July 12, 2018
- Meeting Agenda:
- 1. Discussion about associate member application by Dr. Peter Yingxiao Wang. Here is his application letter. https://drive.google.com/file/d/1LKhwC0_GHnKwTcb0AT-lHLZthxyZm4Ki/view
- 2. Discussion of presentation list of data analyses by data producers. https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0
- August 2, 2018
- Meeting Agenda:
- 1. Presentation by Hakan Ozadam and Sergey Venev (Dekker Lab): Compartment, insulation and dot analysis of Hi-C data for H1-ESCs and HFFc6
- August 9, 2018
- Meeting Agenda:
- 1. Presentation by Ivan Juric (Ming Hu lab) and Miao Yu (Ren Lab): PLAC-seq analysis
- August 23, 2018
- Meeting Agenda:
- 1. Presentation by Christoph Thieme and Alexander Kukalev (Pombo Lab): Comparing chromatin contacts in ESCs by GAM and Hi-C
- August 30, 2018
- Meeting Agenda:
- 1. Presentation by Dr. Peter Yingxiao Wang for his associate member application.
- 2. Discuss how to share the Joint Analysis presentations, including the slides and recordings.
- September 6, 2018
- Meeting Agenda:
- 1. Presentation by Daniel Capurso (Ruan Lab): CTCF motif orientation in ChIA-PET loops at different sequencing depths and in different cell types
- 2. Discuss on associate member application from Dr. Peter Yingxiao Wang
- September 13, 2018
- Meeting Agenda:
- 1. Presentation by Da Kuang (Yue Lab): Identifying differential chromatin interactions with triplet network
- September 20, 2018
- Meeting Agenda:
- 1. The presentation slides can be shared on 4DN joint analysis wiki page now. If you want to share your slides (including past presentations), please send them to Zhangming (Frank). Email: yanzm@ucsd.edu
- 2. Presentation by Andrew Belmont and Liguo Zhang (Belmont Lab): TSA-Seq overview and update
- October 4, 2018
- Meeting Agenda:
- 1. Presentation by Yuchuan Wang (Jian Ma lab at Carnegie Mellon): Updates on Integrative Analysis of Nuclear Compartmentalization for Joint Analysis Cell Lines
- October 18, 2018
- Meeting Agenda:
- 1. Presentation by Gurkan Yardimci (Noble Lab and Shendure Lab): Exploratory analysis of sciHiC data
- October 25, 2018
- Meeting Agenda:
- 1. Presentation by Frank Alber: Update on data integration efforts in genome structure analysis of tier 1 cells.
- 2. Discussion on “planning for the annual meeting” (15 mins)
- November 1, 2018
- Meeting Agenda:
- 1. Presentation by Sofi Quinodoz (Guttman Lab): Update on DNA SPRITE of Tier 1 cell lines
- November 8, 2018
- Meeting Agenda:
- 1. Go over which presentations are ready for the annual meeting
- November 15, 2018
- Meeting Agenda:
- 1. Presentation by Gianluca Pegoraro (IWG): The 4DN Imaging to Omics Working Subgroup
- 2. Discussion about the annual meeting presentations https://docs.google.com/document/d/1Bn2EWLV81ebqt8A8NYOTY8NtCe6QEKpkGH2pIEDrSy4/edit
- November 29, 2018
- Meeting Agenda:
- 1. Presentation by Sheng Zhong: Comparison of RNA-DNA interactions with other 4DN data types
- 2. Discussion about the annual meeting presentations https://docs.google.com/document/d/1Bn2EWLV81ebqt8A8NYOTY8NtCe6QEKpkGH2pIEDrSy4/edit