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 ====== 4DN What's new ======
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 <img src="https://www.4dnucleome.org/Assets/images/4dn-logo_1.png" style="max-height: 200px; display: block;">
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+=====   =====
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+===== 2024 =====
-=====   =====
+[[https://drive.google.com/file/d/1wwOcgucFS-FJeFtcyZLOwbBbLZDSkCVr/view?usp=drive_link|January 2024]]
-===== December 2020 =====
+[[https://drive.google.com/file/d/1Ry1MnTLTK0GLUSS-aqwui6D6CIlkM-O8/view?usp=drive_link|February 2024]]
-  * [[https://drive.google.com/file/d/1t0IizijFhI3s3o8p77hGjc2D3AKzUheH/view?usp=sharing|PDF]]
+[[https://drive.google.com/file/d/12rZcciWci3gyvS4oICO6BDq9wuqHzDj0/view?usp=drive_link|March 2024]]
-===== November 2020 =====
+[[https://drive.google.com/file/d/1IgjVahI2NX6QvOxbCNnhlRMZ0X_dM9eY/view?usp=sharing|April 2024]]
-  * [[https://drive.google.com/file/d/1hNnRq42d32yLpogUwHxPG4rnKBB1vncD/view?usp=sharing|PDF]]
+[[https://drive.google.com/file/d/1iy2bXmjkJSXNseJrEXCNkhOfEH4GUv6p/view?usp=drive_link|May 2024]]
-===== October 2020 =====
+[[https://drive.google.com/file/d/1inwah6M9PXdHUQJW7KoUSMULORfooYqk/view?usp=drive_link|June 2024]]
-  * [[https://drive.google.com/file/d/199emtja_BB50qkCGvbeUYO4KaqLC_4hy/view?usp=sharing|PDF]]
+[[https://drive.google.com/file/d/1mPmXXkmsirnDNVLX1FTT570oXjfLm9hI/view?usp=drive_link|July 2024]]
-===== September 2020 =====
+[[https://drive.google.com/file/d/15IBNLaEtF0h1FHixXuEA8T4j8T5R3R68/view?usp=drive_link|August 2024]]
-  * [[https://drive.google.com/file/d/1wTZ66w2UDiRzIzCdD8yaGQGdOrRwGvL4/view?usp=sharing|PDF]]
+[[https://drive.google.com/file/d/1pLgHrGONir5hE7KijPt27B2dI7Cdrm0H/view?usp=drive_link|September 2024]]
-===== August 2020 =====
+[[https://drive.google.com/file/d/1u4QCtlXLdH-TW6zSOFX3yNJk-8klzgRr/view?usp=drive_link|October 2024]]
-  * [[https://drive.google.com/file/d/1Ki476Fq4WncMQ9XjZaMRCrfcKb1NUa9D/view?usp=sharing|PDF]]
+November 2024
-===== July 2020 =====
+December 2024
-  * [[https://drive.google.com/file/d/1jPCOD1mpvcW0IHLrpaXM0Mp2e0tevsBB/view?usp=sharing|PDF]]
+===== 2023 =====
-===== June 2020 =====
+[[https://drive.google.com/file/d/1Jp9b8rGhrmXSVHQsoCw-dVZWbtG12vLe/view?usp=share_link|January 2023]]
-  * [[https://drive.google.com/file/d/1RAVE_e7pSpsSDuUL4ddL-GTWKAlh60eA/view?usp=sharing|PDF]]
+[[https://drive.google.com/file/d/1kfcHXY6PHcMGJ_kAOVfla2d7N6aMgCLb/view?usp=share_link|February 2023]]
-===== May 2020 =====
+[[https://drive.google.com/file/d/1_dBZuvN6bCqP2M7BWAx0nEOCceixpeDq/view?usp=share_link|March 2023]]
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting 4DN OH (OH@4dnucleome.org). Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
+[[https://drive.google.com/file/d/1kJhhuRfKVgcjLiAgezDg3pQcyEPGZ3xm/view?usp=drive_link|April 2023]]
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * **Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals****. **//Sanford, E. M., Emert, B. L., Cote, A., Raj, A.// [[https://doi.org/10.1101/2020.05.26.116962| https://doi.org/10.1101/2020.05.26.116962]] — Posted: 2020-05-27
-        * **Chromatin folding variability across single-cells results from state degeneracy in phase-separation****. **//Conte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., Nicodemi, M. // [[https://doi.org/10.1101/2020.05.16.099275|https://doi.org/10.1101/2020.05.16.099275 ]]— Posted: 2020-05-16
-        * **Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance****. **//Schep, R., Brinkman, E. K., Leemans, C., Vergara, X., Morris, B., van Schaik, T., Manzo, S. G., Peric Hupkes, D., van den Berg, J., Beijersbergen, R., Medema, R. H., van Steensel, B. // [[https://doi.org/10.1101/2020.05.05.078436|https://doi.org/10.1101/2020.05.05.078436]] — Posted: 2020-05-05
-        * **The qBED track: a novel genome browser visualization for point processes. **//Moudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T., Mitra, R. D. // [[https://doi.org/10.1101/2020.04.27.060061|https://doi.org/10.1101/2020.04.27.060061]] — Posted: 2020-04-29
