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Charlotte Soneson

@csoneson.bsky.social
269 followers 102 following 1 posts
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Reposted by Charlotte Soneson
FMI science @fmiscience.bsky.social · 16/09/2026
We’re hiring! The FMI Computational Biology Facility is seeking a Computational Biologist with experience in proteomics data analysis. Join a collaborative team working with scientists across the FMI to turn complex datasets into biological insight. Apply by Oct 25: www.fmi.ch/education-ca...
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Reposted by Charlotte Soneson
FMI science @fmiscience.bsky.social · 19/02/2026
💫 We're hiring! The Computational Biology Facility is looking for a Computational Proteomics Scientist to collaborate on cutting-edge proteomics projects, develop new analytical approaches, and publish impactful research. Apply by April 12 at: www.fmi.ch/education-ca...
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Reposted by Charlotte Soneson
Bioconductor @bioconductor.bsky.social · 31/10/2025
🚀 Bioconductor 3.22 is released! Thanks to all developers and community members for contributing to the project! 🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...
bioconductor.org
Bioconductor - Bioconductor 3.22 Released
The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and…
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Reposted by Charlotte Soneson
FMI science @fmiscience.bsky.social · 12/09/2025
📣The Turco group is seeking a computational biologist to analyze large omics datasets. Work on cutting-edge 3D organoid models of the human placenta and be embedded in our Computational Biology Platform (part of @sib.swiss). Apply here: www.fmi.ch/education-ca...
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Reposted by Charlotte Soneson
Alexandra Bendel @alexbendel.bsky.social · 25/08/2025
I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel. We used ddPCA to map the genetic architecture of the entire human bZIP interaction network. www.biorxiv.org/content/10.1... Thanks to all our co-authors for the great collaboration!
biorxiv.org
The genetic architecture of the human bZIP family
Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...
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Reposted by Charlotte Soneson
Silvia Barbiero @silviabarbiero.bsky.social · 15/08/2025
We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊 📄 joss.theoj.org/papers/10.2110… (1/3)
joss.theoj.org
ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets
Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882
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Reposted by Charlotte Soneson
Marc Bühler @marcbuhler.bsky.social · 06/07/2025
preprint alert: www.biorxiv.org/content/10.1...
biorxiv.org
Remodeling Activity of ChAHP Restricts Transcription Factor Access to Chromatin
Transcription in eukaryotes is regulated by chromatin-based mechanisms that control nucleosome occupancy, chromatin modifications, and transcription factor binding. We have previously shown that the transcription factor ADNP forms the ChAHP complex with the chromatin remodeler CHD4 and HP1 proteins, acting as a site-specific regulator of transcription and antagonist of CTCF binding. However, the molecular basis of these functions remained unclear. Here, we demonstrate that the CHD4 subunit is essential to antagonize CTCF and silence transcription of transposons, while HP1 proteins are dispensable. Although the remodeling activity of CHD4 is not required for ChAHP chromatin association, it is critical for both transposon repression and CTCF antagonism. Our findings support a model wherein ADNP recruits chromatin remodeling activity in a sequence-specific manner, enabling transcriptional control and local modulation of chromatin architecture. ### Competing Interest Statement The Friedrich Miescher Institute for Biomedical Research (FMI) receives significant financial contributions from the Novartis Research Foundation. Published research reagents from the FMI are shared with the academic community under a Material Transfer Agreement (MTA) having terms and conditions corresponding to those of the UBMTA (Uniform Biological Material Transfer Agreement). Novartis Research Foundation, n.a. Swiss National Science Foundation, grant 310030_188835
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Reposted by Charlotte Soneson
Bioconductor @bioconductor.bsky.social · 20/06/2025
📣 Late-breaking poster call for #EuroBioC2025 is now open! Submit by July 11 to present your work in Barcelona this September. 🔗 forms.gle/ewTGdKzB2xyE... 📅 Notifications by July 15 #Bioconductor #Bioinformatics
forms.gle
EuroBioC2025 late-breaking poster abstract submission
Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…
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Reposted by Charlotte Soneson
Michael Stadler @mbstadler.bsky.social · 18/05/2025
If you look for an easy way to plot OME-zarr images in your scripts, I hope the ez-zarr python package will be useful:
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Reposted by Charlotte Soneson
Bioconductor @bioconductor.bsky.social · 24/04/2025
🎓 New Publication! Our 1st paper on Bioconductor training from the Bioconductor Training Committee is now published in PLOS Comp Biol. We're pleased to share our work with the community. Read here: journals.plos.org/ploscompbiol... Thank you to everyone involved for your contributions!
