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4dn:phase1:newsletter_archive:newsletter_2018

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December 2018

  • 2018 4DN Annual Meeting and 4DN-ASCB Satellite Meeting concluded successfully!
  • 4DN wiki is under maintenance.
  • 4DN Publications: Please add your preprints into 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. * Stats by Dec 31, 2018 * Preprints (bioRxiv 4DN channel): 135 in total
    • Publications (Pubmed): 170 in total.
  • New preprints in December (bioRxiv 4DN channel): * Mayank NK Choudhary, Ryan Z Friedman, Julia T Wang, Hyo Sik Jang, Xiaoyu Zhuo, Ting Wang. Co-opted transposons help perpetuate conserved higher-order chromosomal structures. doi: https://doi.org/10.1101/485342
    • Recent new publications: * Haifeng Wang, Xiaoshu Xu, Cindy M. Nguyen, Yanxia Liu, Yuchen Gao, Xueqiu Lin, Timothy Daley, Nathan H. Kipniss, Marie La Russa, Lei S. Qi. CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Cell. 2018 Nov 15;175(5):1405-1417.e14. doi: 10.1016/j.cell.2018.09.013.
  • Happy New Year 2019!

November 2018

  • 2018 4DN Annual Meeting and 4DN-ASCB Satellite Meeting are coming next week (Dec 4-7). See you in San Diego
  • 4DN Publications: Please add your preprints into 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. * New preprints in November (bioRxiv 4DN channel): * Zhangming Yan, Norman Huang, Weixin Wu, Weizhogn Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhen Chen, Shu Chien, Sheng Zhong. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. doi: https://doi.org/10.1101/47201

October 2018

  • 2018 4DN Annual Meeting registration has been closed on November 1st.
  • 4DN Publications: Please add your preprints into 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. * Stats by Oct 30, 2018 * Preprints (bioRxiv 4DN channel): 113 in total
    • Publications (Pubmed): 170 in total.
  • Recent new publications: * Jesse R. Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera-Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T. Odom, John A. Stamatoyannopoulos, James R. Broach, Ross C. Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M. Gilbert & Feng Yue. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. volume 50, pages1388–1398 (2018). doi: https://doi.org/10.1038/s41588-018-0195-8
  • Scientific Webinar Series this Month: October 26, 2018

Presenter: Martin Falk (Massachusetts Institute of Technology) - “Heterochromatin drives organization of conventional and inverted nuclei”[Link to presenter slides]

Presenter: Andrew Barentine (Yale University) -“3D Nanoscopy of 10,000 Nuclei a Day“[Link to presenter slides]

September 2018

  • 4DN Publications: Please add your preprints into 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. * New preprints in September (bioRxiv 4DN channel): * Sadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D. Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale. doi: https://doi.org/10.1101/266981 — Posted: 2018-09-14
    • Recent new publications: * James H. Sun, Linda Zhou, Daniel J. Emerson, Sai A. Phyo, Katelyn R. Titus, Wanfeng Gong, Thomas G. Gilgenast, Jonathan A. Beagan, Beverly L. Davidson, Flora Tasson, Jennifer E. Phillips-Cremins. Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. Cell. 2018 Sep 20;175(1):224-238.e15. doi: https://doi.org/10.1016/j.cell.2018.08.005.
      • Marc A. Marti-Renom, Genevieve Almouzni, Wendy A. Bickmore, Kerstin Bystricky, Giacomo Cavalli, Peter Fraser, Susan M. Gasser, Luca Giorgetti, Edith Heard, Mario Nicodemi, Marcelo Nollmann, Modesto Orozco, Ana Pombo & Maria-Elena Torres-Padilla. Challenges and guidelines toward 4D nucleome data and model standards. Nature Genetics. volume 50, pages1352–1358 (2018). https://doi.org/10.1038/s41588-018-0236-3
  • Scientific Webinar Series this Month: September 28, 2018
  • Presenter: Adrien Senecal (Albert Einstein College of Medicine) - The p53 transcription factor regulates transcriptional burst frequency and multiple steps of formation and disruption of chromatin on the p21 gene locus [Link to presenter slides]
  • Presenter: Matthew Denholtz (University of California, San Diego) -Neutrophil genome dynamics in development and pathogen encounter[Link to presenter slides]