-      * Recent new publications:
-        * **MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning****. **Ruochi Zhang, Jian Ma//.////Cell Press//  (2020). [[https://doi.org/10.1016/j.cels.2020.04.004|https://doi.org/10.1016/j.cels.2020.04.004]]
-  * **Scientific Webinar Series: April 24****, 2020**
-      * **Presenter: ****Minji Kim**  (Jackson Laboratory) - “Chromatin folding dynamics in loop extrusion” ([[https://drive.google.com/open?id=1UjC3gXRCdKcMcbte88W0z4nKF0NZetk2|Link to presenter slides]])
-      * **Presenter: ****Giancarlo Bonora**  (University of Washington) - “A time course multi-omics study of early mouse development at the single cell level” ([[https://drive.google.com/file/d/1HOMXlYBBnYPkqi_arEMxN9Lj2EpDXft7/view|Link to presenter slides]])
-  * **Upcoming 4DN Meetings (June 2020)**
-      * June 1 (12pm PT, 3pm ET) **Imaging Workgroup**
-      * June 11 (10am PT, 1pm ET) **JAWG**
-      * June 12 (9am PT, 12pm ET) **NOFIC-AICS Workgroup**
-      * June 16 (8am PT, 11am ET) **Steering Committee**
-      * June 22 (11am PT, 2pm ET) **Omics Workgroup**
-      * June 25 (10am PT, 1pm ET) **JAWG**
-      * June 26 (8am PT, 11am ET) **4DN Scientific Webinar**
-      * June 26 (9am PT, 12pm ET) **NOFIC-AICS Workgroup**
-===== April 2020 =====
+[[https://drive.google.com/file/d/11ISbcp83bebUniPIZFYlwBuXzV2urEal/view?usp=drive_link|May 2023]]
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting 4DN OH (OH@4dnucleome.org). Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
+[[https://drive.google.com/file/d/1XvHd0_42XyzDPKP2ao74Q9JvYvz0bFoP/view?usp=drive_link|June 2023]]
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * **HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. **//Jain, D., Chu, C., Alver, B. H., Lee, S., Lee, E. A., Park, P. J. // [[https://doi.org/10.1101/2020.04.27.060145|https://doi.org/10.1101/2020.04.27.060145]] — Posted: 2020-04-28
-        * **Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin. **//Fiorillo, L., Musella, F., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Conte, M., Prisco, A., Pombo, A., Nicodemi, M. // [[https://doi.org/10.1101/2020.04.24.059915|https://doi.org/10.1101/2020.04.24.059915]] — Posted: 2020-04-25
-        * **Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments. **//Chen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C. // [[https://doi.org/10.1101/2020.04.10.036442|https://doi.org/10.1101/2020.04.10.036442]] — Posted: 2020-04-11
-        * **The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes. **//Cote, A. J., Cote, C. J., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Boyden, E. S., Berger, S., Churchman, L. S., Raj, A. // [[https://doi.org/10.1101/2020.04.06.028092|https://doi.org/10.1101/2020.04.06.028092]] — Posted: 2020-04-07
-        * **CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells.**//Naoki Kubo, Haruhiko Ishii, Xiong Xiong, Simona Bianco, Franz Meitinger, Rong Hu, James D. Hocker, Mattia Conte, David Gorkin, Miao Yu, Bin Li, Jesse R. Dixon, Ming Hu, Mario Nicodemi, Huimin Zhao, Bing Ren.// [[https://doi.org/10.1101/2020.03.21.001693|https://doi.org/10.1101/2020.03.21.001693]] — Posted: 2020-03-23
-        * **Cell-type specialization in the brain is encoded by specific long-range chromatin topologies.**//Winick-Ng, W., Kukalev, A., Harabula, I., Zea Redondo, L., Meijer, M., Serebreni, L., Bianco, S., Szabo, D., Chiariello, A. M., Irastorza Azcarate, I., Fiorillo, L., Musella, F., Thieme, C., Irani, E., Torlai Triglia, E., Kolodziejczyk, A. A., Abentung, A., Apostolova, G., Paul, E. J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S., Dechant, G., Ungless, M. A., Nicodemi, M., Castelo-Branco, G., Pombo, A.// [[https://doi.org/10.1101/2020.04.02.020990|https://doi.org/10.1101/2020.04.02.020990]] — Posted: 2020-04-02
-      * Recent new publications:
