I am grateful to @syopasaatio.bsky.social for awarding ma a dissertation grant 🌸 Huge congrats also to @anna-vaharautio.bsky.social!!!

Such a great panel discussion from the leading minds of the innovative cancer care today at #Slush in Helsinki 🧫🔬

🎉 Huge congrats to Oskari on the acceptance of his final PhD paper! He built Histolytics - a Python package for spatial analysis of whole-slide images 🌠🔬 Try it: github.com/HautaniemiLa...

Are you using any of our factor models, such as MOFA? 🛵 You might’ve found it challenging to tailor them to your specific use cases - not anymore! Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n

🥁 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. 🧶⬇️

Online now: Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer

🎉 After almost 3y in making, my first first-author PhD paper is out in Cell Reports Medicine! 🔗 Link: www.cell.com/cell-reports... 🧵 1/3

Our Systema framework for evaluating genetic perturbation response prediction methods is now out in @natbiotech.nature.com ✨ Systema helps to evaluate perturbation response prediction methods by focusing on perturbation-specific effects rather than systematic variation 🎯

🎉This is the energy every PhD paper celebration should have. Just saying 🥂😁 @gik70.bsky.social

Comparative proteomic analysis of the ECM composition of the human omentum and mesentery, the main sites of ovarian cancer metastasis https://www.biorxiv.org/content/10.1101/2025.07.28.667199v1

🎉 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 👇

Tumor Cells Enriched for Interferon and Inflammatory Programs Pre-Exist in High Grade Serous Ovarian Cancer and are Proportionately Significantly Increased Post Chemotherapy https://www.biorxiv.org/content/10.1101/2025.06.24.661404v1

📢ONLINE @naturegenet.bsky.social 📰Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring. By Wenbao Yu, Kai Tan and colleagues. ⬇️ www.nature.com/articles/s41...

📢ONLINE @natgenet.nature.com 📰Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. By Avishay Spitzer, Mario L. Suvà and colleagues. ⬇️ www.nature.com/articles/s41...

📢OUT TODAY @natgenet.nature.com 📰Predicting resistance to chemotherapy using chromosomal instability signatures. By @jsneaththompson.bsky.social, @gmaci.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...

Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment. https://www.biorxiv.org/content/10.1101/2025.06.20.659124v1

Online now: Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma

Early birds today the “Meet the expert” interactive session at the #EACR2025 in Lisbon, discussing KRAS modulators.

Glad to have presented our work on the longitudinal dynamics of transcriptome and chromatin accessibility in HGSC at the #EACR2025 in Lisbon 🇵🇹

Glad to share that the Ida Montinin Fund has awarded me a personal grant to support my doctoral studies at the @helsinki.fi 🤍 Learn about Ida Montini’s legacy (in Finnish): idamontininsaatio.fi Thanks to my supervisor, Sampsa Hautaniemi, and colleagues for their support! 🙌

Online now: Spatial and genomic profiling of residual breast cancer after neoadjuvant chemotherapy unveil divergent fates for each breast cancer subtype Online now:

Improving Differential Expression and Survival Analyses with Sample Specific Compartment Deconvolution. https://www.biorxiv.org/content/10.1101/2025.06.04.657908v1

Optimising Chemotherapy for Locally Advanced High-Grade Serous Ovarian Cancer via Delay-Differential Equations https://www.biorxiv.org/content/10.1101/2025.06.05.658173v1

EpiTrace infers cell mitotic age and evolution from single-cell ATAC-seq data go.nature.com/3QHBfc3 rdcu.be/em31W

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

🔥New Night Science paper!! Discovery happens when your initial plans fall apart but it requires you to have a particular mindset: it's not extraverted, orderly, neurotic or agreeable that's the most important – discovery requires an OPENNESS to new ideas and unexpected insights.

CRISPRai simultaneously activates and represses two genes in single cells go.nature.com/4apFU9q rdcu.be/efe0E

Thrilled to share that our work is now published in Bioinformatics! Tribus helps discover cell identities in multiplexed imaging data. doi.org/10.1093/bioi... Huge thanks to my amazing supervisor @afarkkila.bsky.social and our team @farkkilab.bsky.social — we will keep explore spatial biology 🧬✨

📣 Today marks the official launch of the DYNAMITE project, funded by EP PerMed with Biswa Sahu hosting the event! 💡 DYNAMITE aims to uncover the molecular mechanisms explaining why ovarian cancer cells become resistant to chemotherapy. 👀 We look forward to report on the project progress!

Online now: The IFN-high phenotype: A biomarker-driven breakthrough in colorectal cancer treatment

The Protein Design Archive (PDA): insights from 40 years of protein design go.nature.com/4iNRFLI

Online now! Li et al. show through single-cell and functional data that TME remodeling promotes peritoneal metastasis of colorectal cancer through microbiome dysbiosis, neutrophil recruitment and mesenchymal transition of mesothelial cells. ⬇️ www.nature.com/articles/s43...

Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data go.nature.com/43YySqO rdcu.be/ebBio

📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄 We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks. doi.org/10.1101/2024... 👇

Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer

🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub! - sc.pp.sample replaces subsample with many new features - Sparse Dask support pca - session-info2 package for more reproducible notebooks See the release notes:

Jellyfish visualization tool and the Jellyfisher R package have now been published in OUP Bioinformatics! 🎉 doi.org/10.1093/bioi... #Bioinformatics #DataViz (1/7)

The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community. academic.oup.com/bioinformati... In parallel, we’ll continue expanding benchmarks and developing new applications. Interested in contributing? Reach out! ⬇️

We just released simpleaf v0.19.0 (github.com/COMBINE-lab/...). Make sure to pair it with piscem v0.12 for faster scATAC-seq processing. The other big feature & first explicit @scverse.bsky.social integration point is AnnData format output with the new `--anndata-out` flag!

Today is International Day of Women & Girls in Science. Marie Curie, the first woman to win a Nobel Prize. Her contributions have left an indelible mark on the world of science & health & continue to inspire generations of scientists & innovators. 🔬 #WomenInScience #WomenInSTEM

On Tuesday at 2025-02-04 18:00 CET, @jkobject will talk about scPrint, a transformer model that infers gene networks from scRNA-seq data, at our 2nd community meeting of 2025! For more information, check out the GitHub: https://buff.ly/40RJ3gT & pre-print https://buff.ly/4hwK4Av

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta