The Single-Cell Ninjas

#AGTA2026 returns to Sydney (Roundhouse UNSW), Sept 1316! Confirmed superstar speakers: Braden Tierney Jiwoon Park Martin Smith Lipin Loo Tiffany Boughtwood Justin Wong Joseph Powell Kim-Anh Lê Cao Topics: Population-scale genomics (clinic + non-human) Spatial and Sc omics, disease atlases CRISPR, functional/regulatory genomics AI for genomics and pathology Emerging platforms and automation #AGTA2026 #Genomics #SpatialOmics #CRISPR #SingleCellOmics #AiGenomics #FunctionalGenomics #ClinicalGenomics @agtaGenomics

Hack alert! 🚨 In vivo multiomic Perturb-seq with enhanced nuclear gRNA capture | bioRxiv biorxiv.org/content/10.648…

Spatial perturb-seq: single-cell functional genomics within intact tissue architecture Scale up your in situ CRISPR screens Out in @NatureComms

Hello single cellers and also spatial people! The Single Cell Ninjas are back on the road and would like to offer 1:1 tele-consultations sessions to discuss experimental designs, technologies choices, troubleshooting and so on. All completely free of charge. Please DM us!

Join me and these 4 super legends in the fields of single cell and spatial‑omics for a fast‑paced discussion on innovative benchmarking approaches that address delivering the deepest biological insights per dollar, tailored to your specific study design.

𝗕𝗲𝗻𝗰𝗵𝗺𝗮𝗿𝗸𝗶𝗻𝗴 𝗶𝘀 𝗕𝗿𝗼𝗸𝗲𝗻. 𝗟𝗲𝘁’𝘀 𝗙𝗶𝘅 𝗜𝘁. Single-cell and spatial benchmarking studies dominate journals and conferences. Yet, after the leaderboards are published, you’re still left with the same high-stakes questions: Do these metrics actually inform your next biological move, or just confirm what you already know? When the grant money is on the line, the question isn't just 'what works' - it’s 'what works within reach.' Which platform truly maximizes biological output for your specific budget? Most benchmarking work misses the point. It ranks tools. It crowns winners. But it leaves you to carry the risk when it’s time to design your study and spend your grant. 𝗠𝗼𝘃𝗶𝗻𝗴 𝗕𝗲𝘆𝗼𝗻𝗱 𝘁𝗵𝗲 𝗟𝗲𝗮𝗱𝗲𝗿𝗯𝗼𝗮𝗿𝗱 At AGBT 2026, four of our beloved leaders in the field will challenge the status quo of benchmarking. We aren't talking about which method "wins" or who runs the fastest pipeline. We are questioning the utility of the metrics themselves. This discussion will dive into the hard truths of study design: -𝗜𝗻𝘀𝗶𝗴𝗵𝘁 𝘃𝘀. 𝗠𝗲𝘁𝗿𝗶𝗰𝘀: are you optimizing for biological discovery or just "clean" data? -𝗥𝗲𝗮𝗹𝗶𝘁𝘆 𝘃𝘀. 𝗜𝗱𝗲𝗮𝗹𝗶𝘀𝗺: are you planning studies real labs can afford, or chasing extreme depth that isn't reproducible? -𝗚𝘂𝗶𝗱𝗮𝗻𝗰𝗲 𝘃𝘀. 𝗛𝘆𝗽𝗲: are benchmarks helping you design better experiments or simply feeding a hype cycle? 𝗝𝗼𝗶𝗻 𝘁𝗵𝗲 𝗖𝗼𝗻𝘃𝗲𝗿𝘀𝗮𝘁𝗶𝗼𝗻 If you generate or analyze single-cell or spatial data, this panel will speak directly to your results and your bottom line. Details coming soon. Stay tuned! #Benchmarking #SingleCell #MultiOmics #Bioinformatics #Genomic #SpatialBiology #AGBT2026

As I'm updating my NIH Biosketch for the N-th time this year, I made a Jekyll theme for students to familiarize themselves with this CV structure while building their online presence. Demo: jefworks.github.io/online-biosket… Fork to modify: github.com/JEFworks/onlin… #JustAcademicThings

I just finished reading this beauty from the @KleinLabHMS 🫶🫶🫶 Multistep genomics on single cells and live cultures in subnanoliter capsules. Mazelis et al, recently published Science last December. DOI: 10.1126/science.ady7209 I first saw Ignas start working on this almost five years ago when I was at HMS. It’s unreal, and makes me very happy, to see it go all the way to a Science paper. Legend! In this work, Ignas and team introduce a new single-cell functional genomics platform that lets you: -keep single cells alive -culture them over time -run multi-step biochemical workflows on them -then read out genome-wide signals The big breakthrough is the capsule design. It physically holds cells (and large biomolecules) in place, while still allowing media, enzymes, and reagents to diffuse in and out. Smart idea. Huge impact. To make this work, they built “capsules with amphiphilic gel envelopes,” or CAGEs. These magic capsules: -retain cells and large analytes (so you don’t lose the important stuff) -stay permeable to media, enzymes, and reagents (so complex protocols still work) -support high-throughput processing (so you can scale to tens of thousands of samples) This matters because most functional genomic assays require multiple sequential steps. Those workflows fall apart when you try to scale them across large numbers of living single cells. CAGEs solve that, which allowed the team to: -run high-throughput, multi-step workflows on living single cells (not limited to “one-pot” reactions) -create a DNA library barcoding strategy for CAGE-derived material, so you can pool capsules without losing cell identity -measure how gene expression programs persist through clonal expansion -link lineage-like clonal growth with transcriptome readouts at real scale Most single-cell sequencing methods are great at snapshots. But biology is dynamic. We care about things like: -response to stimuli -stability of cell states -differentiation -expansion of rare clones This platform tackles one of the biggest bottlenecks in the field: Scaling live-cell, multi-step functional measurements to high throughput, while still getting genome-wide readouts!!! Big congratulations to the entire team!