-        * **Distinct features of nucleolus-associated domains in mouse embryonic stem cells.**  Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu & Paul D. Kaufman. //Chromosoma //  (2020). [[https://doi.org/10.1007/s00412-020-00734-9|https://doi.org/10.1007/s00412-020-00734-9]]
-  * **Scientific Webinar Series: April 24****, 2020**
-      * **Presenter: ****Kami Ahmad**  (Fred Hutchinson Cancer Research Center) - “CUT&RUN and CUT&Tag methods for profiling chromatin marks and chromatin structure.” ([[https://drive.google.com/open?id=1bQ2JBKCgwd3zXpJXT1fIleDxHtQqhjIp|Link to presenter slides]])
-      * **Presenter: ****Jiang Xu**  (University of Southern California) - “Cryo-Milling TCC-Based Mapping of Genome-Wide Chromatin Contacts” ([[https://drive.google.com/open?id=1W864AlfFE4jU3-LrjetSNlInKnmYbFbj|Link to presenter slides]])
-  * **Upcoming 4DN Meetings (May 2020)**
-      * May 4 (12pm PT, 3pm ET) Imaging Workgroup
-      * May 8 (9am PT, 12pm ET) NOFIC-AICS Workgroup
-      * May 14 (10am PT, 1pm ET) JAWG
-      * May 22 (8am PT, 11am ET) 4DN Scientific Webinar
-      * May 22 (9am PT, 12pm ET) NOFIC-AICS Workgroup
-      * May 25 (11am PT, 2pm ET) Omics Workgroup
-      * May 28 (10am PT, 1pm ET) JAWG
-=====   =====
+[[https://drive.google.com/file/d/1lQhY0UZMX7F6wzZTVqUBJyp2NJMv_W1g/view?usp=drive_link|July 2023]]
-===== March 2020 =====
+[[https://drive.google.com/file/d/16gpQAzfSfh799my8msuh72c3RoD8WlIG/view?usp=drive_link|August 2023]]
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
+[[https://drive.google.com/file/d/1nfM3saR15lFuc7HBwBkAwEbQbM5YZU1L/view?usp=sharing|September 2023]]
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * SPIN reveals genome-wide landscape of nuclear compartmentalization. Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric-Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., Belmont, A. S., Ma, J. [[https://doi.org/10.1101/2020.03.09.982967|https://doi.org/10.1101/2020.03.09.982967]] — Posted: 2020-03-10
-        * Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping. Welch, L. R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W. F., Welch, J. D., Pombo, A. [[https://doi.org/10.1101/2020.02.10.941047|https://doi.org/10.1101/2020.02.10.941047]] — Posted: 2020-02-12
-        * An Improved 4'-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNA. Wielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J., Lin, H. [[https://doi.org/10.1101/2020.02.29.971317|https://doi.org/10.1101/2020.02.29.971317]] — Posted: 2020-02-29
-        * Detecting chromatin interactions along and between sister chromatids with SisterC. Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker. [[https://doi.org/10.1101/2020.03.10.986208|https://doi.org/10.1101/2020.03.10.986208]] — Posted: 2020-03-11
-        * Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer. Tejaswi Iyyanki, Baozhen Zhang, Qiushi Jin, Hongbo Yang, Tingting Liu, Xiaotao Wang, Jie Xu, Fan Song, Yu Luan, Hironobu Yamashita, Lu Wang, Joshua Warrick, Jay Raman, Joshua J. Meeks, David Degraff, Feng Yue. [[https://doi.org/10.1101/2020.02.26.966697|https://doi.org/10.1101/2020.02.26.966697]]. — Posted: 2020-02-29
-      * Recent new publications:
-        * Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Tsung-Han S. Hsieh, Elena Slobodyanyuk, Anders S. Hansen, Claudia Cattoglio, Oliver J. Rando, Robert Tjian, Xavier Darzacq. //Molecular Cell//, available online 25 March 2020. [[https://doi.org/10.1016/j.molcel.2020.03.002|https://doi.org/10.1016/j.molcel.2020.03.002]]
-        * High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Peiyao A. Zhao, Takayo Sasaki & David M. Gilbert. Genome Biology, 21, Article number: 76 (2020). [[https://doi.org/10.1186/s13059-020-01983-8|https://doi.org/10.1186/s13059-020-01983-8]]
-===== February 2020 =====
+[[https://drive.google.com/file/d/15zJiLUBLiS3d1F6_Q6d1Ff1g95Nm0GDT/view?usp=drive_link|October 2023]]
-  * **Six 4DN RFAs (Phase 2) have been published**. The announcement can be seen on the NIH Common Fund Website ([[https://commonfund.nih.gov/4Dnucleome/funding_opportunities|https://commonfund.nih.gov/4Dnucleome/funding_opportunities]]).