August 2018

  • 4DN Publications: Please add your preprints into 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. * New preprints in August (bioRxiv 4DN channel): * Kim, S., Dunham, M., Shendure, J. A combination of transcription factors mediates inducible interchromosomal pairing. doi: https://doi.org/10.1101/385047. Posted: 2018-08-05
  • Rieger, B., Stallinga, S., Hulleman, C. N., Thorsen, R. O., Grunwald, D., Hammer, M. Photon count estimation in single-molecule localization microscopy. doi: https://doi.org/10.1101/396424. Posted: 2018-08-20
  • Recent new publications: * Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H. Alver, Hanspeter Pfister, Leonid A. Mirny, Peter J. Park and Nils Gehlenborg. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biology. 2018, Aug 24;19(1):125. doi: https://doi.org/10.1186/s13059-018-1486-1.
  • * Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. Journal of Cell Biology. August 28, 2018. DOI: https://doi.org/10.1083/jcb.201807108
  • * Won-Ki Cho, Jan-Hendrik Spille, Micca Hecht, Choongman Lee, Charles Li, Valentin Grube, Ibrahim I. Cisse. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 27 Jul 2018: Vol. 361, Issue 6400, pp. 412-415. doi: https://doi.org/10.1126/science.aar4199
  • * Shasha Chong, Claire Dugast-Darzacq, Zhe Liu, Peng Dong, Gina M. Dailey, Claudia Cattoglio, Alec Heckert, Sambashiva Banala, Luke Lavis, Xavier Darzacq, Robert Tjian. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 27 Jul 2018:Vol. 361, Issue 6400, eaar2555. doi: https://doi.org/10.1126/science.aar2555
  • * Hongtao Chen, Michal Levo, Lev Barinov, Miki Fujioka, James B. Jaynes & Thomas Gregor. Dynamic interplay between enhancer–promoter topology and gene activity. Nature Genetics. 2018 Volume 50, pages1296–1303. doi: https://doi.org/10.1038/s41588-018-0175-z
  • * Sofia A. Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M. Lai, Alexander A. Shishkin, Prashant Bhat, Yodai Takei, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Long Cai, Patrick McDonel, Manuel Garber, Mitchell Guttman. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell. 2018, Volume 174, Issue 3, 26, Pages 744-757.e24. doi: https://doi.org/10.1016/j.cell.2018.05.024
  • Scientific Webinar Series this Month: August 24, 2018
  • Presenter: Roel Neijts (Institute Pasteur) - Exploring the TAD: specific enhancer-promoter interactions within regulatory domains [Link to presenter slides]
  • Presenter: Arturas Petronis (Center for Addiction and Mental Health) -Spatiotemporal dynamics of chromatin: the circadian perspective[Link to presenter slides]

July 2018

  • The NIH Common Fund 4D Nucleome program has released an RFIto solicit feedback from the national and international community on the remaining challenges towards a comprehensive analysis of the mammalian 4D Nucleome. Suggestions from all are welcome. Written responses must be submitted by August 6, 2018to 4DNucleome@mail.nih.gov.
  • 4DN Publications: Please add your preprints into 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. * New preprints in July: * Mayuri Rege, Ji Hun Kim, Jacqueline Valeri, Margaret Dunagin, Aryeh Metzger, Wanfeng Gong, Jonathan Beagan, Arjun Raj, Jennifer E Phillips-Cremins. LADL: Light-activated dynamic looping for endogenous gene expression control. doi: https://doi.org/10.1101/349340. Posted June 18, 2018.
    • New publications in July: * Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng and Sheng Zhong. GIVE: portable genome browsers for personal websites. Genome Biology, 2018, 19:92. doi: https://doi.org/10.1186/s13059-018-1465-6
  • Scientific Webinar Series this Month: July 27, 2018
  • Presenter: Tom Pastinen (McGill University) -Interacting differentially methylated regions (iDMRs) to infer chromosome looping

[Link to presenter slides] https://youtu.be/Q5nUrT_3xnk

  • Presenter: Keji Zhao (NHLBI) -Trac-looping: a novel technique for analysis of chromatin accessibility and interaction

