New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth.
www.biorxiv.org/content/10.6...
Nicolas Altemose, assistant professor of genetics at Stanford Medicine
"Some of the most important future scientific discoveries are currently hidden in unexpected places. That's why we're following our curiosity to explore the dark corners of the genome."
Stanford Medicine magazine: The power of research
Spotlight on Nicholas Altemose, assistant professor of genetics: The Altemose Lab applies new tools and technologies to explore the biology of repetitive areas of the human genome. stanmed.stanford.edu/repetitive-d...
Asked the AI to make a fun slide about potential de-skilling from AI use. Need to specify more clearly what I mean by "fun".
Other highlights:
🧬 ENCODE-rE2G scores now in L2G → 5% gain in selectivity
📊 710 new GWAS Catalog studies → 5,000+ new credible sets (incl. Rand et al., Nat Genet 2025)
⚡ ClickHouse migration complete → ~2x query speed
☁️ Platform data now on AWS Open Data Program
Hey this seems like some good news
District Court strikes down RFK Jr vaccine policies as not based on science
www.nytimes.com/2026/03/16/h...
>60% of all predicted transcriptional activation domains (TADs) overlap with strong degrons
www.biorxiv.org/content/10.1...
A major role for acidic residues in TADs is to prevent degrada-
tion
www.biorxiv.org/content/10.1...
What drives the science behind IGVF?
In this IGVF Q&A, members share how the team is tackling long-standing genomics challenges and building a comprehensive catalog of variant effects to advance human health & research.
Tune in: youtu.be/zPzGIjSQJ4U?...
🧬 @danielibrahim.bsky.social, moderated by @stefanschoenfelder.bsky.social, on enhancer-promoter specificity & how promoter-proximal regions act as molecular filters.
Register: us02web.zoom.us/webinar/regi...
March 5, 4PM UK.
#Genomics #GeneRegulation
The impact is already hitting science agencies hard. The NIH—the world's largest public biomedical research funder—has had to rely on leftover stopgap funds.
New grant awards have slowed to a trickle — exacerbating the effects of a record-long shutdown in October.
(h/t @jeremymberg.bsky.social)
Congress rejected massive cuts to US science budgets for 2026, but much of the money still isn’t flowing to researchers.
The culprit? The White House Office of Management and Budget (OMB) is quietly slow-walking the release of funds. 🧵👇
New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu!
www.science.org/doi/10.1126/...
We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here:
journals.biologists.com/dev/article/...
Interested in transcriptional regulation, enhancers and 3D genome folding?
In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control
www.biorxiv.org/content/10.6...
detailed 🧵👇
Practical utility of sequence-to-omics models for improving the reproducibility of genetic fine-mapping www.biorxiv.org/content/10.64898/2026.02...
Yesterday, five-year-old Liam and his dad Adrian were released from Dilley detention center. I picked them up last night and escorted them back to Minnesota this morning.
Liam is now home. With his hat and his backpack.
We mapped the fitness landscape of the 10kb MYC locus using SpRY-Cas9 saturation mutagenesis. 67% of the essential bps are noncoding. So even for a protein coding gene locus, most genetic information may be encoded outside of coding regions.
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
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...
AlphaGenome is out in @nature.com today along with model weights! 🧬
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
An NIH source tells me that after this story was published, agency leadership held an emergency meeting about Council approval and is looking for ways to speed up the pipeline.
"Better late than never?" the source says.
ICE has detained at least 3,800 kids under the second Trump administration — more than 500 of whom were under 5 years old.
Children shouldn't be locked up by our government.
"Senate Democrats will not provide the votes to proceed to the appropriations bill if the DHS funding bill is included,” Schumer said Saturday evening.
talkingpointsmemo.com/news/democra...
Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions
go.nature.com/4qu2ExZ
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
Excited to share our latest work in @ajhgnews.bsky.social 🧬📄
We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease.
www.sciencedirect.com/science/arti...
The conference (agreement between House and Senate) appropriations bill that includes HHS and NIH was released this morning.
www.appropriations.senate.gov/news/majorit...
1/5
How can we identify circRNAs that might be functional?
Together with @jengreitz.bsky.social, Howard Chang, and team, we found that answering this question is much more challenging than previously thought!
academic.oup.com/nar/article/...
See thread below:
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
Thinking about using Cas13 to screen for functional circRNAs?
Think again!
Thread coming soon