+[[https://drive.google.com/file/d/1c4mhZ1bJjNAFN-kSr-zLUAhtOrypsBWC/view?usp=drive_link|November 2023]]
-      * Slides from 4DN phase 2 information webinar can be viewed here: [[https://commonfund.nih.gov/sites/default/files/4DN_Phase_2_Webinar_slide_deck_508.pdf|Link to the PDF file]]
-  * **Outreach**
-      * Higher-Order Chromatin Architecture in Time and Space:  [[https://www.keystonesymposia.org/ks/Online/Events/2020X3/Details.aspx?EventKey=2020X3|click here to register]]
-        * The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
-        * When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
-        * Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
-      * The Four-Dimensional Genome symposium:  [[https://www.embo-embl-symposia.org/symposia/2020/EES20-03/|Click here to register]]
-        * This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
-        * When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
-        * Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia. Yang, H., Zhang, H., Luan, Y., Liu, T., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Perez-Andreu, V., Xu, J., Iyyanki, S., Kuang, D., Reshmi, S. C., Gastier-Foster, J., Smith, C., Pui, C., Evans, W. E., Hunger, S. P., Platanias, L. C., Relling, M. V., Mullighan, C. G., Loh, M. L., Yue, F., Yang, J. J. [[https://doi.org/10.1101/2020.02.23.961672|https://doi.org/10.1101/2020.02.23.961672]] — Posted: 2020-02-25
-        * GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F. [[https://doi.org/10.1101/2020.01.30.927061|https://doi.org/10.1101/2020.01.30.927061]] — Posted: 2020-01-31
-  * **Scientific Webinar Series: February 28****, 2020**
-      * **Presenter: ****Brian Glenn St Hilaire**  (Baylor College of Medicine) - "ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL" ([[https://drive.google.com/open?id=1dXfMhllYePiJbT-ly6GguRX6wbC32qwN|Link to presenter slides]])
-      * **Presenter: ****Lisa Bashkirova **  (Columbia University) - "Nuclear architecture regulates the anatomic pattern of olfactory receptor expression in the olfactory epithelium" ([[https://drive.google.com/open?id=1iGvehhPO2Cjkqiry4z-Aw4bHEOLDDCU8|Link to presenter slides]])
-===== January 2020 =====
-  * **Six 4DN RFAs (Phase 2) have been published**. The announcement can be seen on the NIH Common Fund Website ([[https://commonfund.nih.gov/4Dnucleome/funding_opportunities|https://commonfund.nih.gov/4Dnucleome/funding_opportunities]]).
+[[https://drive.google.com/file/d/1Gg9S5aP97lK7JNqJb5s3pTFC8_IeP3-W/view?usp=drive_link|December 2023]]
-      * Slides from 4DN phase 2 information webinar can be viewed here: [[https://commonfund.nih.gov/sites/default/files/4DN_Phase_2_Webinar_slide_deck_508.pdf|Link to the PDF file]]
-  * **4DN Directory system:** <font inherit/inherit;;#e74c3c;;inherit>**Please update your email and profile on [[https://people.4dnucleome.org/|people.4dnucleome]]**</font> * After the launch of people.4dnucleome, we have consolidated all the email addresses of members.
-      * If 4DN announcements are going to email address(es) that you didn't use before, or you cannot send 4DN announcements to working groups anymore, please consider updating your email address to your preferred one.
-      * Your email address can be updated by:
-        * Login to people.4dnucleome ([[https://people.4dnucleome.org/|https://people.4dnucleome.org/]]);
-        * Click "My profile" on the left;
-        * Update your email address (see [[https://docs.google.com/presentation/d/1YPNUUZZ1XdCYn84GWlcOuVTQCY5X3M3R2fBwfcAW_Yw/edit?usp=sharing|this Google Slides]] for reference);
-        * Click "UPDATE" to save.