[Link to presenter slides] https://youtu.be/qjTZWtLJ7Cg

June 2018

  • Cell line WTC-11 has been moved from a Tier 2 to a Tier 1 cell line, as approved by the Cells WG. We now have 5 cell lines on Tier 1. Check the cell line wiki page for more details.
  • Job Opportunities: Please check the 4DN Job Advertisement Page for detailed information. * 2 new job opportunities: * Bioinformatics Scientist – Harvard Medical School - DCIC (Link to details)
    • Senior Bioinformatics Scientist – Harvard Medical School - DCIC (Link to details)
  • 6 previous job opportunities are still open.
  • 4DN Publications: Please add your preprints into bioRxiv 4DN channel. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome. * New preprints in June: * Kim, J., Han, K. Y., Khanna, N., Ha, T., Belmont, A. S. Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles. doi: 10.1101/34795. Posted: 2018-06-15
    • New publications in June: * Ipek Tasan Gabriela Sustackova Liguo Zhang Jiah Kim Mayandi Sivaguru Mohammad HamediRad Yuchuan Wang Justin Genova Jian Ma Andrew S Belmont, Huimin Zhao. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Research, Published: 15 June 2018. doi: https://doi.org/10.1093/nar/gky501
      • Ji Hun Kim, Katelyn R.Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer E.Phillips-Cremins. 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Methods, Volume 142, 1 June 2018, Pages 39-46. doi: https://doi.org/10.1016/j.ymeth.2018.05.005
      • Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. O'Neill, David M. Gilbert, Jian Ma. Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. Cell Systems. Published Online: June 20, 2018. doi: https://doi.org/10.1016/j.cels.2018.05.022
      • Weizhong Chen, Zhangming Yan, Simin Li, Norman Huang, Xuerui Huang, Jin Zhang, Sheng Zhong. RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. iScience . Volume 4, p204–215, 29 June 2018. doi:https://doi.org/10.1016/j.isci.2018.06.005
      • Ruochi Zhang Yuchuan Wang Yang Yang Yang Zhang Jian Ma. Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinformatics , Volume 34, Issue 13, 1 July 2018, Pages i133–i141. doi:https://doi.org/10.1093/bioinformatics/bty248
  • Scientific Webinar Series this Month: June 22, 2018
  • Presenter: Nicola Neretti (Brown University)- Inference and Validation of Chromosomes' 3D Structure

[Link to presenter slides]

  • Presenter: Andrew Field (Harvard Medical School) - Elucidating the role of nascent RNA at enhancers

[Link to presenter slides]https://youtu.be/PC5v5axTSFs

May 2018

  • Job Opportunities: Please check the 4DN Job Advertisement page for detail information. * 1 new job opportunity: * Postdoc positions (multiple, including NIH-funded Nucleomics project) – California Institute of Technology (Link to detail)
    • 5 previous job opportunities are still open.
  • 4DN Publications * Stats by May 31, 2018 * Preprints (bioRxiv 4DN channel): 108 in total
    • Publications (Pubmed):157 in total, 2 new publications in May
  • New publications in May: * Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM. Allele-specific control of replication timing and genome organization during development. Genome Res. 2018 May 7 [Epub ahead of print]. doi: 10.1101/gr.232561.117
    • Marchal C, Sasaki T, Vera D, Wilson K, Sima J, Rivera-Mulia JC, Trevilla-García C, Nogues C, Nafie E, Gilbert DM. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.Nat Protoc . 2018 May;13(5):819-839. doi: 10.1038/nprot.2017.148
  • Scientific Webinar Series this Month: May 25, 2018 * Presenter: Amin Allahyar (Hubrecht Institute)- Looking beyond pairwise 3D conformation of the genome by MC-4C HD

[<font 10pt/inherit;;inherit;;inherit><font inherit/arial, sans-serif;;inherit;;inherit><font inherit/inherit;;inherit;;inherit>Link to presenter slides</font></font></font>] https://youtu.be/PFskL_9TfI4

  • Presenter: Brad Cairns (University of Utah) and Antonio Giraldez (Yale University) - How the Genome Awakens in Zebrafish

