Who's who?
11.03.2026 15:45
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Who's who?
We invite you to join our seminar at UCSF Mission Bay campus with Paul Norman from @cuanschutz.bsky.social
humangenetics.ucsf.edu/ihg-seminar-...
📣New from Kumar & co!
📄MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes
🖥️ github.com/karinkumar/M...
Nice to see this out! Great work by Kiran Kumar and Sebastian Zöllner!
Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!
Connecting to some recent threads here:
Finally, today's offering! www.biorxiv.org/content/10.6...
This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social
My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs https://www.biorxiv.org/content/10.64898/2026.02.26.708346v1
My lab is seeking to co-hire another postdoctoral fellow with the @shaonsengupta.bsky.social team. See details below!
careers.chop.edu/us/en/job/10...
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
Two post-doc post in ARG space and loads of internal and external collaboration
Postdoctoral Research Associate in quantitative genomics
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Postdoctoral Research Associate in quantitative genetics and breeding
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Super cool to see more nuanced models of heritability and genetic architecture for medically relevant definitions.
postdoc recruitment still open!
Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...
The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action:
Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...
The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io
Our Perspective paper "Toward informed batch correction for single-cell transcriptome integration" is out now in Nature Computational Science! 📄✨
We review a decade of batch-correction methods and propose a move from "blind" integration to "informed" modeling. 🧵👇 🔗 rdcu.be/e4cSp
I used my JAX-based skills for codex to port the excellent Python3 LDSC spec to JAX and Polars.
My intent here was to stress test my JAX skill definitions and find how I could improve rules and contexts--NOT to develop a replacement github.com/mancusolab/j...
Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!
Buscamos una/un postdoc entusiasta y motivada para unirse al grupo de Paleogenómica y Biología Evolutiva en @liigh-unam.bsky.social para liderar un proyecto enfocado a muestras humanas prehispánicas. Interesadxs por favor enviar CV y carta de intención a fsanchez@liigh.unam.mx. Por favor #RT.
(Observation 3) Qualitative trends of portability can depend on the measure of prediction accuracy used. For some traits our measure of group-level prediction accuracy often drops where at the individual level, it increases.
(19/27)
Relatedly, some cool recent work from @roshnipatel.bsky.social, Jeffrey Spence, @jkpritch.bsky.social et al. dives deep into expectations, based on models of natural selection, for allele frequency in a group B conditional on allele frequency in group A.
academic.oup.com/genetics/art...
(16/27)
(Observation 1) Previous work suggested genetic distance from the GWAS sample largely explains variation in PGS performance. However, what we see empirically is that prediction accuracy is extremely noisy at the individual level.
(5/27)
Our work on the generalizability of polygenic scores (PGS) from the @arbelharpak.bsky.social Lab is now officially out!
We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.”
rdcu.be/e0LAr
(1/27)
The number of people arguing, following the #NeurIPS2025 case, that a bit of systematically bad scholarship and borderline academic misconduct is OK because doing things the right way is tedious and time-consuming is concerning.
Yes, doing things well might be boring. But doing them badly is... bad
1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...
Choice of phenotype scale is critical in biobank-based GxE tests https://www.biorxiv.org/content/10.64898/2026.01.20.694695v1
Balancing selection maintains some remarkable biological diversity, but detecting it from genomic data alone can be tricky. This may bias our view of its true prevalence. We investigated what makes balancing selection more or less detectable in genomic scans. + in thread & preprint!
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