-        * This email address will be used for delivery of all 4DN-related messages and shall be used to send all 4DN-related group emails.
-        * If you have any questions, please let us know at oh@4dnucleome.org
-  * **Outreach**
-      * Higher-Order Chromatin Architecture in Time and Space:  [[https://www.keystonesymposia.org/ks/Online/Events/2020X3/Details.aspx?EventKey=2020X3|click here to register]]
-        * The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
-        * When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
-        * Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
-      * The Four-Dimensional Genome symposium:  [[https://www.embo-embl-symposia.org/symposia/2020/EES20-03/|Click here to register]]
-        * This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
-        * When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
-        * Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
-      * Recent new publications:
-        * MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Dechao Tian, Ruochi Zhang, Yang Zhang, Xiaopeng Zhu and Jian Ma. //Genome Res//. January 6, 2020, doi: [[https://doi.org/10.1101/gr.250316.119|https://doi.org/10.1101/gr.250316.119]]
-        * Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Mayank NK Choudhary, Ryan Z. Friedman, Julia T. Wang, Hyo Sik Jang, Xiaoyu Zhuo & Ting Wang. //Genome Biology//. Volume 21, Article number: 16 (2020). [[https://doi.org/10.1186/s13059-019-1916-8|https://doi.org/10.1186/s13059-019-1916-8]]
-        * Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Elizabeth H. Finn, Gianluca Pegoraro, Hugo B. Brandão, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny and Tom Misteli. //Cell//. Volume 176, Issue 6, 7 March 2019, Pages 1502-1515.e10. [[https://doi.org/10.1016/j.cell.2019.01.020|https://doi.org/10.1016/j.cell.2019.01.020]]
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * Cell cycle dynamics of lamina associated DNA. van Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B. [[https://doi.org/10.1101/2019.12.19.881979|https://doi.org/10.1101/2019.12.19.881979]] — Posted: 2019-12-19
-        * Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. Giusti-Rodriguez, P. M., Sullivan, P. F. [[https://doi.org/10.1101/406330|https://doi.org/10.1101/406330]] — Posted: 2019-01-30
-        * Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild. Humble, E., Dobrynin, P., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Lieberman Aiden, E., Wildt, D., Oliagi, S., Tamazian, G., Pukazhenthi, B., Ogden, R., Koepfli, K.-P. [[https://doi.org/10.1101/867341|https://doi.org/10.1101/867341]] — Posted: 2019-12-08
-        * Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. Ma, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A. [[https://doi.org/10.1101/2020.01.16.909333|https://doi.org/10.1101/2020.01.16.909333]] — Posted: 2020-01-17
-        * High-Resolution 3D Fluorescent Imaging of Intact Tissues. El-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R. [[https://doi.org/10.1101/855254|https://doi.org/10.1101/855254]] — Posted: 2019-11-26
-        * Probing multi-way chromatin interaction with hypergraph representation learning. Zhang, R., Ma, J. [[https://doi.org/10.1101/2020.01.22.916171|https://doi.org/10.1101/2020.01.22.916171]] — Posted: 2020-01-23
-  * **Scientific Webinar Series**: **January 24, 2020**
-      * **Presenter: Leo Barinov**  (Princeton University) - “Interplay between chromatin organization and transcriptional activity”
-      * **Presenter: Mathias Hammer**  (University of Massachusetts medical school) - “A study on effects of fixation with Formaldehyde and Paraformaldehyde”
-=====  =====
-===== Archive: 2019 =====
+===== 2022 =====
-**[[:4dn:phase1:newsletter_archive:newsletter_2019|Newsletter Archive: 2019]]**
+[[https://drive.google.com/file/d/1QSuAXx37yip1Jelipt-EC2Iit0GdwzCF/view?usp=sharing|January 2022]]
