🗓️📍Save the date for UCSF PROPEL’s 6th Annual Symposium on June 1st!! 🧑‍🔬🧫Come support and celebrate our scholars as they present research talks and posters! We look forward to seeing you there!

My goodness SF is beautiful. I had never seen a night rainbow before!!! #doLookUp

Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...

David Botstein has passed away. A true pioneer in the genetics and biotechnology industry, known methods to map genes. While at Stanford he collaborated with Pat Brown in microarrays, co-founded the Gene Ontology and became the CSO of Calico. He worked again with Pat Brown at Impossible Foods. RIP.

1. Kevin Gross and I have a new paper out today PLOS Biology. We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

"In particular, these models highlight a pernicious feedback loop: increasing submissions to top journals exhausts the pool of suitable peer reviewers, resulting in lower quality peer reviews that encourage yet more authors to take a chance on submitting their paper to a prestigious venue."

www.biorxiv.org/content/10.6... Glad to see this paper out. I attended Prof. Gürsoy's talk during last year's probgen and the claims were scary. You can literally reverse-engineer GWAS summary statistics and public single-cell RNA-seq data to identify subjects.

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza. Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

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...

🚨 Proud to share that our paper on the genetic links between type 2 diabetes (T2D) and hypertension is now published in @natcomms.nature.com! We dissect the genetic relationship between T2D and hypertension and show it is not driven by a single shared pathway. 🧬 (1/N)

academic.oup.com/genetics/adv... #histbio #hps

My colleagues at @sfsu.bsky.social used 3 decades of data to show that students with low undergrad GPA have equal PhD completion rates compared to students with high GPA. @sfstatebio.bsky.social journals.plos.org/plosone/arti...

Sad. We are a country in decline www.chronicle.com/article/has-... #gradschool #phd

So excited to have this study live! Lead by @ee-reh-neh.bsky.social's teram and in collaboration with an incredible team at MRIN in Indonesia. This is the culmination of ~5 years of work including a ton of effort in the field. Really proud of how this came together! www.biorxiv.org/content/10.6...

Very nice work led @drghawkes.bsky.social, showing convergence between rare and common genetic associations, using whole-genome sequencing data to evaluate the contribution of rare non-coding variants for commonly studied anthropometric traits 🧪🧬 www.nature.com/articles/s41...

Science Bluesky is now much better than Science Twitter is… but I still miss peak pre-pandemic Science Twitter.

My daughter Maya, who had to wear a scoliosis brace for 2 years, wants to connect with other teens who live with invisible diseases. www.under-the-iceberg.com/about

“Success in US science has come from sustained funding and welcoming the best talent from around the world, yet both of these advantages are in decline” www.science.org/doi/10.1126/...

We are in the middle of MCB graduate admissions interviews. It has renewed my sense of hope—there are so many bright, empathic and resilient young people ready to help advance knowledge and make a difference.

It took scientists 11 years to compute 1-2/3=1/3

Balancing selection alert!! 🧬🧪 New preprint where we try to quantify how likely (or rather, unlikely) it is for balancing selection to maintain stable polymorphism, and how easy (or rather, challenging) it is to identify its signatures in genomes. #Popgen #MolecularEvolution #EvoBio #Science

A new preprint from the lab, with postdoc @deboraycb.bsky.social and collaborators @aidaandres.bsky.social and Tim Connallon: “Characterising the detectable and invisible fractions of genomic loci under balancing selection” www.biorxiv.org/content/10.6...

Hey MD/PhD-bound Scholars 👋 Prepare for MSTP Program applications with PROPEL! This is an opportunity you don't want to miss! 📆 Feb 6 – Sign up for AMCAS essay reviews by MSTP grad students (QR code) 📆 Feb 13 – Submit essay draft for review 📆 Feb 20 – Receive Feedback

PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5! *Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.

The meeting will take place at the gorgeous IslandWood Resort on Bainbridge Island, a short ferry ride from downtown Seattle. Registration is free. We will cover travel and lodging for graduate students, and at least partially subsidize those costs for postdocs and assistant professors.

Excited to share our new preprint from the @arbelharpak.bsky.social Lab! How do recruitment into genetic studies and study characteristics impact what we infer about the genetic bases of traits, and what are the consequences? (1/21) www.biorxiv.org/content/10.6...

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

Here's my latest contribution to the @nytimes "Lost Science" series. Brenna Henn's sweeping study of African genetics has been frozen. Gift link: nyti.ms/3Ypmm1A

Oh come on… it is January SECOND. Who ALREADY broke our cluster?? #Wyntoff

This story is heartbreaking. Brenna Henn is a wonderful scientist, and the work their lab does is truly insightful. Anger and rage… www.nytimes.com/2026/01/02/s...

I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post: substack.com/home/post/p-...

Putting on my hat as @asn-amnat.bsky.social ASN President for a minute for a string of announcements, please share widely!!! 1. Student research awards are open for applications, to fund research expenses for 10 graduate students ($2000 each) nam10.safelinks.protection.outlook.com?url=https%3A...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

What a beautiful paper! www.nature.com/articles/s41...

Our latest preprint revisits the classic model of mutation-selection balance. Do human recessive genes fit Haldane's 100-year old model? This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io www.biorxiv.org/content/10.6...

Normalization of glucose in people with prediabetes, i.e. achieving remission, is linked to halving of major cardiovascular adverse events over ensuing decades www.thelancet.com/journals/lan...

Faculty at OHSU, UIowa, UCSF, UW–Madison, and VCU: Your next amazing mentee could be one 10‑minute conversation away. PROPEL Virtual Matchmaking Event is Jan 30: 9–1 PT. Faculty registration deadline extended to 5pm PT on Wed Dec 10: propelscholars.org/matchmaking-...

"Prebunking works by exposing people to the techniques used to create misleading arguments before they encounter them in the wild."

Amazing to be at the #CAGI7 conference. As a data PRODUCER, no less! Fascinating discussions about variants of unknown significance, and how to get rid of them. Sad they are almost always acronymized as VUS, and only once was it VOUS.

My quote of the day The probability that we may fail in the struggle ought not to deter us from the support of a cause we believe to be just. Abraham Lincoln

A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...

Did you publish with researchers outside your lab during grad school? Or published as faculty with a student not under your supervision? I’m collecting examples of cross-lab collaboration in graduate training. Please share your experience & this post! Repository: bit.ly/4pT66BE

The era of coding agents is here. How do we approach this as scientists? Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science. www.youtube.com/watch?v=Rbhs...

"I love Slate! Everything is so intuitive and seamless!!" - No grad program director or program manager I've ever met... For those who attempted to submit your apps to PhD programs and have gotten strange errors, my apologies for the added stress... Folks are working hard to resolve issues!! 🤞🏽

I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...

It's the home stretch teaching undergrad Evolutionary Genetics with @aneil-agrawal.bsky.social using my Primer of Mol Pop Gen text! Grateful it's free for all 67 of our students courtesy @uoftlibraries.bsky.social LMK if you use it and suggestions for improvements! global.oup.com/academic/pro...

Reminder to everyone - mental health issues and depression generally do not just magically go away - it is important to be vigilant if you or ones you love have or are going through such issues www.espn.com/nfl/story/_/...

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

PROPEL builds community in science! Hear directly from our scholars at our 5th annual PROPEL Symposium!

For the first time in my career, I can’t tell people to trust what the CDC website says. And that is an incredibly sad and devastating place for this country to be.