Charlotte Soneson (@csoneson) — Bluesky Profile

2 weeks ago

💫 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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4 months ago

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…

🚀 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_...

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5 months ago

📣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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6 months ago

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...

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!

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6 months ago

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

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)

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8 months ago

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

preprint alert: www.biorxiv.org/content/10.1...

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8 months ago

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…

📣 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

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9 months ago

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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10 months ago

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…

🎓 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!

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10 months ago

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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10 months ago

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…

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

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11 months ago

Eleven quick tips for writing a Bioconductor package

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...

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11 months ago

Eleven quick tips for writing a Bioconductor package

Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social

journals.plos.org/ploscompbiol...

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1 year ago

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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1 year ago

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…

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! 🙌

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1 year ago

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!

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1 year ago

📣 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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1 year ago

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.

#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 !

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1 year ago

This is great @lcolladotor.bsky.social! Maybe one link to add to the document would be the iSEE-verse website: isee.github.io

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1 year ago

[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...

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

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