-===== Archive: 2018 =====
+[[https://drive.google.com/file/d/11jr-rWyRfoAXg_buGU46C08lzJgpmAuX/view?usp=sharing|February 2022]]
-**[[:4dn:phase1:newsletter_archive:newsletter_2018|Newsletter Archive: 2018]]**
+[[https://drive.google.com/file/d/1vBIKJyNS1rg-kC8KzJ-zu6rN-opzvtEB/view?usp=sharing|March 2022]]
+[[https://drive.google.com/file/d/1JgbhnfTz19DaE8KJP8B02ICUKwZPbRZl/view?usp=sharing|April 2022]]
+[[https://drive.google.com/file/d/1AHsA6RSZ2KT_IFVQ7D_89CyLpE_Ip8kW/view?usp=sharing|May 2022]]
+[[https://drive.google.com/file/d/1fU-twnf8pppg4Q1MNwmOPp0bhBHMwbfQ/view?usp=sharing|June 2022]]
+[[https://drive.google.com/file/d/1uubNq30mIgHJWRBNA3FurOVMB4WUsnDG/view?usp=sharing|July 2022]]
+[[https://drive.google.com/file/d/18LcTaw7HmN9FQZDR00KuRC8Euf3LnVqA/view?usp=sharing|August 2022]]
+[[https://drive.google.com/file/d/1y0l0MnOKhADrh3tiN2jGx-7eku01a_Fp/view?usp=share_link|September 2022]]
+October 2022
+[[https://drive.google.com/file/d/1GBKS_p_k7BJrH8KBVNMhcNfnavMD1LPP/view?usp=share_link|November 2022]]
+[[https://drive.google.com/file/d/1m_BJ76vjfYucURLpwTfeb9fuf-l5rkRW/view?usp=share_link|December 2022]]
+===== 2021 =====
+  * [[https://drive.google.com/file/d/1BRR9LNiagx6g3FoUfWFWfAPojUmHS7OQ/view?usp=sharing|December 2021]]
+  * [[https://drive.google.com/file/d/1sjpP8yGnpCyJQeJ2DHCS7THz1iB0Nx8k/view?usp=sharing|November 2021]]
+  * [[https://drive.google.com/file/d/1XNsREk8bxcluzqSB1FLLNBR_OhuSPaNj/view?usp=sharing|October 2021]]
+  * [[https://drive.google.com/file/d/1p0dBDDZU_8LXmmrorJzyQpYWkse0ElB7/view?usp=sharing|September 2021]]
+  * [[https://drive.google.com/file/d/1jsq4e9YbL6qtWR9K2YCztuOrg72N-igr/view?usp=sharing|August 2021]]
+  * [[https://drive.google.com/file/d/1tU6_iA8aef_pycbRff5ptZi9tHLqWqZm/view?usp=sharing|July 2021]]
+  * [[https://drive.google.com/file/d/1ubs7VDsoUzwYBCSE75cLTTdgR670m3u7/view?usp=sharing|June 2021]]
+  * [[https://drive.google.com/file/d/1AlWAbaG_On8UTmAAI4VBujqMvGgkPwhF/view?usp=sharing|May 2021]]
+  * [[https://drive.google.com/file/d/129KgLKgwdhx-79SKyGGBhRKipABcMFwR/view?usp=sharing|April 2021]]
+  * [[https://drive.google.com/file/d/1E5kKgQpTpzs009vbBe9FIpxnyy7_HJWd/view?usp=sharing|March 2021]]
+  * [[https://drive.google.com/file/d/1FiiG3oTPhcq02p4AQnE3L_7Ul_zXnWv_/view?usp=sharing|February 2021]]
+  * [[https://drive.google.com/file/d/1qnFVh1XYj1S8ge4ovkucp5xG0jyuOXOS/view?usp=sharing|January 2021]]
+===== 2020 =====
+  * [[https://drive.google.com/file/d/1t0IizijFhI3s3o8p77hGjc2D3AKzUheH/view?usp=sharing|December 2020]]
+  * [[https://drive.google.com/file/d/1hNnRq42d32yLpogUwHxPG4rnKBB1vncD/view?usp=sharing|November 2020]]
+  * [[https://drive.google.com/file/d/199emtja_BB50qkCGvbeUYO4KaqLC_4hy/view?usp=sharing|October 2020]]
+  * [[https://drive.google.com/file/d/1wTZ66w2UDiRzIzCdD8yaGQGdOrRwGvL4/view?usp=sharing|September 2020]]
+  * [[https://drive.google.com/file/d/1Ki476Fq4WncMQ9XjZaMRCrfcKb1NUa9D/view?usp=sharing|August 2020]]
+  * [[https://drive.google.com/file/d/1jPCOD1mpvcW0IHLrpaXM0Mp2e0tevsBB/view?usp=sharing|July 2020]]
+  * [[https://drive.google.com/file/d/1RAVE_e7pSpsSDuUL4ddL-GTWKAlh60eA/view?usp=sharing|June 2020]]
-===== Archive 2017 =====
+  * [[https://drive.google.com/file/d/1qkDYgObEwI62SGi2sjzYY-TuBizupaFp/view?usp=sharing|May 2020]]
-**[[:4dn:phase1:newsletter_archive:newsletter_2017|Newsletter Archive: 2017]]**
+  * [[https://drive.google.com/file/d/1YevZkOi_DDflFENUGSWbHTiuxrbibxda/view?usp=sharing|April 2020]]
-===== February 2020 =====
+  * [[https://docs.google.com/document/d/10C6qUSaQSr0EmVv0wc4rCB_-Pn0kkhgdmBl9OkfNg1k/edit?usp=sharing|March 2020]]
-  * **Six 4DN RFAs (Phase 2) have been published**. The announcement can be seen on the NIH Common Fund Website ([[https://commonfund.nih.gov/4Dnucleome/funding_opportunities|https://commonfund.nih.gov/4Dnucleome/funding_opportunities]]).
