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4dn:phase1:working_groups:ja_presentations
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Joint Analysis Presentations Archives
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
Archives 2019
| Date | Presenter | PI/Lab | Tentative Title | Slides | Data accession | Other info | Other info | Other info |
|---|---|---|---|---|---|---|---|---|
| 1/31/2019 | Sheng Zhong and Weizhong Chen | Zhong Lab | Defining the relative positions of the genome to nuclear envelope | 4DNESNGESP28; 4DNESTCJSP7W; 4DNESXZ4FW4T; 4DNESXKBPZKQ | ||||
| 01/31/2019 | Jian Ma | Ma Lab | SPIN States for Nuclear Compartmentalization in H1 and HFF | |||||
| 02/07/2019 | Frank Alber | Alber Lab | Update on comparative genome structure analysis for tier 1 cells | |||||
| 02/07/2019 | Alexander Kukalev | Pombo Lab | Promoter centered chromatin interactions detected by PLAC-seq, GAM and Hi-C in H1hESC | |||||
| 02/14/2019 | Sheng Zhong and Weizhong Chen | Zhoang Lab | Comparisons of global RNA-DNA interaction data (iMARGI) and other 4DN omics data | |||||
| 02/14/2019 | Rieke Kempfer | Pombo Lab | Allelic chromatin organization and structure in mouse embryonic stem cells (F123) | |||||
| 02/21/2019 | Sofi Quinodoz | Guttman Lab | DNA SPRITE on 4DN Tier I Cell Lines | |||||
| 02/21/2019 | Daniel Capurso | Ruan Lab | Comparative analysis of chromatin interactions from in situ ChIA-PET and in situ Hi-C | |||||
| 02/28/2019 | Nils Krietenstein | Rando/Mirny/Dekker labs | Micro-C vs Hi-C | |||||
| 03/07/2019 | Tarik Salameh | Yue Lab | PIKACHU: A supervised machine learning method to identify chromatin loops from genome-wide interaction data | |||||
| 03/14/2019 | Xiaotao Wang | Yue Lab | Cross-platform comparisons | |||||
| 03/14/2019 | Peiyao Zhao | Gilbert Lab | High Res Repli-seq (H1, H9, HCT116, F121-9 ESC and NPC) | |||||
| 03/28/2019 | Alber/Ma Labs | Structural models vs SPIN | ||||||
| 03/28/2019 | Bill/Erez Labs | ENCODE to present their 4D Nucleome related work | ||||||
| 04/04/2019 | Sheng Zhong | Zhong Lab | Using native RNA for remote sensing in 3D | |||||
| 05/23/2019 | Burak Alver | DCIC | Updates from DCIC: Assay Curation, Pipelines, Supplementary Page Support, portal updates | |||||
| 05/30/2019 | Nils Krietenstein | Rando, Mirny, Dekker Labs | Genome conformation at nucleosome resolution, Micro-C vs Hi-C | |||||
| 06/06/2019 | Thomas C Bishop (bishop@latech.edu) | Louisiana Tech University | G-Dash: A Genome Dashboard Integrating Modeling and Informatics | |||||
| 07/11/2019 | Liguo Zhang | Belmont Lab | Development and Application of TSA-Seq 2.0 to Measuring 3D Genome Organization Relative to Nuclear Compartments | |||||
| 07/25/2019 | Daniel Capurso | Ruan Lab | Comparative analysis of methods for protein-enriched chromatin interactions | |||||
| 08/15/2019 | Tarik Salameh | Yue Lab | A supervised learning framework for chromatin loop detection in genome-wide contact maps | |||||
| 09/05/2019 | Kyle Xiong | Ma Lab | SNIPER - call subcompartments by imputing inter-chromosomal chromatin interactions | |||||
| 09/26/2019 | Jie Liu | 4DN association member applicant | Computational methods for high resolution chromatin organization | |||||
| 10/03/2019 | Jennifer E. Phillips-Cremins | Cremins Lab | ||||||
| 10/31/2019 | Frank Alber | Alber Lab | Comparative genome structure analysis (H1/HFF/GM12878) | |||||
