I develop Cell Ranger at 10x Genomics, Homebrew, and developed ABySS for my PhD at UBC. I cook, sing, travel, see theatre, and play boardgames for fun. 🏳️🌈
Vancouver, Canada
Joined September 2007
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🧬 10x Genomics is hiring! My first three months at 10x have been fantastic. My colleagues are friendly and helpful. 10x is based in Pleasanton, CA. Remote work may be possible, depending on the position. Check out open positions at grnh.se/c3f537b11
Shaun Jackman retweeted
First, a link to the preprint describing the method (PFlogPF) that produced the amazing results shown above: biorxiv.org/content/10.1101/…
The work was led by @sinabooeshaghi who is first and corresponding author, w/ important contributions by @IngileifBryndis & @agalvezmerchan. 4/
Shaun Jackman retweeted
Except it isn't. Not even close. In a project that is four years in the making, we show that another transformation massively outperforms existing methods on the Ahlmann-Eltze & Huber benchmarks (red dots below). Moreover, it's optimal. What is this new method? How can it be? 3/
Shaun Jackman retweeted
The standard normalization is log(x/s*K+1) w/ K=10,000 in Seurat and Scanpy. It's been used in hundreds of thousands of studies. AI agents nowadays run it routinely.
In an expansive benchmark in @naturemethods, Ahlmann-Eltze & Huber conclude it's pretty much best in class. 2/
Shaun Jackman retweeted
Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale + log. Move on.
Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/
Shaun Jackman retweeted
The impossible is here: introducing Atera, uncompromised #spatialbiology that lets you analyze up to 800 1 cm2 whole transcriptome samples/year with #singlecell sensitivity. Register now for an in-depth look at our 4/21 webinar: bit.ly/4leeJ8X
Shaun Jackman retweeted
Studying biology has long meant working with fragmented tools. With Atera, for the first time ever, biology can be measured as a complete system in its native context, at scale, removing the constraints that have held spatial biology back: bit.ly/48bYvYF
ALT 10x Genomics introduces Atera, a new platform to redefine how biology is measured and understood.
ALT Atera removes the trade-offs that have constrained research, unlocking a new era of insight that will transform our understanding of science and human health.
ALT Atera delivers whole-transcriptome spatial data with single-cell sensitivity at scale.
Shaun Jackman retweeted
Last night we unveiled the impossible. Now see it yourself! Check out Atera at booth #3217; or, if you're not at #AACR26, register for one of our webinars starting 4/21 to get a deeper look into the future of #spatialbiology: bit.ly/4leeJ8X
ALT Uncompromised Spatial: Only on Atera
Shaun Jackman retweeted
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv biorxiv.org/content/10.64898…
Figure 1 shows they key result
Shaun Jackman retweeted
If you haven't heard about this, kudos to the PSF for standing for its values (which are also my values).
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10…
🧵
pyfound.blogspot.com/2025/10…
Shaun Jackman retweeted
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10…
🧵
pyfound.blogspot.com/2025/10…
Shaun Jackman retweeted
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies academic.oup.com/nar/advance… 🧬🖥️🧪 github.com/danledinh/scRNAse…
Shaun Jackman retweeted
Congrats to @Muzz_Haniffa & team for the @BBCNews feature on how human skin develops from stem cells! 🙌 Using #singlecell & #spatialtranscriptomics, this #HumanCellAtlas study could lead to anti-aging breakthroughs: bit.ly/3UbjK5y (Link to paper in comments)
Shaun Jackman retweeted
📢 New Feature Alert 🎉 The beta version of Automated Cell Annotation is live in Cloud Analysis! Reduce the burden of manual annotation & visualize cell types instantly to get more accurate #singlecell insights faster. Try it now: bit.ly/3XVOdHe
Shaun Jackman retweeted
Globally, millions of individuals are affected by endometrial / uterine disorders, yet the #endometrium and the role of its #cellular #heterogeneity in these disorders have been hugely understudied compared with other human tissues and diseases.
Shaun Jackman retweeted
Congratulations to all involved in creating this cellular map of the endometrium, the inner lining of the uterus, during multiple phases of the menstrual cycle. This work helps advance understanding of the healthy endometrium and conditions such as endometriosis. @NatureGenet
Globally, millions of individuals are affected by endometrial / uterine disorders, yet the #endometrium and the role of its #cellular #heterogeneity in these disorders have been hugely understudied compared with other human tissues and diseases.
Shaun Jackman retweeted
Technology impacts the reliability of your #singlecell data. An independently conducted study reported that our Chromium Flex and 3' assays outperformed other technologies. See how the others stacked up: biorxiv.org/content/10.1101/…
Shaun Jackman retweeted
We're honored to have been funded by @cziscience in cycle 6 of their EOSS program & look forward to bringing some recent algorithmic advances to widely-used tools & building some new ones as well! Excited to work with @scarecrow00007, @daniel_c0deb0t, @_NoahCape & others on this!
Rob Patro (@nomad421) is receiving $400K from @ChanZuckerberg to advance open-source transcriptomics tools! This grant will enhance gene expression analysis, improving software performance and interoperability, and fostering open science.
Learn more: go.umd.edu/1p7t
Shaun Jackman retweeted
Excited to share our Seurat update supporting VisiumHD data from @10xGenomics. We explore and validate the ability of HD to map the spatial localization of individual cell types:
satijalab.org/seurat/article…
Shaun Jackman retweeted
We had a great meeting & and are moving forward with a GitHub org. for planning & developing foundational building blocks for sequence analysis & related tasks in @rustlang. The org. "rust-seq" can be found here github.com/rust-seq. Reach out if you're interested in joining!
Shaun Jackman retweeted
@10xGenomics released new single cell GEM-X assays in March, and we were quick to try it out. FHIL benchmarked 5’ GEM-X against 5’ Next GEM v2 chemistry with sorted T-cells from healthy donor PBMCs and targeted the recommended max for each assay, 20k and 10k respectively.(1/8)