+  * [[https://docs.google.com/document/d/1BvEmAWyYERixnXC7wyVRkFCpf8V8wzVc5XCv4hKmuZc/edit?usp=sharing|February 2020]]
-      * Slides from 4DN phase 2 information webinar can be viewed here: [[https://commonfund.nih.gov/sites/default/files/4DN_Phase_2_Webinar_slide_deck_508.pdf|Link to the PDF file]]
-  * **Outreach**
-      * Higher-Order Chromatin Architecture in Time and Space:  [[https://www.keystonesymposia.org/ks/Online/Events/2020X3/Details.aspx?EventKey=2020X3|click here to register]]
-        * The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
-        * When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
-        * Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
-      * The Four-Dimensional Genome symposium:  [[https://www.embo-embl-symposia.org/symposia/2020/EES20-03/|Click here to register]]
-        * This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
-        * When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
-        * Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia. Yang, H., Zhang, H., Luan, Y., Liu, T., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Perez-Andreu, V., Xu, J., Iyyanki, S., Kuang, D., Reshmi, S. C., Gastier-Foster, J., Smith, C., Pui, C., Evans, W. E., Hunger, S. P., Platanias, L. C., Relling, M. V., Mullighan, C. G., Loh, M. L., Yue, F., Yang, J. J. [[https://doi.org/10.1101/2020.02.23.961672|https://doi.org/10.1101/2020.02.23.961672]] — Posted: 2020-02-25
-        * GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F. [[https://doi.org/10.1101/2020.01.30.927061|https://doi.org/10.1101/2020.01.30.927061]] — Posted: 2020-01-31
-  * **Scientific Webinar Series: February 28****, 2020**
-      * **Presenter: ****Brian Glenn St Hilaire**  (Baylor College of Medicine) - "ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL" ([[https://drive.google.com/open?id=1dXfMhllYePiJbT-ly6GguRX6wbC32qwN|Link to presenter slides]])
-      * **Presenter: ****Lisa Bashkirova **  (Columbia University) - "Nuclear architecture regulates the anatomic pattern of olfactory receptor expression in the olfactory epithelium" ([[https://drive.google.com/open?id=1iGvehhPO2Cjkqiry4z-Aw4bHEOLDDCU8|Link to presenter slides]])
-===== January 2020 =====
-  * **Six 4DN RFAs (Phase 2) have been published**. The announcement can be seen on the NIH Common Fund Website ([[https://commonfund.nih.gov/4Dnucleome/funding_opportunities|https://commonfund.nih.gov/4Dnucleome/funding_opportunities]]).
+  * [[https://docs.google.com/document/d/1F-MShtLJklCnxe4SXlO0Uz2UcHrfp0zfYMmQrbHX71o/edit?usp=sharing|January 2020]]
-      * Slides from 4DN phase 2 information webinar can be viewed here: [[https://commonfund.nih.gov/sites/default/files/4DN_Phase_2_Webinar_slide_deck_508.pdf|Link to the PDF file]]
-  * **4DN Directory system:** <font inherit/inherit;;#e74c3c;;inherit>**Please update your email and profile on [[https://people.4dnucleome.org/|people.4dnucleome]]**</font> * After the launch of people.4dnucleome, we have consolidated all the email addresses of members.
-      * If 4DN announcements are going to email address(es) that you didn't use before, or you cannot send 4DN announcements to working groups anymore, please consider updating your email address to your preferred one.
