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Ronan Chaligné @ronanchaligne.bsky.social · 15/04/2026

We may be slightly overusing the “unwrapping” metaphor at this point, but if you work on single-cell genomics, this is probably one GIFT worth opening :-)

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Ronan Chaligné @ronanchaligne.bsky.social · 15/04/2026

This project was a true team effort, many thanks to Sydney Blattman, Nabih Maslah, @austinv11.com, Karolis Kumpaitis, @danapeer.bsky.social, and also @10xgenomics.bsky.social for the partnership and support. A special thanks to @caleblareau.bsky.social for the close collaboration throughout.

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Ronan Chaligné @ronanchaligne.bsky.social · 15/04/2026

The result: scalable, high-accuracy (>99%) genotype-to-phenotype mapping at single-cell resolution, now applied across large patient cohorts to resolve clonal structure and mutation-driven cell states

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Ronan Chaligné @ronanchaligne.bsky.social · 15/04/2026

GIFT enables direct genotyping of hundreds of loci alongside whole transcriptomes in single cells, using a probe-based gap-filling strategy that works across transcripts, and even in fixed and FFPE samples.

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Ronan Chaligné @ronanchaligne.bsky.social · 15/04/2026

Super excited to share our lastest bioRxiv preprint from @mskcancercenter.bsky.social introducing GIFT (Genotyping In Fixed Transcriptomes): Preprint: doi.org/10.64898/202...

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Ronan Chaligné @ronanchaligne.bsky.social · 23/06/2025

- Experience in molecular biology or genomics is essential - We're looking for someone curious, detail-oriented, and collaborative 📍 Based in NYC – learn more about us: sail.mskcc.org 📩 Interested? Get in touch: chalignr@mskcc.org #Genomics #SpatialBiology #Jobs

sail.mskcc.org

Single-cell Analytics Innovation LabChaligne Lab Website

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Ronan Chaligné @ronanchaligne.bsky.social · 23/06/2025

🚨🚨 We're hiring! 🚨🚨 The Single-cell Analytics Innovation Lab (SAIL) at @mskcancercenter.bsky.social is looking for a Junior Technician to join our wet lab team! You'll work with spatial genomics and single-cell technologies, helping us push the boundaries of cutting-edge analysis in cancer research.

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Reposted by Ronan Chaligné

danapeer.bsky.social @danapeer.bsky.social · 26/05/2025

The Single-cell Analytics Innovation Lab @mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t

bit.ly

Computational Biologist (Single-cell Genomics / ML) – Single-cell Analytics Innovation LabChaligne Lab Website

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Reposted by Ronan Chaligné

Caleb Lareau @caleblareau.bsky.social · 14/03/2025

Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1

media.tenor.com

a baby is eating a piece of food while sitting on the ground .

ALT: a baby is eating a piece of food while sitting on the ground .

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Ronan Chaligné @ronanchaligne.bsky.social · 13/03/2025

This publication is deeply meaningful to us, as Ignas tragically passed away last year from a sudden and aggressive cancer. Proud that his incredible scientific legacy lives on through this work. We will never forget him, and it has only strengthened our dedication to the work we do at MSKCC.

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Ronan Chaligné @ronanchaligne.bsky.social · 13/03/2025

Building on the foundation of DOGMA-seq (standing on the shoulders of @psmibert.bsky.social, Eleni Mimitou, and @caleblareau.bsky.social), SAIL—especially Ignas Masilionis—further optimized the protocol to enhance mitochondrial coverage, called here "HighLLL".

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Ronan Chaligné @ronanchaligne.bsky.social · 13/03/2025

So happy to see this work published! It all began when @agnelsfeir.bsky.social and her lab joined @mskcancercenter.bsky.social and reached out to SAIL for help in assessing mtDNA heteroplasmy at the single-cell level. Huge thanks to the Sfeir Lab for trusting us with this endeavor! 🙂

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Reposted by Ronan Chaligné

Stand Up for Science! @standupforscience.net · 09/03/2025

But our work is far from done—science is still under attack. We’ve got ideas, but we want to hear from you. What’s worrying you most? What should we do next? How can we grow this movement together? Fill out this quick form to share your thoughts & stay connected: forms.gle/QAxH4wD4Y3sg...

forms.gle

How do we keep Standing Up for Science?

A heartfelt thank you for everyone that Stood Up for Science with us on March 7th—whether it be volunteering, donating, sharing, or attending in event, we're forever indebted to people like you who ca...

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Ronan Chaligné @ronanchaligne.bsky.social · 21/02/2025

Excited to present the incredible work happening at the Single-cell Analysis Innovation Lab (SAIL) @mskcancercenter.bsky.social! Tune in to discover the impactful research SAIL has helped drive with its amazing collaborators: Susan DeWolf, Robert Stanley, Omar Abdel-Wahab, @caleblareau.bsky.social

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Ronan Chaligné @ronanchaligne.bsky.social · 21/02/2025

Huge thanks for the shoutout, Andrea! 🙌 Roshan is an incredible teacher, and I can’t recommend his online class enough for anyone looking to deepen their understanding of single-cell analysis.

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Reposted by Ronan Chaligné

New York Times Opinion @nytopinion.nytimes.com · 14/02/2025

"I've spent over five decades as a scientist in academia and the federal government," Harold Varmus, the former director of the N.I.H., writes in a guest essay. "Never before have I seen my profession so politicized as it is now under the Trump administration."

nytimes.com

Opinion | American Science is Under Attack

The Trump administration hobbles research and endangers the public health.

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Ronan Chaligné @ronanchaligne.bsky.social · 30/12/2024

🔗 More infos: sail.mskcc.org 📧 Pls contact me directly at chalignr@mskcc.org if interested! #SingleCell #SpatialGenomics #ResearchJobs

sail.mskcc.xn--org-pk23b

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Ronan Chaligné @ronanchaligne.bsky.social · 30/12/2024

🔬 We’re Hiring! 🧪 The Single-cell Analytics Innovation Lab @mskcancercenter.bsky.social is expanding and looking for Junior Research Technician! Join our team based in NYC to work on cutting-edge single-cell & spatial genomics methods in collaboration with leading research labs.

sail.mskcc.org

Single-cell Analytics Innovation LabChaligne Lab Website

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