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Ricardo O. Ramirez Flores

@ricoramirez.bsky.social
583 followers 657 following 17 posts

🇲🇽 Staff Scientist at EMBL-EBI (@ebi.embl.org and @saezlab.bsky.social) studying the molecular biology of multicellular disease processes, cellular cooperation and its parallels to ecology and social systems

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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 09/07/2026
🧵 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/
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Saez-Rodriguez Group @saezlab.bsky.social · 13/05/2026
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 17/03/2026
🧵 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.
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Saez-Rodriguez Group @saezlab.bsky.social · 12/03/2026
🧵 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
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Saez-Rodriguez Group @saezlab.bsky.social · 12/02/2026
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 ⬇️
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Alejandro Montenegro @aemonten.bsky.social · 01/12/2025
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!
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 06/11/2025
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...
nature.com
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 ...
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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 06/11/2025
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...
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Ricard Solé @ricardsole.bsky.social · 02/10/2025
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
royalsocietypublishing.org
Philosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1936
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Saez-Rodriguez Group @saezlab.bsky.social · 15/09/2025
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
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Maria Brbic @mariabrbic.bsky.social · 25/08/2025
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 🎯
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Nature Methods @natmethods.nature.com · 04/08/2025
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...
nature.com
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 22/07/2025
🎉 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 👇
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PLOS Biology @plosbiology.org · 25/06/2025
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
plos.io
Too poor to science: How wealth determines who succeeds in STEM
From student to researcher, a career in science can come with a high price tag. This Perspective explores how persistent financial barriers limit who can succeed in science, revealing how wealth shape...
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Nature Reviews Nephrology @natrevneph.nature.com · 19/06/2025
nature.com
Leveraging data as a patient–scientist: frustrations and opportunities
Nature Reviews Nephrology, Published online: 19 June 2025; doi:10.1038/s41581-025-00968-9The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability have led to frustration, collaboration bodes well for a future in which patients will have access to more personalized information.
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Anshul Kundaje @anshulkundaje.bsky.social · 24/01/2025
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/
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Reposted by Ricardo O. Ramirez Flores
MwahahahahahadScientist @mads100tist.bsky.social · 22/04/2025
Read preprints. Cite preprints. Email people and tell them you loved their preprint. Email people you hated their preprint. Embrace preprints, preprints are good.
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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 07/05/2025
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
nature.com
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...
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Jovan Tanevski @tanevski.bsky.social · 22/04/2025
🚨 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...
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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025
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...
Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.
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Biology Open @biologyopen.bsky.social · 25/03/2025
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
Fast & Fair peer review

A new initiative offering high-quality peer review within 7 working days of submission

Biology Open
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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 14/03/2025
📄 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... 👇
Performance of multimodal GRN inference methods. SCENIC+ and Dictys outperform others.
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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 17/03/2025
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...
embl.wd103.myworkdayjobs.com
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...
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Reposted by Ricardo O. Ramirez Flores
Saez-Rodriguez Group @saezlab.bsky.social · 25/02/2025
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)
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Shoval Miyara @shovalmiyara.bsky.social · 19/02/2025
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...
cell.com
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 20/02/2025
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! ⬇️
academic.oup.com
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
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Britta Velten @brittavelten.bsky.social · 31/01/2025
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!
shorturl.at
Scientific programmer
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
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Reposted by Ricardo O. Ramirez Flores
Eric Topol @erictopol.bsky.social · 22/01/2025
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
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eLife @elife.bsky.social · 26/11/2024
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 buff.ly/4f8vIpk
buff.ly
Learning resources for scientists · eLife
A collections of articles that provide practical resources and guidance for researchers and academics
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Reposted by Ricardo O. Ramirez Flores
Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
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/
biorxiv.org
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...
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Florian Ederer @florianederer.bsky.social · 23/12/2024
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
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 23/12/2024
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!!
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Adam MacLean @adamlmaclean.bsky.social · 28/11/2024
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...
nature.com
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 26/11/2024
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
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Raymond Hames @rayhames.bsky.social · 19/11/2024
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....
pnas.org
Cultural evolution: Where we have been and where we are going (maybe)
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Saez-Rodriguez Group @saezlab.bsky.social · 20/11/2024
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
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Jenine Harris @jenineharris.bsky.social · 19/11/2024
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
Grumpy cat with the caption, “you must like dummy variables since they were named after you”
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P(aul) Frazee @pfrazee.com · 15/11/2024
Can you believe this whole site runs on a mac mini m4
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Will Macnair @willmacnair.bsky.social · 15/11/2024
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.
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Laura Helmuth @laurahelmuth.bsky.social · 14/11/2024
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)
scientificamerican.com
From Civil Rights to Black Lives Matter
Protest expert Aldon Morris explains how social justice movements succeed
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 15/11/2024
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.
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Pau Badia i Mompel @paubadiam.bsky.social · 14/11/2024
POV: you try to run any multimodal GRN inference method 🫠
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 11/11/2024
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
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The Company of Biologists @biologists.bsky.social · 12/11/2024
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.
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Saez-Rodriguez Group @saezlab.bsky.social · 11/11/2024
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...
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 11/11/2024
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
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/11/2024
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
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Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 24/11/2023
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
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Richard Sever @richardsever.bsky.social · 04/10/2023
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...
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Anne Carpenter @drannecarpenter.bsky.social · 03/10/2023
“…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
statnews.com
The Karikó problem: Lessons for funding basic research
"Fund people not projects" is easier said than done. A better way to fund science is to bend over backward to fund a truly diverse range of people and ideas, even including those perceived as unpopula...
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