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#bioinformatics

11 posts10 participants2 posts today
Public
Bose-Einstein-Kondensat

A few images from yesterdays first #HoloDeck presentation at Prof. Varshneys #lab at the #Indian Institute of #Science (#IISc) in #Bangalore (#India), where people enjoyed 'playing molecules'.

Holodeck, also known as the Rechenkraft.net #Molecular #AR Environment is our #OpenSource approach - based on the @tiltfive hardware - to visualize molecular #structures in #3D for #education & #research & #development purposes.

#DIYbio#instruments#bioinformatics
Public
Nicola Romanò

Our new preprint is now out!

Dynamic transcriptional heterogeneity in pituitary corticotrophs

biorxiv.org/content/10.1101/20

We analysed publicly available single-cell RNA sequencing data of pituitary gland tissue and looked at corticotrophs, cells that are central to mediate stress responses.

We identified several transcriptional states in these cells that are related to how they respond to stress. Cells are able to transition between these states and this might be helpful for them to respond to stress coming at unpredictable times.

We also highlight issues related to using scRNAseq to look at functional subpopulations of cells.

bioRxiv · Dynamic transcriptional heterogeneity in pituitary corticotrophsA large body of evidence has shown that corticotrophs, the anterior pituitary cells central to the generation of hormonal stress responses, exhibit heterogeneous functional behavior, suggesting the presence of functional sub-populations of corticotrophs. We investigated whether this was the case at the transcriptomic level by conducting a comprehensive analysis of scRNA-seq datasets from rodent pituitary cells. We envisaged two alternative scenarios, one where robust subtypes of corticotrophs exist, and the other where these subpopulations were only transient states, possibly transitioning into one another. Our findings suggest that corticotrophs transition between multiple transcriptional states rather than existing as rigidly defined subpopulations. We employed marker gene-based comparisons and whole transcriptome label transfer approaches to analyze transcriptional signatures across datasets. Marker-based clustering revealed strikingly low similarity in the identified subpopulations across datasets. This analysis evidenced the presence of transcriptional states with different functional relevance, related to different stages of hormonal signalling. Similarly, the label transfer approach, which considers non-linear interactions across the entire transcriptome showed that transcriptional states could be detected across independent datasets. This classification relied on broader gene expression patterns rather than conventional marker genes, reinforcing the notion of continuous rather than discrete cell states. Furthermore, trajectory analysis by RNA velocity indicated dynamic transitions between transcriptional states, suggesting the presence of transcriptional mechanisms facilitating rapid recruitment of corticotrophs in response to physiological demands. Our findings align with evidence from other endocrine cell types, such as lactotrophs and pancreatic β-cells, where hormone secretion is linked to fluctuating transcriptional activity. The observed transitions in corticotroph states suggest a mechanism allowing flexible hormonal responses to unpredictable and time-varying stressful events. Additionally, this study highlights the challenges associated with scRNA-seq methodologies, including data sparsity, batch effects, and pseudoreplication, underscoring the need for rigorous experimental design and reproducibility in single-cell transcriptomics research. These insights contribute to a broader understanding of pituitary cell plasticity and endocrine adaptation mechanisms. ### Competing Interest Statement The authors have declared no competing interest.
#scrnaseq#stress#physiology
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Luke Pembleton

Cloud computing: where you're not just a bioinformatician, you’re also the finance manager, compliance officer, and IT support, all while carrying a hefty dose of mental fatigue. I miss those PhD days with a inhouse HPC when all you had to do was sbatch every parameter combo under the sun to test your research question… then complain about queue times and who was clogging the damn cluster with their BLAST jobs 😅
#bioinformatics

Public
SIB Swiss Bioinformatics

@bgeedb was used to design stem-cell based vaccines 💉against #cancer in mouse models, opening a door to a potential application with humans.

🔎 This is an example of the impact that #bioinformatics databases and tools developed by SIB groups have. Researchers use them to make sense of their data and tackle essential societal challenges.

👉 Learn more: sib.swiss/services/open-softwa

@marcrr @fbastian

#SIBResourceImpacts#OpenSoftwareAndDatabases
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Benjamin Carr, Ph.D. 👨🏻‍💻🧬

#Genetic data repo #OpenSNP to self-destruct before authoritarians weaponize it
The reason, according to #bioinformatics researcher Bastian Greshake Tzovaras, one of the founders of the project, is the dissolution of genetic testing biz #23andMe and the potential weaponization of genetic data by #farright #authoritarian regimes.
theregister.com/2025/04/01/ope

The Register · Genetic data repo OpenSNP to self-destruct before authoritarians weaponize itBy Thomas Claburn
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Bioconductor

🎉 Announcing the EuroBioC2025 Sticker Design Winner! 🎉

🏆 Winner: Chaima Hkimi

🎨 Chaima’s design draws on some of Barcelona’s most iconic landmarks, featuring the Sagrada Família and the vibrant colours of Park Güell. She even swapped the 'i' in 'BioC' for the Bioconductor logo — a creative nod to the project!

Thanks to everyone who submitted a design. You’ll be able to pick up Chaima’s sticker at EuroBioC2025!

EuroBioC2025 hex sticker design featuring the Sagrada Família in the centre, vibrant mosaic patterns inspired by Park Güell at the bottom, and other Barcelona landmarks like the crane and towers. The Bioconductor logo replaces the "i" in "BioC", and "bioconductor.org" is written across the top left. The overall shape is a yellow-bordered hexagon.
#EuroBioC2025#Bioconductor#Bioinformatics
Public
Headlines Africa

Africa: Continued Partnership to Enhance Pathogen Genomic Surveillance and Bioinformatics for Public Health in Africa: [Africa CDC] In a strategic move to bolster Africa's preparedness for future pandemics, the Africa Centres for Disease Control and Prevention (Africa CDC), in partnership with the African Society for Laboratory Medicine (ASLM) and with support from the Mastercard… newsfeed.facilit8.network/TJs8 #PublicHealth #GenomicSurveillance #AfricaCDC #Bioinformatics #PandemicPreparedness

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