Reposted by Ricardo O. Ramirez FloresSaez-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/ 1165
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 13/05/20261/🧵 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... 174
Reposted by Ricardo O. Ramirez FloresSaez-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. 1155
Reposted by Ricardo O. Ramirez FloresSaez-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 22411
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 12/02/2026On 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 ⬇️ 072
Reposted by Ricardo O. Ramirez FloresAlejandro Montenegro @aemonten.bsky.social · 01/12/2025In 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! 1133
Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 06/11/2025Great 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.comA cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling - Nature CommunicationsCardiac 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 ... 060
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 06/11/2025Our 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... 165
Reposted by Ricardo O. Ramirez FloresRicard Solé @ricardsole.bsky.social · 02/10/2025How 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.socialroyalsocietypublishing.orgPhilosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1936 17331
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 15/09/2025Introducing 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 12216
Reposted by Ricardo O. Ramirez FloresMaria Brbic @mariabrbic.bsky.social · 25/08/2025Our 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 🎯 1258
Reposted by Ricardo O. Ramirez FloresNature Methods @natmethods.nature.com · 04/08/2025An 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.comDeep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature MethodsThe 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... 06425
Reposted by Ricardo O. Ramirez FloresSaez-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 👇 16129
Reposted by Ricardo O. Ramirez FloresPLOS Biology @plosbiology.org · 25/06/2025From 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/4edGlY4plos.ioToo poor to science: How wealth determines who succeeds in STEMFrom 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... 02619
Reposted by Ricardo O. Ramirez FloresNature Reviews Nephrology @natrevneph.nature.com · 19/06/2025nature.comLeveraging data as a patient–scientist: frustrations and opportunitiesNature 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. 0107
Reposted by Ricardo O. Ramirez FloresAnshul Kundaje @anshulkundaje.bsky.social · 24/01/2025I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/ 211523
Reposted by Ricardo O. Ramirez FloresMwahahahahahadScientist @mads100tist.bsky.social · 22/04/2025Read preprints. Cite preprints. Email people and tell them you loved their preprint. Email people you hated their preprint. Embrace preprints, preprints are good. 834878
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 07/05/2025The 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 levelnature.comLearning tissue representation by identification of persistent local patterns in spatial omics data - Nature CommunicationsSpatial 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... 12611
Reposted by Ricardo O. Ramirez FloresJovan 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... 13117
Reposted by Ricardo O. Ramirez FloresChiara Schiller @chiaraschiller.bsky.social · 15/04/20251/ 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... 13712
Reposted by Ricardo O. Ramirez FloresBiology Open @biologyopen.bsky.social · 25/03/2025We 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 25026
Reposted by Ricardo O. Ramirez FloresSaez-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... 👇 25018
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 17/03/20256 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.comPostdoctoral fellow - Saez-Rodriguez GroupYour 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... 13127
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 25/02/2025Congrats 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) 185
Reposted by Ricardo O. Ramirez FloresShoval Miyara @shovalmiyara.bsky.social · 19/02/2025It’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.comCold and hot fibrosis define clinically distinct cardiac pathologiesMiyara 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... 2194
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 20/02/2025The 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.comNetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networksAbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage 04420
Reposted by Ricardo O. Ramirez FloresBritta Velten @brittavelten.bsky.social · 31/01/2025JOB 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.atScientific programmerPost a job in 3min, or find thousands of job offers like this one at jobRxiv! 0711
Reposted by Ricardo O. Ramirez FloresEric Topol @erictopol.bsky.social · 22/01/2025BioChatter, 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 38817
Reposted by Ricardo O. Ramirez FloreseLife @elife.bsky.social · 26/11/20241/ 🧵 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/4f8vIpkbuff.lyLearning resources for scientists · eLifeA collections of articles that provide practical resources and guidance for researchers and academics 1115075
Reposted by Ricardo O. Ramirez FloresAnshul Kundaje @anshulkundaje.bsky.social · 25/12/2024Our 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.orgChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variantsDespite 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... 723189
Reposted by Ricardo O. Ramirez FloresFlorian Ederer @florianederer.bsky.social · 23/12/2024Academics 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 20666277
Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 23/12/2024Check @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!! 0131
Reposted by Ricardo O. Ramirez FloresAdam MacLean @adamlmaclean.bsky.social · 28/11/2024Just 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.comDevelopmental hematopoietic stem cell variation explains clonal hematopoiesis later in life - Nature CommunicationsClonal 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... 07315
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 26/11/2024We 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 29632
Reposted by Ricardo O. Ramirez FloresRaymond Hames @rayhames.bsky.social · 19/11/2024Excellent 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.orgCultural evolution: Where we have been and where we are going (maybe) 22313
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 20/11/2024We 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 13012
Reposted by Ricardo O. Ramirez FloresJenine Harris @jenineharris.bsky.social · 19/11/2024I 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 012917
Reposted by Ricardo O. Ramirez FloresP(aul) Frazee @pfrazee.com · 15/11/2024Can you believe this whole site runs on a mac mini m4 70916309834
Reposted by Ricardo O. Ramirez FloresWill Macnair @willmacnair.bsky.social · 15/11/2024Restarting 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. 154918
Reposted by Ricardo O. Ramirez FloresLaura Helmuth @laurahelmuth.bsky.social · 14/11/2024Racial 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.comFrom Civil Rights to Black Lives MatterProtest expert Aldon Morris explains how social justice movements succeed 121530251
Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 15/11/2024Am 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. 352
Reposted by Ricardo O. Ramirez FloresPau Badia i Mompel @paubadiam.bsky.social · 14/11/2024POV: you try to run any multimodal GRN inference method 🫠 131
Reposted by Ricardo O. Ramirez FloresRicardo O. Ramirez Flores @ricoramirez.bsky.social · 11/11/2024As 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 084
Reposted by Ricardo O. Ramirez FloresThe Company of Biologists @biologists.bsky.social · 12/11/2024Welcome 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. 1018271
Reposted by Ricardo O. Ramirez FloresSaez-Rodriguez Group @saezlab.bsky.social · 11/11/2024What 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... 02610
Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 11/11/2024As 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 084
Reposted by Ricardo O. Ramirez Flores🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/11/2024Hi 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 23923
Ricardo O. Ramirez Flores @ricoramirez.bsky.social · 24/11/2023Explore 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 051
Reposted by Ricardo O. Ramirez FloresRichard Sever @richardsever.bsky.social · 04/10/2023The 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... 311179
Reposted by Ricardo O. Ramirez FloresAnne 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’Brienstatnews.comThe 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... 03616