Writing this piece has been quite fulfilling (and scary). I spent half of last year putting in order some of my thoughts regarding how to study multicellular coordination with single-cell and spatial data. If you are interested please read the manuscript below. 😊

I'm thrilled to share with you that #visiumStitched led by Nick Eagles has now been published Our #RStats / @Bioconductor 📦provides a framework for stitching together multiple #Visium @10xgenomics capture areas together https://t.co/T5SIJjrKY2

@jan_lanzer and I have been preparing this work for a while, and happy that we can finally share with you all. Please don't hesitate to provide feedback on the pre-print ☺️

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!

I made a genomic scientists trained in Mexico 🇲🇽 starter pack. I'd like for our voices to be heard! If you can help spread the word, that'd be great! Thank you! @CDSBMexico @nnb_unam @RBioinformatica @lcgunam @lcgunam @ccg_unam @ibt_unam @LIIGH_UNAM

Our work with @schirmerlab in multiple sclerosis (MS) is out today in @NatureNeuro. We investigated lesion progression and cell-cell communication events in MS using snRNA-seq and spatial transcriptomics 🧠 See below ⬇️ https://t.co/j6LIwv4IgU

📢 Introducing CORNETO: a unified, knowledge-driven framework for multi-sample network learning & modeling via constrained optimization, supporting a wide variety of network methods and prior knowledge 💻Code: https://t.co/OuM9Acrs9U 📜Paper: https://t.co/XFjEbKMAAL 🧵👇

Starting today as a Staff Scientist at @emblebi! I will continue my work @saezlab on multicellular processes with multi-scale omics. Excited to join the Genome Campus community and see where the science takes us! ☺️ Happy to catch up with friends and colleagues in Cambridge.

How good is our understanding of signaling pathways? In this study together w/ @savitski_lab @EMBL, we combine multiple state-of-the-art resources to evaluate signaling pathway inference using phosphoproteomics and kinase-substrate networks https://t.co/T2iIKGYuiZ

Kidney fibrosis as a molecular process is poorly understood. In this new study together w/ Pepperkok lab @EMBL, we present a time-resolved #multiomics + computational network modeling approach in combination w/ phenotypic assays to study #kidneyfibrosis https://t.co/9I1axrjUYl

"Several members of my faculty [told] me, 'You can't get a job at Berkeley without a Cell, Science or Nature paper'. These [same] people had gotten jobs at Berkeley without a [CNS] paper...We believe this to be true to an extent that's irrational" @mbeisen

And they cost ~1% of journal articles (~0.01% of research). So whatever you think of peer review (we need more vs less vs different vs none), supporting a mechanism that provides rapid and universal free access to knowledge should be a no-brainer

🚀 Excited to share our new publication in @NatureBiotech! We explore scalable strategies for phenotypic screening using innovative methods with to address the challenges when the number of candidates is simply too large. Check out the details https://t.co/C0oan6L18a! (1/10)

"When I suggested the data were uninterpretable given the sample size and methods, she responded that the journal had an Impact factor in the high 30s (suggesting that regardless of my opinion, it was worth attention)"

🚀 Exciting postdoc opportunity in collaboration with @AstraZeneca. Our EAZPOD fellowships push the boundaries of cutting-edge computational biology in oncology. Combine method development & modelling with preclinical multiomics data. Find out more 👇 https://t.co/BhJHh2Mv8i

STAMP is OUT! Sequencing-free #singlecell RNA and Protein profiling. Game-changing approach for scalable and cost-efficient analysis of single cells. The future starts today! Amazing ⁦@LGMartelotto⁩ ⁦@DrJasPlummer⁩

👉Consider joining us for a post-doc at @emblebi & @ASTRAZENECAUK as part of the EAZPOD program to study multicellular mechanisms associated with #cancer treatment resistance! #postdoc https://t.co/Pfyp0P1fEf

Posting a preprint only after your paper is rejected by a journal is not the way to do it..

For those interested in repurposing factor models for patient-level comparisons and inference of multicellular programs have a look at the great overview given by Leo of the foundation work and the applications/packages that we have built! Thanks for this 😊

Check out our work on fibroblast activation patterns in HF models! Huge thanks to my co-lead @LauraWienecke 🙏 from @LeuschnerLab!

"Peer review...for centuries the standard tool to determine an academic paper’s suitability for publication". https://t.co/G7kuGKxTa5 No. The term is only a few decades old and Nature itself didn't it routinely until the 1970s. 1/3