@jeffspence.github.io
assistant professor at ucsf interested in genetics, statistics, etc…
@stairwaytokevin.bsky.socialReposted by @jeffspence.github.ioNew work to share! Pangenome studies treat gene presence/absence independently, but genes work together in pathways. By focusing on the covariance of gene loss, we show the Arabidopsis dispensable genome has modular co-evolutionary structure reflecting the biological organization of the plant 1/
@jeffspence.github.ioI've always wondered about that. I guess it reduces the amount of trust one needs from needing to trust the whole argument to just entrusting that the theorem statement was encoded correctly into Lean. And it's an interesting point that it could be a different proof in Lean than what's in the text.
@deboraycb.bsky.socialReposted by @jeffspence.github.ioNow that it's officially out, I have to say I'm quite proud of this work🙂 I got involved in it after a bit of a failure in another proj. Took way longer than it could. Started pregnant, published close to baby's 3rd bday😅 Very grateful for my patient mentors and collaborators
doi.org/10.1093/molb...
@epigenci.bsky.socialReposted by @jeffspence.github.ioWe then applied the theory to human demography and deduced a provisional estimate of stabilizing selection in humans accounting for LD. The key machinery is Roshni Patel's conditional frequency spectra. With SDEs, this becomes a PDE scheme.
@epigenci.bsky.socialReposted by @jeffspence.github.ioWe studied the evolution of genome-wide linkage disequilibrium and its influence on genetic architecture with genetic drift. We found that the Bulmer effect is population size and demography dependent. For nerds: genetic architecture follows from solving PDEs.
@roshnipatel.bsky.socialReposted by @jeffspence.github.ioSo excited about this work with @nasalab.bsky.social! Led by Stephanie Gogarten & with help from @daphmarts.bsky.social, we use LLMs as judges to evaluate the use of population descriptors in the entirety of the GWAS Catalog (~4,000 papers published 2007-2025) www.biorxiv.org/content/10.6...
@rdhernand.bsky.socialReposted by @jeffspence.github.ioThe BMI PhD program @ucsanfrancisco.bsky.social is recruiting!
Want to use computing to advance our understanding of biology and disease?
Virtual Info Session: Tue 10/27, 1-2pm PT.
Learn about our research, our approach to training, and what makes a strong app!
Register: tiny.ucsf.edu/BMI2026
@benoitbruneau.bsky.socialReposted by @jeffspence.github.ioHappy Pluripotency Day! #Oct4
@chriscrsmith.bsky.socialReposted by @jeffspence.github.ioI'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! We're a computational lab working on spatial demographic inference using genomic data and machine learning. You can apply here: indiana.peopleadmin.com/postings/34508
@masakanai.bsky.socialReposted by @jeffspence.github.ioOur single-nucleus immune multiome atlas is now out in @nature.com! 🧬
10M PBMCs from 1,108 @finngen.bsky.social donors recruited by Finnish Blood Service, profiled at @broadinstitute.org with chromatin accessibility and gene expression in the same nuclei, to trace how disease variants act 🧵👇
@ellenleffler.bsky.socialReposted by @jeffspence.github.ioMy department at University of Utah is recruiting new faculty, with "Human" and "Genetics" broadly defined. It is a fantastic place to start a lab, with collaboration, creativity and conviviality encouraged. Applications due Oct 16. Please share and apply!
utah.peopleadmin.com/postings/208...
@genetics-gsa.bsky.socialReposted by @jeffspence.github.ioThe September issue of #GENETICS features work from @jonj-udd.bsky.social, @jeffspence.github.io, & Co which determines how genes associated with human recessive disorders fit the predictions of the classic theory of mutation–selection balance.
@ihgatucsf.bsky.socialReposted by @jeffspence.github.ioWe invite you to join our seminar at UCSF Mission Bay campus with @ygilad.bsky.social from the University of Chicago
humangenetics.ucsf.edu/ihg-seminar-...
@tombooker.bsky.socialReposted by @jeffspence.github.ioI’m keen to share this preprint. There is growing evidence that associative overdominance leads to the maintenance heterozygosity and we wondered how this would affect variance for traits under stabilizing selection:
@yun-s-song.bsky.socialReposted by @jeffspence.github.ioPlease help spread the word! We are recruiting multiple Postdoctoral Fellows as part of the recently launched Bakar Computational Biomedicine Initiative (BCBI) at UC Berkeley and UCSF.
BCBI website: bcbi.berkeley.edu
Apply by Nov 1, 2026: berkeley.infoready4.com#freeformComp...
(1/n)
@mexpositoalonso.bsky.socialReposted by @jeffspence.github.io📣 We are looking for a PhD student in 2027!
Interested in studying rapid evolutionary dynamics of species in changing climates?
Apply to the MOI LAB by Nov 19!
Flyer below & tinyurl.com/flyerphdmoilab
@ucberkeleyofficial.bsky.social
@innovativegenomics.bsky.social
@hhmi-science.bsky.social
@jeffspence.github.ioNot a blog post, but @yundeng.bsky.social and co. convincingly showed (IMO) that it was a statistical artifact here: academic.oup.com/genetics/art...
@adamauton.bsky.socialReposted by @jeffspence.github.ioWhat can we learn about a single rare variant? Published today in Science: the 23andMe Research Institute and Dana-Farber studied the EGFR T790M in 10.1M 23andMe research participants. The variant has OR = 25.2 for lung cancer, rising to 61.7 in never-smokers(!). 🧵
@mollyprz.bsky.socialReposted by @jeffspence.github.ioWork by Matin Saeidi and @will-milligan.bsky.social modeling mutator allele dynamics in humans, and asking what types of mutators we should expect to find by surveying offspring in trios.
@biorxiv-genomic.bsky.socialReposted by @jeffspence.github.ioPRDM9-mediated meiotic hotspot specification is constrained in humans despite extensive sequence diversity https://www.biorxiv.org/content/10.64898/2026.09.10.750150v1