[<font 10pt/inherit;;inherit;;inherit><font inherit/arial, sans-serif;;inherit;;inherit><font inherit/inherit;;inherit;;inherit>Link to presenter slides</font></font></font>] https://youtu.be/vzy4WbU5Y5Q

April 2018

  • Announcing Collaboration plaza, a new wiki page for seeking collaboration opportunities within the 4DN network.
  • 4DN Publications * Stats by Apr 30, 2018 * Preprints (bioRxiv 4DN channel): 108 in total, 3 new preprints in April
    • Publications (Pubmed): 156 in total.
  • New preprints in April: * RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome. Weizhong Chen, Zhangming Yan, Simin Li, Norman Huang, Xuerui Huang, Jin Zhang, Sheng Zhong. doi: https://doi.org/10.1101/300483
    • Pattern-Driven Navigation in 2D Multiscale Visual Spaces with Scalable Insets. Fritz Lekschas, Michael Behrisch, Benjamin Bach, Peter Kerpedjiev, Nils Gehlenborg, Hanspeter Pfister. doi: https://doi.org/10.1101/301036
    • TSA-Seq Mapping of Nuclear Genome Organization. Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont. doi: https://doi.org/10.1101/307892
  • Scientific Webinar Series this Month:

April 27, 2018

Presenter: Karla Neugebauer (Yale University)- The Cell Nucleus under Stress

Presenter: Steve Henikoff (Fred Hutchinson Cancer Research Center)- CUT&RUN: Efficient genome-wide profiling of the epigenomic landscape [Link to presenter slides]


  • March 2018
  • Announcing Collaboration plaza, a new wiki page for seeking collaboration opportunities within the 4DN network.
  • Senior Computational Biologist – The Florida State University (FSU) Center for Genomics (CGPM)
  • Computational biology postdoc position to analyze chromatin architecture in cancer – Jane Skok and Richard Bonneau New York University School of Medicine and NYU Data Sciences
  • Postdoc position to study chromatin architecture in cancer: experience in chromosome conformation and capture AND CRISPR preferred – Jane Skok and New York University School of Medicine
  • Postdoc position to study dynamic chromatin architecture and transcription in developmental systems – Thomas Gregor, Princeton University (USA) and Institut Pasteur (France)
  • Assistant in Research (12 month salaried, Molecular Biology) – Florida State University Department of Biological Science Core Facility
  • Scientific Webinar Series this Month:

March 23, 2018

Presenter: Rajarshi P Ghosh (Stanford University)- Chromatin dynamics: Motional signatures of transcriptional state

February 2018

February 23, 2018

Presenter: Paul Fields (University of Washington)- Dynamics of Genome Reorganization during Human Cardiogenesis

Presenter: Caroline Bartman (University of Pennsylvania)- Frequency modulation of polymerase recruitment via transcriptional bursting is a dominant mode of transcriptional regulation [Link to presenter slides]
* 4DN Publications * Stats by Feb 28, 2018 * Preprints (bioRxiv 4DN channel): 105 in total, 64 out of them unpublished. 5 new preprints in Feb 2018.

  • Publications (Pubmed): 155 in total.
  • Job Opportunities: *
 Position/Title Employer Job Type Post Date Deadline Status Apply methods / contacts Detail Link
1Senior Computational BiologistThe Florida State University (FSU) Center for Genomics (CGPM)Full-time non-tenure-trackFeb 10, 2018NAOpenOnline apply

Indeed

January 2018</font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font> * 4DN Program Announces Associate Membership.Read the PDF file for more information. January 26, 2018</font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font> * Scientific Webinar Series this Month: Presenter: Yi Kou (University of Southern California) - Mapping genome 3D structure by direct DNA-DNA photo-crosslinking and click enrichment Presenter: Paul Olivier (University of Toronto) - Developing a new framework to detect and link protein complexes to specific chromatin interactions Presenter: Meizhen Zheng (The Jackson Laboratory of Genomic Medicine) -Multiplex Chromatin Interaction Analysis with Single Molecule Precision

4dn/phase1/newsletter_archive/newsletter_2018.1550617048.txt.gz · Last modified: 2025/04/22 16:21 (external edit)

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