Ricardo O. Ramirez Flores

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...

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.

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...

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...

Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.

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...

Fast & Fair peer review A new initiative offering high-quality peer review within 7 working days of submission Biology Open

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... 👇

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...

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)

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...

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

Learning resources for scientists · eLife A collections of articles that provide practical resources and guidance for researchers and academics

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!!

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life - Nature Communications Clonal hematopoiesis becomes increasingly common with age. Here the authors track stem cell dynamics in monozygotic twins and provide evidence that clonal hematopoiesis in later life reflects weak sel...

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

Grumpy cat with the caption, “you must like dummy variables since they were named after you”

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

And to be fair, I still don’t have the guts to reply to editors in that way 🙈

But for sure, I wish that at least privileged institutions gave it a chance to open reviewing processes in pre-print servers

I agree, those computational papers are the ones that surprise me the most whenever they aren’t public by submission. 😅😅

I never thought of this, but it is a good point. It is hard to compete already in those circumstances, and this doesn’t get easier with a community not embracing reviewed pre-prints as something meaningful, will keep this in mind. Thanks :)