Bárbara Zita Peters Couto

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳

📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org

OmniPath integrates 160+ resources for multi-omics analysis & modeling.

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17.09.2025 13:09 — 👍 35    🔁 20    💬 1    📌 0

👀 we are involved in projects 1 & 6 on the list:

1️⃣ Multicellular molecular characterisation of inflammatory bowel disease
6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents

📅 Application deadline is 30th September ❗

14.08.2025 09:05 — 👍 3    🔁 5    💬 0    📌 0

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇

22.07.2025 15:23 — 👍 61    🔁 29    💬 1    📌 1

🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org

This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/

12.06.2025 06:36 — 👍 35    🔁 7    💬 0    📌 2

What is the current bottleneck in mapping molecular interaction networks? Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

In this Voices article, our @martingarridorc.bsky.social & @juliosaezrod.bsky.social discuss key strategies for building context-specific molecular networks: knowledge and data-driven methods, + future directions in the field bridging to structures and perturbations tinyurl.com/z8t6yych

30.05.2025 06:27 — 👍 3    🔁 4    💬 0    📌 0

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4

23.05.2025 07:37 — 👍 47    🔁 20    💬 1    📌 2

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

09.05.2025 10:49 — 👍 321    🔁 103    💬 9    📌 13

The nitroplast: A nitrogen-fixing organelle A bacterial endosymbiont of marine algae evolved to an organelle

Move over mitochondria, a new organelle called the nitroplast is here.

In a Science study last year, researchers reported that a nitrogen-fixing organelle has been identified in a marine alga.

Learn more in this #SciencePerspective: scim.ag/49GjClc #ScienceMagArchives

29.04.2025 17:48 — 👍 151    🔁 32    💬 2    📌 2

MCML Blog: 🚨 Hate speech spreads fast — and it’s not just about detecting hate or profiling its authors. Who reshares it?

Dominique Geissler, Abdurahman Maarouf & PI Stefan Feuerriegel analyzed the profiles of hate speech spreaders on social media. 🔍

📄 Read more: mcml.ai/news/2025-04...

30.04.2025 08:49 — 👍 2    🔁 1    💬 0    📌 0

Members of saezlab enjoying the good weather in Ascona.

Wrapping up in beautiful Ascona ☀️ for the Modern Benchmark Conference sites.google.com/view/ascona2.... Great to see the community discussing a field that’s essential yet often overlooked and challenging @smuellerdott.bsky.social @barbarazpc.bsky.social @ivanovaos.bsky.social @paubadiam.bsky.social

27.03.2025 09:11 — 👍 18    🔁 2    💬 0    📌 1

🇺🇦💙🇬🇧 Standing with Ukraine—enhancing OSINT for a safer future!

Since day one, OSINT Industries has supported Ukrainian law enforcement with free access. Recently, EUAM Ukraine led a 4-day OSINT training at ХНУВС in Vinnytsia, equipping officers with advanced skills.

Proud to support this mission!

25.02.2025 06:28 — 👍 5    🔁 3    💬 0    📌 2

Vevo Therapeutics Open Sources Tahoe-100M, the World's Largest Single-Cell Dataset, as the Inaugural Contribution to Arc Institute's New Virtual Cell Atlas /PRNewswire/ -- In a landmark move to advance AI-driven biological research, Arc Institute and Vevo Therapeutics announced today that they have partnered on...

Vevo therapeutics released their 100M perturbed single cell atlas!

- git repo: github.com/ArcInstitute...

- press release: www.prnewswire.com/news-release...

26.02.2025 09:04 — 👍 4    🔁 0    💬 0    📌 0