Overall, this work has spurred many new hypotheses by pinpointing which genes and contexts are relevant for each disease. As usual, this project was not without it's challenges - I have to give a huge shoutout to my PhD mentors Shamil Sunyaev + Peter Kharchenko and all of our fantastic collaborators
Our method found evidence explaining ~2x the number of GWAS loci compared to pseudobulk eQTLs. We dove deep into several disease-specific findings, especially relating to Parkinson's disease (TRPV2 may be a protective gene, supported by recent studies).
Therefore, our method leverages eQTL models with continuous cell state interactions. While such models are now more commonly used, we specially adapted their output to enable eQTL-GWAS colocalization testing across the cell state space.
Uniquely, scJLIM does NOT require clustering cells before eQTL mapping. Arbitrary clustering cutoffs can kill statistical power for detecting eQTLs when you cluster too finely or too coarsely, and we typically don't know the expected resolution to look at a priori.
Super excited that my paper describing the scJLIM single-cell genetic colocalization tool is finally out on bioRxiv! scJLIM enables you to identify the specific cell states where GWAS genetic variants impact gene expression. Check it out! www.biorxiv.org/content/10.1...
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch
Delighted to introduce our new spatial transcriptomics tool, SpottedPy, allowing the identification of tumour hotspots at different scales and the exploration of distances and overlap with tumour microenvironment niches: genomebiology.biomedcentral.com/articles/10....
1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...
Cancer escapes immunotherapies by mutating its surface, meaning even groundbreaking #CARTCell therapies fail too often. But what if #GenerativeAI could design CAR-T with de novo binders faster, targeting resistant tumors? 🧵 www.biorxiv.org/content/10.1... (1)
ctDNA isn't great at detecting small, early stage cancers which don't shed much DNA. Could the systemic anti-cancer immune response be used for early detection? Interesting data here from colorectal cancer
Paper found with researchbriefing.com.
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
#paperoftheweek @jackiheraudfarlow.bsky.social & Co report that GGNBP2-CNOT10/11 complex formation promotes MDA5 sensing of immunogenic self dsRNAs, upon ADAR1 mutation. Congrats to all involved! 👏🏻
www.science.org/doi/10.1126/...
Now online in Cancer Discovery: PKN2 Is a Dependency of the Mesenchymal-like Cancer Cell State - by Shane Killarney, Kris Wood and colleagues doi.org/10.1158/2159...
Researchers at the Crick and UCL have developed a tool to analyse genes linked to the ability of tumours to hide from the immune system.
The findings were led by first author Clare Puttick as part of the TRACERx study funded by Cancer Research UK
www.crick.ac.uk/news-and-rep...
That's a really interesting system from Georgia Tech. Immune Organoids! The research team used synthetic hydrogels which can make a microenvironment for B cells, isolated from human tonsils and blood, to mature and produce antibodies.
Published in Nature Materials.
news.gatech.edu/news/2024/11...
Hot off the press: @mathonco.bsky.social members, including
Anna Gaffney, Matt Froid, and yours truly, working with the Lynch lab, use #MathOnco #ABM models to describe the bone ecosystem in Multiple #Myeloma:
link.springer.com/article/10.1...
This one dramatically increased my awareness of how much we might be wrong with our current view of gene regulation by chromatin - and genesdev.cshlp.org/content/36/1...
wake up babe, new george church skincare routine just dropped
www.biorxiv.org/content/10.1...
Spatialomics reveals T cell behaviors in metastatic breast cancer: infiltration vs. exclusion. Cool work from @KlughammerLab www.nature.com/articles/s41...
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment www.sciencedirect.com/science/arti...
Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
Exciting to see the SciTwitter community rebuild and take off this week at Blue Sky.
We are interested in 3D Genome Structure and Function and long-range gene regulation.
Reposting from Twitter some of the things that came out of the lab ( www.ashansenlab.com ) over the last year or so.
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
Starter packs are genius, but I was surprised there wasn't a list of them for people to find.
So I built it:
blueskydirectory.com/starter-pack...
The website monitors the packs being shared and adds the ones it finds to the database.
Missed your stater pack? Message me and I'll get it added.
