Hunter Shain @ShainLab
Associate Professor, Dermatology, UCSF. part of HTAN. Melanoma, skin cancer, single-cell, DNA/RNA-seq, spatial transcriptomics, cancer, dermatology, pathology shainlab.ucsf.edu San Francisco, CA Joined November 2017-
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Hunter Shain retweeted
Delighted to share our latest review on 3D multi-omics tumor atlases. A major @theNCI #HTAN team work w/ @deniswirtz @AshleyKiemen @StimulatedRaman @SStevenWang, kudos to my phenomenal postdoc @Miao__Liu and co-contributors Jorge, Andre, & Xiaolong, on this team work! 🥰
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@LupinCambridge Very interesting! I don't want to read too much into a small blip, but the mutation burden seems to go down from 2 to 4 months? Is it feasible for tissue to shed high mutation burden cells as a mechanism to lower their mutation burdens over time?
I am worried this is a mirage, caused by the fact that only the top third of grants are discussed. It is hard to make it into the top third if a single reviewer gives your grant a 5
The two factors are clearer and understandable. As a result, scores are much more consistent now, than in the past. It is a rare occurrence to see spread of preliminary overall scores of 3 points or more between three reviewers (eg 2, 2, and 5). (6/10)
Hunter Shain retweeted
Incredible to see our work out today in Cell: "Plasma signals of lung tumor promotion for molecular cancer prevention." cell.com/cell/fulltext/…
@aemonten The blue place is not really any better. LI is where I get the most scientific engagement these days, but it is not an ideal platform for many things
Hunter Shain retweeted
Heading to #ASCO this week and really looking forward to the energy and the science. On a personal note, I’m proud to share some work my team is presenting this year. I want to briefly highlight why I think these results matter.
Hunter Shain retweeted
1/ Thrilled to share our new paper, out today in @ScienceMagazine! We built a pan-cancer spatial atlas of tertiary lymphoid structures (TLSs) and developed computation and AI frameworks to study TLS biology at scale. science.org/doi/10.1126/sc…
@JohnStreicher1 SABV was created with good intentions, but it turned into a stock reviewer critique. That is frustrating.
@RongFan8 Is this where Crick and Watson would brainstorm the structure of DNA over beer? Nice!
@srikosuri One could go even further to account for differences in class difficulties, such as an ELO score -- similar to what they do in college sports to account for scheduling differences.
@SyedAAhmad5 This is misleading. The Kaplan-Meier curves represent physicians "in this study population that are not currently practicing (N = 521)". It helps compare men vs women who left but not overall rates of attrition
Hunter Shain retweeted
Marty Makary misunderstood something fundamental about the FDA There is not, and never has been, a ‘deep state’ to shove aside statnews.com/2026/05/16/mar…
Hunter Shain retweeted
On Friday, I hosted a forum with the top 5 Democrats running for governor of California on how they'd fix the state's housing crisis. Some really interesting moments, including this one, from @katieporterca, on California Forever and master-planned communities. Full forum on podcast apps/Youtube.
Hunter Shain retweeted
Excited to share SapiensOntoCellMap! 🚀 An open-source tool for ontology-aware, hierarchical cell type annotation of scRNA-seq and spatial transcriptomics data. Built at @UCSF to solve a major gap: moving beyond simple labels to true biological context. 🧵👇
Hunter Shain retweeted
Excited to see this in print! Kudos to Haikuo, Bo, and the entire team including @MinaXu7 @yalepathology @zhou_jingtian @arcinstitute to explore this clinically relevant area of lymphoma transformation with truly innovative technology. @theNCI #HTAN nature.com/articles/s4146…
Now do San Francisco
@TheStalwart Yeah it's 70% human capital, 15% the food (underrated not overrated), 8% the subway, 6% that NYC is actually really pretty and 1% the Knicks when they're winning.
Original publication is here, though the software has been through many versions since the original manuscript was published. link.springer.com/article/10.118…
STmut can be downloaded here. github.com/limin321/stmut. Thanks to @liminchen15 for creating the software and continually updating it to handle higher resolution spatial transcriptomics, as they are rolled out. Thanks to Vignesh Arunachalam for generating the present figures.
STmut can now operate on Atera data from @10xGenomics. Here is a breast cancer that was profiled on the Atera platform
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