journals.plos.org
Learning and teaching biological data science in the Bioconductor community
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and…
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Reposted by Charlotte Soneson
Robert Castelo @robertclab.bsky.social · 22/04/2025
Participate in the Bioconductor community by sharing your work in a meeting designed to maximize interactivity and productivity at the seafront of Barcelona! 👩‍💻🏖️🧬 #EuroBiocC2025
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Reposted by Charlotte Soneson
Bioconductor @bioconductor.bsky.social · 16/04/2025
Bioconductor 3.21 is released! A huge thank you to all developers and community members for your contributions. Explore what’s new in the full release announcement: bioconductor.org/news/bioc_3_... #Bioconductor #RStats
bioconductor.org
Bioconductor - Bioconductor 3.21 Released
The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and…
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Reposted by Charlotte Soneson
BF Francis Ouellette @bffo.bsky.social · 20/03/2025
From @csoneson.bsky.social , @mramos148.bsky.social, @jorainer.bsky.social & colleagues in @plos.org #Computational #Biology | Eleven quick tips for writing a #Bioconductor package | #Bioinformatics #Education #Rstats #PLOSCBQT 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...
journals.plos.org
Eleven quick tips for writing a Bioconductor package
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Reposted by Charlotte Soneson
Hans-Rudolf Hotz @hrhotz.bsky.social · 20/03/2025
Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social journals.plos.org/ploscompbiol...
journals.plos.org
Eleven quick tips for writing a Bioconductor package
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Reposted by Charlotte Soneson
PomBase: The S. pombe knowledgebase @pombase.bsky.social · 26/02/2025
This work is not only an amazing resource for the community, it is also a total masterclass in code reusability, data FAIRness and reproducibility. Hopefully, this is the future!
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Reposted by Charlotte Soneson
Merle Skribbe @merleskribbe.bsky.social · 26/02/2025
www.sciencedirect.com/science/arti... I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬 Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌
sciencedirect.com
A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin
Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyce…
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Reposted by Charlotte Soneson
Davide Risso @davi1893.bsky.social · 27/01/2025
Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!
CSAMA 2025 flyer
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Reposted by Charlotte Soneson
FMI science @fmiscience.bsky.social · 16/12/2024
📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...
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Reposted by Charlotte Soneson
Stefano Mangiola @stemang.bsky.social · 17/06/2024
#tidyomics made it to #NatureMethods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽 Will, Timothy, and Team! 32 researchers | 26 institutes | 10 countries | 4 continents A #crowd/#community-research success nature.com/articles/s41... #CZI, Thanks @mikelove.bsky.social !
nature.com
The tidyomics ecosystem: enhancing omic data analyses - Nature Methods
tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.
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Reposted by Charlotte Soneson
🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 13/04/2024
New: "A user perspective on using #iSEE interactive websites" for @LIBDrstats 📽️ youtu.be/i5I_mFOsGks 📓 docs.google.com/document/d/1... #rstats #Bioconductor #RNAseq #datavis @federicomarini.bsky.social @csoneson.bsky.social
youtu.be
[2024-04-12] A user perspective on using iSEE interactive websites
For more information on Leonardo Collado-Torres, check https://twitter.com/lcolladotor.For more information about the materials discussed in this video, chec...
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