-      * Your email address can be updated by:
-        * Login to people.4dnucleome ([[https://people.4dnucleome.org/|https://people.4dnucleome.org/]]);
-        * Click "My profile" on the left;
-        * Update your email address (see [[https://docs.google.com/presentation/d/1YPNUUZZ1XdCYn84GWlcOuVTQCY5X3M3R2fBwfcAW_Yw/edit?usp=sharing|this Google Slides]] for reference);
-        * Click "UPDATE" to save.
-        * This email address will be used for delivery of all 4DN-related messages and shall be used to send all 4DN-related group emails.
-        * If you have any questions, please let us know at oh@4dnucleome.org
-  * **Outreach**
-      * Higher-Order Chromatin Architecture in Time and Space:  [[https://www.keystonesymposia.org/ks/Online/Events/2020X3/Details.aspx?EventKey=2020X3|click here to register]]
-        * The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
-        * When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
-        * Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
-      * The Four-Dimensional Genome symposium:  [[https://www.embo-embl-symposia.org/symposia/2020/EES20-03/|Click here to register]]
-        * This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
-        * When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
-        * Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
-  * **4DN Publications:**  Please add your preprints into the [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]] by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
-      * Recent new publications:
-        * MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Dechao Tian, Ruochi Zhang, Yang Zhang, Xiaopeng Zhu and Jian Ma. //Genome Res//. January 6, 2020, doi: [[https://doi.org/10.1101/gr.250316.119|https://doi.org/10.1101/gr.250316.119]]
-        * Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Mayank NK Choudhary, Ryan Z. Friedman, Julia T. Wang, Hyo Sik Jang, Xiaoyu Zhuo & Ting Wang. //Genome Biology//. Volume 21, Article number: 16 (2020). [[https://doi.org/10.1186/s13059-019-1916-8|https://doi.org/10.1186/s13059-019-1916-8]]
-        * Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Elizabeth H. Finn, Gianluca Pegoraro, Hugo B. Brandão, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny and Tom Misteli. //Cell//. Volume 176, Issue 6, 7 March 2019, Pages 1502-1515.e10. [[https://doi.org/10.1016/j.cell.2019.01.020|https://doi.org/10.1016/j.cell.2019.01.020]]
-      * Recent new preprints added to [[http://connect.biorxiv.org/relate/content/66|bioRxiv 4DN channel]]:
-        * Cell cycle dynamics of lamina associated DNA. van Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B. [[https://doi.org/10.1101/2019.12.19.881979|https://doi.org/10.1101/2019.12.19.881979]] — Posted: 2019-12-19
-        * Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. Giusti-Rodriguez, P. M., Sullivan, P. F. [[https://doi.org/10.1101/406330|https://doi.org/10.1101/406330]] — Posted: 2019-01-30
-        * Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild. Humble, E., Dobrynin, P., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Lieberman Aiden, E., Wildt, D., Oliagi, S., Tamazian, G., Pukazhenthi, B., Ogden, R., Koepfli, K.-P. [[https://doi.org/10.1101/867341|https://doi.org/10.1101/867341]] — Posted: 2019-12-08
-        * Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. Ma, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A. [[https://doi.org/10.1101/2020.01.16.909333|https://doi.org/10.1101/2020.01.16.909333]] — Posted: 2020-01-17
-        * High-Resolution 3D Fluorescent Imaging of Intact Tissues. El-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R. [[https://doi.org/10.1101/855254|https://doi.org/10.1101/855254]] — Posted: 2019-11-26
-        * Probing multi-way chromatin interaction with hypergraph representation learning. Zhang, R., Ma, J. [[https://doi.org/10.1101/2020.01.22.916171|https://doi.org/10.1101/2020.01.22.916171]] — Posted: 2020-01-23
-  * **Scientific Webinar Series**: **January 24, 2020**
-      * **Presenter: Leo Barinov**  (Princeton University) - “Interplay between chromatin organization and transcriptional activity”
-      * **Presenter: Mathias Hammer**  (University of Massachusetts medical school) - “A study on effects of fixation with Formaldehyde and Paraformaldehyde”
-=====  =====
-===== Archive: 2019 =====
+===== 2019 =====
 **[[:4dn:phase1:newsletter_archive:newsletter_2019|Newsletter Archive: 2019]]**
-===== Archive: 2018 =====
+===== 2018 =====
 **[[:4dn:phase1:newsletter_archive:newsletter_2018|Newsletter Archive: 2018]]**
-===== Archive 2017 =====
+===== 2017 =====
 **[[:4dn:phase1:newsletter_archive:newsletter_2017|Newsletter Archive: 2017]]**

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