Amazing pub from an even more amazing team! Congratulations to everyone!

TY @Aiims1742! Thrilled to share our new @AGA_CMGH paper! Using FixNCut scRNA-seq, we uncover novel acinar metaplastic cell states and precancer programs in pancreas disease. sciencedirect.com/science/articl… Led by the amazing @Aney_Katie and Woo-Jeong 👏🧵👇

Early Spatial Adopters Develop Standards, Resources for Quality Control and Data Benchmarking | ⁦@GenomeWeb⁩ genomeweb.com/sequencing/ear…

Single Cell Imaging is the new Single Cell Sequencing. The very first STAMP at CCI following El Maestro. STAMP in the quest to Zero Childhood Cancer. @LGMartelotto @DrJasPlummer @CytoNology @KidsCancerInst

Goliath effort to help with standards in the field of spatial trancriptomics … can only be more amazing when done with @LGMartelotto @mason_lab 🚀 Paper: nature.com/articles/s4158… Touchstone portal: spatialtouchstone.org Spatial touchstone protocols: protocols.io/view/spatial-t…

What started with three amigos’ shared frustration with weak quality metrics and SOPs in spatial omics grew into a framework built to help the community raise standards. From frustration to focused progress. @mason_lab @DrJasPlummer stjude.org/media-resource…

Very happy to finally present our work! “𝘚𝘵𝘢𝘯𝘥𝘢𝘳𝘥𝘪𝘻𝘦𝘥 𝘮𝘦𝘵𝘳𝘪𝘤𝘴 𝘧𝘰𝘳 𝘢𝘴𝘴𝘦𝘴𝘴𝘮𝘦𝘯𝘵 𝘢𝘯𝘥 𝘳𝘦𝘱𝘳𝘰𝘥𝘶𝘤𝘪𝘣𝘪𝘭𝘪𝘵𝘺 𝘰𝘧 𝘪𝘮𝘢𝘨𝘪𝘯𝘨-𝘣𝘢𝘴𝘦𝘥 𝘴𝘱𝘢𝘵𝘪𝘢𝘭 𝘵𝘳𝘢𝘯𝘴𝘤𝘳𝘪𝘱𝘵𝘰𝘮𝘪𝘤𝘴 𝘥𝘢𝘵𝘢𝘴𝘦𝘵𝘴” Spatial transcriptomics promises deep insight into tissue architecture - but inconsistent data quality across labs and platforms has been a major barrier. A new study from a global consortium addresses this by releasing the Spatial Touchstone (ST): a harmonized, multi-site, multi-platform dataset using six tissue types and two widely imaging used technologies. We introduce SpatialQM, an open-source quality-control software, and a public repository, Spatial Touchstone Portal (STP), that hosts ~33M cells and ~7B transcripts. With standardized metrics for sensitivity, reproducibility, signal-to-noise, false discovery rates, and cell-type annotation, this framework gives labs a way to benchmark and compare spatial transcriptomics data reliably. This effort sets a foundation for more robust, reproducible spatial-omics research — and helps unlock cross-study comparability across institutions and platforms. I’m incredibly thankful to my amazing collaborators across the globe and an special shout out to my dear friends @DrJasPlummer and @mason_lab and their super amazing teams for literally working they brains out to make this happen. Felipe, Jiwoon , David, Luke, Maycon, Yutian, Arjumand, Hannah, Kellie, Alex, Lisa, Alicia, Roberto and many more! @WeillCornell @StJudeResearch nature.com/articles/s4158…

Calling all #singlecell #spatial officianados. Join fellow @GESTALT_sp members in our workshop at NextGenOmics Spatial & Data 2025 @naveedishaque Musa Mhlanga @SManiatis73425 @ahmetfcoskun Free registration for GESTALT members Nov 13-14 in London UK! @ioavlachos @LGMartelotto

New in Nature Reviews Genetics: my Review on how advanced genomic technologies are redefining cellular reprogramming: mapping trajectories, dissecting chromatin dynamics, + lineage tracing & synthetic circuits to push the boundaries of cell identity. rdcu.be/eLv1Z

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 It started from my frustration with the depressing effect that the current publishing system has on the well-being of myself, my team, and pretty much every scientist I know (maybe you’ve noticed from my stupid jokes… :) I was exhausted of dealing with the huge delays, reviewers that can be abusive, and how arbitrary it all is. Unfortunately, the most important factors are often WHO your reviewers are and who YOU are... It’s clear we need alternatives or at least ways to improve the situation. So, together with a really special and talented team we worked to develop this idea into “qed” a platform where you can get CONSTRUCTIVE feedback on your own work or CRITICALLY assess other people’s papers. It can be a real difference maker if many of you join us (thousands have tried it already, but today we release a NEW and much stronger version ;) Let’s harness qed to put the power back in the scientists’ hands, to do, to read & to publish science on our own terms. I’m dying for you to TRY IT, and it’s very simple - just drop a paper (the link to the website is in the replies👇) - it’s completely secure, private, and free, and you get results fast. Please show your support, SHARE, tell your friends, and let’s be the revolution 🫵!

@AnnaEnim @CellGenomics @LGMartelotto @JudeNicho @NIH @BWFUND It’s a fantastic technique. Easily the best genotyping + RNA technique available at the moment. Do not sleep on this one!!! Great work @AnnaEnim and @LGMartelotto

RT @LGMartelotto: YES!!! It’s out! 🔥 One of the most amazingly beautiful collaborations. I’ve admired @AnnaEnim since her original GoT -…