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...

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...

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

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 🎯

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...

🎉 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

🚨 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... 👇

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...

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)

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...

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! ⬇️

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

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/

Academics from poorer socio-economic backgrounds are more likely to - not publish - have outstanding publication records - introduce more novel scientific concepts - less likely to receive recognition, as measured by citations, Nobel Prize nominations, and awards. www.nber.org/papers/w33289

Check @paubadiam.bsky.social 's herculean work where he proposes the modularization of GRN reconstruction methods to evaluate their stability, similarity and performance in distinct tasks. Surprising results about the lack of agreement between methods and poor causal sufficiency. Congrats Pau!!

Just in time for thanksgiving our paper is out ☄️ using fluctuating methylation clocks as barcodes we show that the variation in the hematopoietic stem cell pool that (in most of us) leads to clonal hematopoiesis in later life is likely present *before birth* 👉🏼 www.nature.com/articles/s41...

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

Excellent history of evolutionary anthropology as it relates to human behavior and culture. The take home point is that both human behavioral ecology and evolutionary psychology need to account for culture per se more effectively and intergratively. Open access at www.pnas.org/doi/epub/10....

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you) Also juliosaezrod.bsky.social has recently joined Bluesky go.bsky.app/5ZtPHPz

I have an Easter egg in my syllabus where anyone who sends me a stats meme gets an extra point. In all the years I’ve done it, this one is my fave…. #rstats #rladies

Can you believe this whole site runs on a mac mini m4

Restarting a previous discussion on here: How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅 I see them used everywhere, but I don't know of any really good way to validate them... More importantly, I don't know of any *non-simulated* training data.

Racial justice is a science story. www.scientificamerican.com/article/from... Environmental justice is a science story. www.scientificamerican.com/article/the-... Reproductive justice is a science story. www.scientificamerican.com/article/abor... (8/n)

Am I wrong by rejecting to review manuscripts that haven't been submitted to pre-print repositories? I feel this is the only way to support newer publication systems.

POV: you try to run any multimodal GRN inference method 🫠

As the philosopher Celine Dion once said: My heart will go on🫀🔬 We've expanded our multi-study heart failure reference and proposed new multicellular analyses to get the best from scell and bulk data, all of this while learning how cells cooperate and divide labor in tissues! t.co/aRDqdQxC5j

Welcome to our Bluesky account. With so many of our community members now present on Bluesky, we felt it was the right time to join. We will use this account to bring you news from the Company, our journals and our community sites.

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...

As the philosopher Celine Dion once said: My heart will go on🫀🔬 We've expanded our multi-study heart failure reference and proposed new multicellular analyses to get the best from scell and bulk data, all of this while learning how cells cooperate and divide labor in tissues! t.co/aRDqdQxC5j

Hi everyone! Here's a starter pack of genomics scientists trained in Mexico 🇲🇽 including from #LCG-UNAM #LCG-EJ-UNAM undergrads, #RMB / #NNB-UNAM / @cdsbmexico.bsky.social workshops, and more It's in an early stage and I'm trying to get more to join us here at #AcademicSky go.bsky.app/5bWBN5V

Explore disease at a multicellular level, capturing variations in patient samples across cell types, tissue features, studies, and technologies with Multicellular Factor Analysis, peer-reviewed by Review Commons and now published @elife.bsky.social elifesciences.org/articles/93161

The past, present and future of science publishing. New article from me on a history not always told correctly, the reality of the journal world, and choices for the future doi.org/10.1371/jour...

“…and who started in a non-tenure track position only to get demoted from there. Let’s give her a few million dollars in unrestricted funding over the next 10 years.”” www.statnews.com/2022/02/01/k... H/T Lucy O’Brien

The strain on scientific publishing 📄: We've got issues. Scientists overwhelmed, editors overworked, constant special issue invites, mass article retractions, journal delistings… JUST WHAT IS GOING ON!? See: arxiv.org/abs/2309.15884 A 🧵1/n #AcademicChatter #PublishOrPerish #PhDAdvice #PhDChat

Sorry, but this is hogwash. The reason nobody talks about Science being a non-profit is that it has for decades behaved in a way that is indistinguishable from its for-profit brethren. If they want to be known as a non-profit, they should act like one. www.science.org/doi/10.1126/...

#HiSciSky I am also joining the exodus from that other platform. I'm a 🇲🇽 computational biologist in saezlab.org interested in studying multicellularity by integrating bulk, spatial and single-cell omics data. 😄 First-gen and #QueerInSTEM 😊 Short-form writing, and more here: roramirezf.github.io