| 11/14/2019 | Christoph Thieme and Teresa Szczepinska | Pombo, Plewczynski, Nicodemi Labs | GAM versus Hi-C comparisons mESC and H1 hESC | |||||
| 11/21/2019 | Yijun Ruan | Ruan Lab | Brief updates on 1) methods comparison; 2) human ChIA-Drop data | |||||
| 11/21/2019 | Job Dekker | Dekker Lab | Hi-C protocol parameter sweep | |||||
| 12/12/2019 | Xiaotao Wang and Andy Schroeder | Yue Lab and DCIC | Sharing analysis products within the JAWG via the DCIC |
Archives 2018
| Date | Presenter | PI/Lab | Tentative Title | Slides | Data accession | Other info | Other info | Other info |
|---|---|---|---|---|---|---|---|---|
| 03/08/2018 | Soo Lee | DCIC | DCIC Data Processing Pipeline Status | |||||
| 03/15/2018 | Wouter de Laat | De Laat group | Multi-contact 4C | |||||
| 03/22/2018 | Kami Ahmad | Henikoff/AHMAD Lab | CUT&RUN for chromatin structure | |||||
| 03/29/2018 | Karla Neugebauer | Neugebauer Lab | The Cell Nucleus under Stress | |||||
| 04/05/2018 | Sheng Zhong | Zhong Lab | Global mapping of RNA-genome interactions | |||||
| 04/12/2018 | Jian Ma | Ma Lab | Computational methods for probing nuclear compartmentalization | Update on Oct 4 | ||||
| 04/19/2018 | Jie Liu | Noble Lab | Unsupervised Embedding of Single-cell Hi-C Data | |||||
| 04/26/2018 | Alexander Kukalev and Warren Winick-Ng | Pombo Lab | Update on H1 hESC GAM data production and QC | |||||
| 05/10/2018 | Nicola Neretti | Neretti Lab | Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data | |||||
| 05/24/2018 | Maxwell Libbrecht and Michael Hoffman | Libbrecht Lab and Hoffman Lab (associate member) | Understanding large-scale genome regulation through joint analysis of chromatin state and chromatin conformation | |||||
| 06/14/2018 | David Gilbert | Gilbert Lab | 16 fraction repliseq | |||||
| 06/28/2018 | Kai Tan | Tan Lab (associate member) | Associate member application | |||||
| 08/02/2018 | Hakan Ozadam and Sergey Venev | Dekker Lab | Compartment, insulation and dot analysis of Hi-C data for H1-ESCs and HFFc6 | |||||
| 08/09/2018 | Ivan Juric and Miao Yu | Ming Hu Lab and Ren Lab | PLAC-seq analysis | |||||
| 08/23/2018 | Christoph Thieme and Alexander Kukalev | Pombo Lab | Comparing chromatin contacts in mouse ESCs by GAM and Hi-C | |||||
| 08/30/2018 | Peter Yingxiao Wang | Wang Lab (associate member) | Associate member application | |||||
| 09/06/2018 | Daniel Capurso | Ruan Lab | CTCF motif orientation in ChIA-PET loops at different sequencing depths and in different cell types | |||||
| 09/13/2018 | Da Kuang | Yue Lab | Identifying differential chromatin interactions with triplet network | |||||
| 09/20/2018 | Andrew Belmont and Liguo Zhang | Belmont Lab | TSA-Seq overview and update | |||||
| 10/04/2018 | Yuchuan Wang | Ma Lab | Updates on Integrative Analysis of Nuclear Compartmentalization for Joint Analysis Cell Lines | |||||
| 10/18/2018 | Gürkan Yardımcı | Noble Lab | Exploratory analysis of sciHiC data | |||||
| 10/25/2018 | Frank Alber | Alber Lab | Update on comparative genome structure analysis for tier 1 cells | |||||
| 11/01/2018 | Sofia Quinodoz | Guttman Lab | DNA SPRITE on 4DN Tier 1 Cell lines | |||||
| 11/15/2018 | Gianluca Pegoraro | IWG | The 4DN Imaging to Omics Working Subgroup | |||||
| 11/29/2018 | Sheng Zhong | Zhong Lab | Comparisons of global RNA-DNA interaction data (MARGI) and other 4DN omics data |
4dn/phase1/working_groups/ja_presentations.1600883260.txt.gz · Last modified: 2025/04/22 16:21 (external edit)