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 :-)

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.

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

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.

Super excited to share our lastest bioRxiv preprint from @mskcancercenter.bsky.social introducing GIFT (Genotyping In Fixed Transcriptomes):

Preprint: doi.org/10.64898/202...

- 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

🚨🚨 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.

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

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 .

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

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.

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".

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! 🙂

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...

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...

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

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.

Opinion | American Science is Under Attack The Trump administration hobbles research and endangers the public health.

"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."

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...

🔗 More infos: sail.mskcc.org

📧 Pls contact me directly at chalignr@mskcc.org if interested!

#SingleCell #SpatialGenomics #ResearchJobs

🔬 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.