Category: News

Paper Published

New paper by Dr Soya Shinkai has been published.

Understanding how chromosomes move inside living cells requires quantitative models linking genome structure to chromatin dynamics. Here, using genome-wide live-cell imaging together with our PHi-C technology, a Hi-C data-constrained polymer modeling approach, we built an integrative, physics-based “digital twin” of the fission yeast genome that reproduces its spatiotemporal chromatin dynamics. The model captures known architectural features, reveals characteristic chromatin relaxation times, and shows that low-frequency forces generated outside the nucleus propagate through the spindle pole body and centromeres to drive genome-wide chromatin displacement. This work provides a physical framework for understanding how nuclear mechanics shapes genome dynamics and function.

Reference

S. Shinkai, T. Namba, T. Sugawara, S. Hagiwara, S. Onami, T. Haraguchi, Y. Hiraoka, A. Awazu, M. Ueno, & S. Tate, Integrative modeling of the genome structure and dynamics in fission yeast, Proc. Natl. Acad. Sci. U.S.A. 123 (37) e2612002123, (2026). doi: 10.1073/pnas.2612002123

Call for RIKEN Research Engineer Fellow

RIKEN has established the RIKEN Research Engineer Fellow Program to foster the next generation of “research engineers” — young professionals who combine research experience with advanced skills in data science, AI, and information technology. Applications for the program opened in September 2026.

Through this program, RIKEN aims to nurture a new generation of young professionals who bring together research expertise and advanced information technology skills, including the use of data and AI. RIKEN expects these individuals to go on to make broad contributions to the advancement of science and technology in academia and industry, both in Japan and around the world.

RIKEN Research Engineer Fellow Program

Overview of the program

Call for Applications: FY 2027 RIKEN Research Engineer Fellow Program

Our laboratory is a host laboratory for this program. If you are interested in joining our laboratory as a RIKEN Research Engineer Fellow, please feel free to contact us.

236 GFP-tagged C. elegans strains from the Onami Lab released in WormTagDB

We have released information for 236 endogenously GFP-tagged Caenorhabditis elegans strains in WormTagDB, a community resource for endogenously tagged worm strains. With this contribution, our laboratory is now the second-largest contributor of tagged alleles in the database. Notably, approximately 150 of the genes in our collection had not previously been tagged, making this a substantial contribution toward expanding proteome-wide fluorescent tagging resources in C. elegans.


The strains were generated as part of our efforts to systematically visualize protein expression and localization during embryonic development. We plan to continue expanding the collection and developing associated imaging resources.


WormTagDB: https://wormtagdb.rc.duke.edu

SSBD:BFF Explorer Released

A new feature, SSBD:BFF Explorer, has been implemented in the SSBD database to facilitate the discovery, organization, filtering, and visualization of bioimaging datasets through metadata. The tool enables efficient exploration of large-scale bioimaging datasets in OME-Zarr format directly in a web browser and also supports links to datasets managed in OMERO, thereby promoting the reuse and accessibility of bioimaging data.

Read more: https://biosciencedbc.jp/news/20260622-01.html (In Japanese Only)

Reference

  • Meharry, S.L., Borensztejn, A., Gaudreault, N. et al. Search, organize, aggregate and share image data with BioFile Finder (BFF). Nat Methods (2026). doi: 10.1038/s41592-026-03130-w

Zallery — OME-Zarr Image Gallery

We released Zallery, a lightweight web application for browsing OME-Zarr image datasets as a study-level gallery.
Zallery was started during the OME Community Meeting 2026 Hackathon as part of our effort to publish SSBD image data in OME-Zarr format. It reads tabular metadata files and provides gallery views, metadata-based filtering, and links to OME-Zarr image resources.

Live: https://openssbd.github.io/zallery/
Resource: https://github.com/openssbd/zallery

foundingGIDE Community Event 2025 registration is open

We’re excited to announce that registrations are now open for the foundingGIDE Community Event 2025, taking place in Brisbane, Australia on October 17–18. Join us for 1.5 days of collaboration and engagement with the global imaging data community. More details below.

The foundingGIDE Community Event is positioned between two major data-centric conferences and offers a unique opportunity for professionals engaged in research data management, imaging, and digital infrastructure to connect with the global data research community. FoundingGIDE Community Event (October 17-18) is following International Data Week 2025 (October 13–16) and preceding eResearch Australasia 2025 (October 20–24) all at the same location, Brisbane Convention and Exhibition Centre, Australia. These three events bring together communities working toward the FAIR data principles and advancing practices in data sharing, stewardship, and interoperability across scientific domains.

To find out more about the event and to register, visit https://founding-gide.eurobioimaging.eu/community-event-2025/.

Logo of foundingGIDE

 

EU emblem and funding statement

foundingGIDE has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101130216. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Join us at GloBIAS 2025 – Registration is open!

We are delighted to invite you to join us at the GloBIAS Bioimage Analysis Conference 2025 from Oct 26, 2025 – Oct 31, 2025 in Kobe, Japan at the RIKEN Kobe Campus.

The Conference will consist of several events:

  • Training school, hackathon and taggathon from 26 October to 29 October, 
  • Symposium with poster session, Open-source Software Lounge, Call4Help sessions from 29 October to 31 October

Important dates:

  • Abstract submission deadline: 15 May 2025
  • Training school application deadline: 15 May 2025
  • Training School Trainee, Travel grants, Poster/Oral notification: 15 June 2025

More information can be found on our website: https://www.globias.org/activities/bioimage-analysis-conference-2025-in-kobe

There you can also find the link to the registration form.

We look forward to welcoming you in Kobe!

[Press Release]Discovery of a new mechanism by which changes in the distance between genes regulate their expression

Drs Hiroaki Oishi, Hiroshi Ochiai, (Kyushu University, respectively) and Soya Shinkai et al. found a novel mechanism of gene expression regulation involving changes in the spatial distance between genes. Understanding the mechanisms of gene expression regulation is crucial not only for molecular biology but also for medical research, as it directly links to identifying disease causes and therapeutic targets.

Learn more about the study on Press Release by Kyushu University, RIKEN and JST. (In Japanese only)

Reference

Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H. (2024). Transcription-coupled changes in genomic region proximities during transcriptional bursting. Sci. Adv. 10, eadn0020. DOI:10.1126/sciadv.adn0020