Jeff Spence
@jeffspence.github.io
980 followers 730 following 86 posts
assistant professor at ucsf interested in genetics, statistics, etc… jeffspence.github.io
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Reposted by Jeff Spence
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by Jeff Spence
Hi #ashg2025! Lookin forward to another exciting event! If any trainee would like to chat, either about career advice or submitting their work to @hggadvances.bsky.social pls don't hesitate to reach out!
Reposted by Jeff Spence
I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.
Reposted by Jeff Spence
We have a postdoc position in my team. Join us if you are passionate about genomics, human genetics, synthetic biology and agentic AI!

careers.gene.com/us/en/job/20...
Reposted by Jeff Spence
📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).
Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications
This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.
www.nature.com
This was such a fun read 🤯🤯🤯
Reposted by Jeff Spence
This paper is bananas and shows there is still so much to be learned about gradient descent behavior. [ODEs are so hot right now]

centralflows.github.io
Understanding Optimization in Deep Learning with Central Flows
centralflows.github.io
Reposted by Jeff Spence
Do check out our new manuscript, now out in G3 on modelling theoretical expectations of ghost introgression in sampled genomes. Just in time for Halloween! 🎃 👻
New in #G3journal: @arunsethuraman.bsky.social et al. describe biases in summary statistics, such as genetic differentiation, diversity, Tajima’s D, and estimates of theta, migration rates, and divergence for understanding genomic signatures from extinct ghost populations. buff.ly/7fGnPXj
Reposted by Jeff Spence
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:

1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs

bsky.app/profile/bior...
Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
Reposted by Jeff Spence
Fine-tuning sequence to function deep learning models on large-scale proteomic data improves the accuracy of variant effect prediction https://www.biorxiv.org/content/10.1101/2025.09.26.678908v1
This should be the “Methods number” for a paper! Like an “Erdős number” or a “Bacon number”. Some papers might have lower Erdős numbers than Methods numbers!
Reposted by Jeff Spence
Any academic folks on H1B visas (even with stamps in passports) please get legal advice from your University attorneys before leaving the US.
Reposted by Jeff Spence
/2 OUTRAGEOUS! Fri. afternoon (night in most of the US), providing less than 25 hr notice of a BIG new fee. Looks like it is not just new post-docs but those who are now overseas. (Note—our academic year starts Monday.) "If you have an H-1B visa & are outside the U.S., you must return immediately"
Reposted by Jeff Spence
OH NO!
"The White House issued a proclamation today, Sept. 19, 2025, around 4:36 PM PDT imposing a $100,000 fee for each H-1B visa holder who enters the U.S. after Sept. 21, 2025, 12:01 AM EDT. In CA, this will take effect tomorrow, Sept. 20, 2025, at 9:01 PM PDT." Emergency notice at Stanford.
Reposted by Jeff Spence
My team has a postdoc position available now, join us!

careers.gene.com/us/en/job/20...
Reposted by Jeff Spence
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:

The E2G Portal! e2g.stanford.edu

This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.

Uses cases 👇

1/
Reposted by Jeff Spence
New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT
Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
Faculty Recruitment
chemh.stanford.edu
Very cool! Do you have a link to the paper?
Reposted by Jeff Spence
SINGER, our ARG inference method, is finally published and freely available online:

doi.org/10.1038/s415...

It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org
Reposted by Jeff Spence
SINGER is a fantastic method for ARG Inference and based on some of the analyses I've seen definitely the best trade off between accuracy and sample size
SINGER, our ARG inference method, is finally published and freely available online:

doi.org/10.1038/s415...

It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org