🧵 ParTIpy, our Python package for Pareto Task Inference just got published in Molecular Systems Biology (Peer reviewed at Review Commons) 🔗 Manuscript: link.springer.com/article/10.1... 💻 Code: github.com/saezlab/part... 📚 Docs: partipy.readthedocs.io/en/latest/

1/🧵 New preprint! We built a patient-level map of systemic lupus erythematosus using single-cell blood transcriptomics, linking multicellular immune coordination to patient heterogeneity, future disease activity, and potential tissue pathology. ➡ doi.org/10.64898/202...

🧵 What does single-cell transcriptomics reveal about individual patients with acute (AKI) and chronic (CKD) kidney 🫘 disease? Can we use it to find new biomarkers? In our new preprint 👇, we asked this using biopsies from 150+ participants from the Kidney Precision Medicine Project.

🧵 See 👇 our new preprint on shared and organ-specific gene expression programs of fibrotic diseases 🧬 📄 Paper: doi.org/10.64898/202... 📊 Explore the data: organfibrosis.saezlab.org

On March 4th, our @ricoramirez.bsky.social will share how we can currently study tissue remodelling with spatial transcriptomics data at a webinar from @training.ebi.embl.org. This webinar series includes a great lineup of speakers. For free registration see link below ⬇️

EMBL-EBI Training@training.ebi.embl.org · 7mo ago

We're pleased to announce that our next webinar series is now live. Decoding spatial transcriptomics through sequences, pixels, and bioinformatics will run from 18 February – 8 April 2026: www.ebi.ac.uk/training/eve... Coordinated by: @ajaymishra24.bsky.social, Kristy Ou, and Flaminia Zane. 🧬🖥️📊

In writing, there's two things you can do with words, select them and arrange them. In scientific writing, words should be: Precise Simple Necessary Note that "necessary" is third on the list: one should try to be succinct and avoid extra words, but if you need more words to be precise, so be it!

Great to see our patient map of heart failure across patient cohorts, scales, and techs out. Hope that our work shows how we can transform molecular data into interpretable tissue features that describe remodeling and associate with clinical outcomes. www.nature.com/articles/s41...

A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling - Nature Communications

Cardiac tissue remodeling in heart failure is driven by interactions between multiple cell types, but existing studies have not fully captured these coordinated responses. Here, the authors show that ...

nature.com

Our revised consensus transcriptional patient map of human heart failure across patient cohorts and single-cell and bulk technologies is now published @natcomms.nature.com www.nature.com/articles/s41...

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map doi.org/10.1101/2024...

How dit life originate in our planet? How can we create it in the lab?Our @royalsocietypublishing.org Theme Issue "Origins of Life: the possible and the actual", coedited with @sfiscience.bsky.social C Kempes and Susan Stepney is out! royalsocietypublishing.org/toc/rstb/202... @manlius.bsky.social

Philosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1936

royalsocietypublishing.org

Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics. 🔗 Manuscript: www.biorxiv.org/content/10.1... 💻 Code: partipy.readthedocs.io

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 🎯

Nature Biotechnology@natbiotech.nature.com · 12mo ago

Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation - @mariabrbic.bsky.social @mornitzan.bsky.social go.nature.com/4791kda

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social www.nature.com/articles/s41...

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods

The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

nature.com

🎉 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 👇

From student to researcher, a #career in #science can come with a high price tag. @drcraigmc.bsky.social ‬explores how wealth shapes opportunity in #STEM and proposes structural changes to support #equity and inclusion. 🧪 plos.io/4edGlY4

I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/

Read preprints. Cite preprints. Email people and tell them you loved their preprint. Email people you hated their preprint. Embrace preprints, preprints are good.

The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level

Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications

Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...

nature.com

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

1/ Ever wondered how to best quantify cell-cell neighbor preferences in tissues? We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨ Read more: doi.org/10.1101/2025...

We are excited to be launching the next phase of our Fast & Fair peer review initiative: offering high-quality peer review within 7 working days. #fastandfairpeerreview Read the Editorial by EiC Daniel Gorelick @danielgorelick.bsky.social at: bit.ly/4kYD1mL

📄 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... 👇

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

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

6 days left to apply to the Post-doc opening in our lab @ebi.embl.org to develop&apply #bioinformatics & #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data: embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Postdoctoral fellow - Saez-Rodriguez Group

Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...

embl.wd103.myworkdayjobs.com

Congrats to @shovalmiyara.bsky.social,Miri Adler, @eldadtzahor.bsky.social & @urialonlab.bsky.social on this great work! We're glad to have supported the translation of findings from theoretical and animal models to human myocardial infarction data using LIANA+ (liana-py.readthedocs.io)

Shoval Miyara@shovalmiyara.bsky.social · last yr.

It’s finally here! My PhD work, five years in the making, is now published @CellSystems @cellpress.bsky.social 🚨 Cold and hot fibrosis define clinically distinct cardiac pathologies. www.cell.com/cell-systems...

It’s finally here! My PhD work, five years in the making, is now published @CellSystems @cellpress.bsky.social 🚨 Cold and hot fibrosis define clinically distinct cardiac pathologies. www.cell.com/cell-systems...

Cold and hot fibrosis define clinically distinct cardiac pathologies

Miyara et al. identify two types of fibrosis in cardiac pathologies: “hot fibrosis,” involving macrophage-myofibroblast interactions in chronic injuries, and acute-injury-driven “cold fibrosis,” contr...

cell.com

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! ⬇️

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

AbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage

academic.oup.com

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵 Paper: doi.org/10.1101/2024... Docs: networkcommons.readthedocs.io

JOB OPPORTUNITY: Join us as a scientific programmer to advance tools for multi-omics data at Heidelberg University. Details can be found at shorturl.at/OcnOa and please spread the word!

BioChatter, a new open-source platform for large language of life models, "to bridge the gap between complex custom solutions and close-source commercial platforms" www.nature.com/articles/s41... @slobentanzer.bsky.social @juliosaezrod.bsky.social

1/ 🧵 Free resources for scientists 💡 Covering research skills, careers, #SciComm, leadership, activism and more, everything in this thread appears on our Learning Resources page, with tips for researchers and academics at any career stage. #AcademicChatter #ECRChat https://buff.ly/4f8vIpk

Learning resources for scientists · eLife

A collections of articles that provide practical resources and guidance for researchers and academics

buff.ly

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

biorxiv.org

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.