CENTRA Centrality-Based Exploration of Network Topologies from Regulatory Assemblies

👉 ngs-info.medizin.uni-halle.de/shiny/CENTRA/

🧪🧬🖥️ #AcademicSky #MedSky #CENTRA #MolecularBiology #Bioinformatics #NetworkBiology #SystemsBiology #GraphTheory #Centrality #FractalNetworks

CENTRA Centrality-Based Exploration of Network Topologies from Regulatory Assemblies

We’d love to hear your thoughts. Tried CENTRA yet? Feedback, bugs, ideas, or a module that completely surprised you? Tell us, we’re already shaping the next updates.

💬 DMs are open, or visit ngs-info.medizin.uni-halle.de/shiny/CENTRA/ for more contact options.

CENTRA Centrality-Based Exploration of Network Topologies from Regulatory Assemblies

👉 ngs-info.medizin.uni-halle.de/shiny/CENTRA/

🧪🧬🖥️ #AcademicSky #MedSky #CENTRA #MolecularBiology #Bioinformatics #NetworkBiology #SystemsBiology #GraphTheory #Centrality #FractalNetworks

Thinking about using CENTRA for functional exploration?

The browser comes with built-in functions to:
📚 parse gene metrics
🔍 generate ready-to-publish graphs
🧠 explore module functions across all networks

Everything is fully accessible without any account or login.

🔀 CENTRA assesses the variance of betweenness to see how stable a gene’s bridging role really is.

📉 By randomly rewiring our networks we control for underrepresented genes in the dataset.

🛡️ What remains are genuine, robust information brokers or hidden functional master regulators.

CENTRA Centrality-Based Exploration of Network Topologies from Regulatory Assemblies

👉 ngs-info.medizin.uni-halle.de/shiny/CENTRA/

🧪🧬🖥️ #AcademicSky #MedSky #CENTRA #MolecularBiology #Bioinformatics #NetworkBiology #SystemsBiology #GraphTheory #Centrality #FractalNetworks

🧠 CENTRA uses Latent Dirichlet Allocation (LDA) to cluster gene sets by their semantic content.

🗂️ Each cluster becomes a distinct biological topic.

🕸️ This transforms unstructured text into functional gene networks.

Each gene in CENTRA comes with its own radar plot visualizing key topological properties:
📡 Centrality
🌿 Local fractality
🛡️ Robustness

Perfect for comparing genes across different biomedical topics.

CENTRA’s topics span a wide biological landscape, including:
🧠 Neurodevelopment
🔬 DNA damage response
🦠 Immune regulation
💥 Apoptosis
🧫 Cancer metabolism

…besides many others. Each topic forms its own network with distinct functional hubs.

🧩 CENTRA identifies modules using Louvain clustering.

🔍 Each module is tested for functional coherence via Overrepresentation Analysis.

📊 The resulting modules often align with coordinated biological processes and pathways.

🌿 Some genes reveal structure not by connections alone, but by how complex their local neighborhood is.

CENTRA uses Local Fractal Dimension to capture this, a measure of how dense the surroundings of a gene become in the network.

✨ High LFD can hint at elevated information density.

⭐ Some genes stand out because of who they’re connected to.

CENTRA uses eigenvector centrality to identify these influence hubs, genes linked to other highly connected players across the network.

✨ High eigenvector values can hint at strong regulatory relevance.

🔀 Some genes quietly sit at the crossroads of biological information flow.

CENTRA uses betweenness centrality to find these hidden mediators, genes that bridge modules and shape how information moves through a network.

✨ High betweenness can hint at regulatory leverage.

How do we define a key gene in a network?

CENTRA uses multiple centrality measures:
🔹 Betweenness
🔹 Eigenvector
🔹 Local Fractal Dimension

These combine to reveal functional importance across contexts.

CENTRA is available as interactive browser app:

🧭 Explore topic-specific networks
🔍 Search genes or terms
🌐 Visualize modules, metrics, enrichments

🚨 Our CENTRA paper is out in NAR Genomics and Bioinformatics!
CENTRA shows how centrality and fractal geometry uncover functional master regulators across biological networks. You can explore everything instantly, completely open access.

doi.org/10.1093/narg...

The idea is to decouple the journals from the review step. They’ll still exist, but they’ll need to add other value. They’ll highlight, curate, add new perspectives. If they do a good job they can still be prestigious (like Scientific American or Wired) (1.2) 👇

IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Weinflasche kröver Nacktarsch

Auch hier ist nicht drin was drauf steht. Verbieten!

🚨 Two manuscripts accepted at Nature Communications within one week!🎉 Both papers deal with GPCRs. Thank you, Anette Kaiser and Tobi Langenhan, the wonderful collaborations! 😀 More details will follow. @unihalle.bsky.social @unileipzig.bsky.social

🧪 And this is the second Nature Communications @natcomms.nature.com paper where we contributed:
www.nature.com/articles/s41...
@academic-chatter.bsky.social @academicsky.org #teammassspec
@unileipzig.bsky.social @unihalle.bsky.social

Friday Papers Club! 🍿In light of Pubmed going down, the collapse of social media, and my recent success at getting recommendations for interesting papers from those still around, I am starting a new tradition! - Recommend a good scientific manuscript! 👇

Can't stop loving this one: "Dilution of expertise in the rise and fall of collective innovation" by Duran-Nebreda et al.

www.nature.com/articles/s41...

Foggy morning view of a cable-stayed bridge with a tall central pylon and multiple suspension cables, silhouetted against the rising sun shining through the mist, with tram lines and street lamps in the foreground.

The gentle rays of morning hint at summer’s end.

Mit saisonaler Regelmäßigkeit tauchen dort verloren geglaubte Fahrradhandschuhe auf 😅

Is the Sagrada Família a Masterpiece or Kitsch? In the century since Antoni Gaudí died, his wild design has been obsessively realized, creating the world’s tallest church—and an endlessly debated icon.

D. T. Max writes about the slow becoming of one of the world’s most unusual—and soon to be tallest—churches: the Sagrada Família.

Our manuscript "Conserved hydrophilic checkpoints tune FocA-mediated formate:H+ symport" has just been accepted at Nature Communications!🎉🎉 I feel truly honored to be part of this work that was headed by Panos Kastritis and Gary Sawers.More information to follow! @unihalle.bsky.social
#Academicsky

Thank you Prof. Mirta Galesic (University of Vienna and Santa Fe Institute) for the inspiring talk “Collective moderation of public discourse” at CCS 2025!