We promise that GIFT is something that you're going to want to unwrap soon-- we've been floored by how well this method works. Check out the preprint to learn more! www.biorxiv.org/content/10.6... 8/n
It's cool to see we aren't the only ones that think rationally designed probes + gapfilling is the future. Check out a corroborating workflow from @mgrillo.bsky.social, @lgmartelotto.bsky.social, Anna Nam, and colleagues: bsky.app/profile/mgri... 7/n
I lied-- here's a fourth thing you should know. GIFT is fully loaded and ready to go in your lab.
> The experimental protocol is fully open-sourced.
> We have 3 git repos for probe design, parsing, and downstream analyses
> We've validated it in primary samples and preserved FFPE tissues 6/n
3. This design enables genotyping hundreds of loci in individual cells at an accuracy much higher than other workflows for genotyping off of flex. GIFT simply works incredibly well. 5/n
2. GIFT builds on the 10x Genomics Flex kit, enabling a multi-step combinatorial barcoding that scales cell capture for genotype-to-phenotype mapping by ~an order of magnitude. 4/n
The three things you need to know:
1. GIFT uses short DNA probes to enable genotyping anywhere in a transcript and reads out potential mutations with a short 'gapfilling' reaction between adjacent probes. 3/n
At the risk of duplicating a fairly long primer on the method, I'll share some of the highlights here but refer everyone to this thread on twitter/X 2/n x.com/CalebLareau/...
We’re unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
Really pleased to see this out @natsmb.nature.com: www.nature.com/articles/s41.... MitoPerturb-Seq combines #singlecell #CRISPR screening with whole-cell Multiome, to identify nuclear modifiers of mtDNA dynamics. @mitocamb.bsky.social @mrc-mbu.bsky.social @prudentlab.bsky.social and Stephen Burr
I defended my PhD 10 years ago today. That was the least remarkable thing that happened that day. Sharing something I wrote about it last year. Since then "the horrors persist but so do we." And with dignity.
Breast cancer mortality dropped 58% from 1975 to 2019.
Localized, early detected breast cancer has a 99% 5 year survival rate.
Modern mammogram tech was developed by NASA for telescopes.
Last year, RFK Jr. cancelled 87 research grants on breast cancer.
www.nytimes.com/2026/03/16/u...
Those who know me, know I’m not someone who changes his preferences & behaviors lightly. As Ron Swanson said, “I regret nothing. The end.” Well, let me tell you about our new study, out from The Perry Lab @mskcancercenter.bsky.social in @cp-immunity.bsky.social, which is the exception. /1
🖨️ Hot off the press 🍾 :
I am super excited to share that our article on the host control of persistent EBV infection has just been published in Nature Magazine, in an accelerated article preview version:
rdcu.be/e4Lg8
Wellcome Connecting Science Single Cell Biology hybrid conference Conference dates: 10-12 June 2026 Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online. Bursary deadline: 16 March 2026 Abstract deadline: 30 March 2026 In person registration deadline: 11 May 2026 Virtual registration deadline: 1 June 2026 Image of a conference delegate presenting a scientific poster.
Registration for Single Cell Biology 2026 is now open! #SingleCell26
Join us as we explore new single cell research insights and discoveries beyond the traditional model organisms🧬
🗓️ 10-12 June
📍 Wellcome Genome Campus, UK
Bursaries available
📎 bit.ly/4pyTK21
#SingleCell #Spatial #Genomics
Excited to share my first preprint on federated conditional analysis of rare single variant and aggregate association tests across six genetically-inferred ancestry groups in All of Us and UK Biobank doi.org/10.64898/202...
Preprint from @lpachter.bsky.social lab argues journals should treat results as machine-readable objects, not just PDFs. Narratives stay for humans, but claims, evidence, and evaluations should ship in structured form so machines can index and verify. www.biorxiv.org/content/10.6... 1/ 🧵
I feel like vegemite jokes are an untapped market wdyt @psmibert.bsky.social
Thanks for the enthusiastic support and charting the path 🙏
Re-analysis of human population-scale whole genome seq data elucidates genetic architecture of EBV DNA persistence, a framework for the broader human virome
@nature.com @caleblareau.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social @ryandhindsa.bsky.social
www.nature.com/articles/s41...
This was a fun and rewarding collaboration! A great example of extracting biological signal from data hiding in plain sight
There is also a wonderful summary of our work (including some important limitations) from Kristen Wade & Jill Hollenbach www.nature.com/articles/d41...
EBV infection is a major detriment to human health. @ryandhindsa.bsky.social, Slavé, and I discussed the impact of this work with @bloomberg.com and some future outlooks
www.bloomberg.com/news/article...
What's been particularly gratifying about this study is the corroboration by independent groups that have arrived at complementary conclusions. Those preprints are here:
www.medrxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.medrxiv.org/content/10.6...
Our prior thread digesting this work is available here. The key findings are the same from the preprint, but there's a boatload of new analyses for corroboration and interpretation of this new biomarker.
bsky.app/profile/cale...
Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection.
Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social
www.nature.com/articles/s41...
The Cancer Signaling & Microenvironment Program at Fox Chase Cancer Center is looking for tenure track faculty (assist./assoc./full) in computational & experimental protein design. CV & 3-page research statement by Feb 15.
More info here:
www.linkedin.com/feed/update/...
Questions: DM/Email me.
i see this all the time with no mention of structural suppression:
- Electoral College winner-take-all
- working day elections
- voter registration burden
turnout in battleground states is fairly high. people aren't lazy. they are responding to disincentivization and disenfranchisement.
We've summarized a detailed thread on this work over on X/Twitter (x.com/CalebLareau/...).
As newcomers to this protein design field, we’d very much welcome thoughts, feedback, missing citations, or ideas on how to steer this work next!
We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—
