How does human genetics research live in the information ecosystem? Is it misused? Misrepresented? In my paper with @sramach.bsky.social, we tackle this question with 25 years of Wikipedia data, AI chatbot responses, and pages from Grokipedia www.biorxiv.org/content/10.6...

From Wikipedia to AI: Measuring 25 years of synthesis of human genetics research in the public-facing information ecosystem

Genetics research frequently intersects with ethnicity, nationality, and race, making it uniquely vulnerable to misrepresentation. Yet, 25 years after the initial sequencing of the human genome, there...

biorxiv.org

Officially recruiting postdocs at GW. If you are interested in genetic novelty, structural variation, or evo genetics please get in touch! We have data sets on mulitple organisms with large population sizes (Drosophila, Megalonaias nervosa) and species in decline (fireflies, mussels, elephants).

Took my frustration with current OMB/OSTP proposals and turned it into an op-ed for my hometown newspaper! Here's my better-late-than-never contribution to the #McClintockLetters: herald-zeitung.com/opinion/morr...

MORRISON: Federal funding brought me from Canyon H.S. to cancer research – cuts threaten the next generation

Cuts to federal funding for American science are disrupting research, halting clinical trials, and imperiling the next generation of scientists. As a scientist and a proud graduate of Texas schools,

herald-zeitung.com

Very cool pair of papers demonstrating little link between amount of additive genetic variation and amount of nucleotide variation within species: journals.plos.org/plosbiology/... www.pnas.org/doi/10.1073/...

Levels of additive genetic variation vary substantially between species

Adaptive potential determines how populations respond to environmental change. This study compiles evolvability estimates from over 170 multicellular species, revealing substantial variation across th...

journals.plos.org

Good news! Our paper (with @aabiddanda.github.io @sarahaj34.bsky.social @codushlaine.bsky.social and Priya Moorjani) is now officially online! www.science.org/doi/10.1126/...

Recovering signatures of archaic hominin introgression using ancestral recombination graphs

Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unad...

science.org

Yulin Zhang@yulinzhang.bsky.social · 5mo ago

Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history! www.biorxiv.org/content/10.6...

@ihgatucsf.bsky.social and @ucsfstemcell.bsky.social are excited to inform you about the annual Genotech Symposium, taking place on 9/23. The goal is to foster collaboration and cross-fertilization between industry and academia in genetics and genomics. Hope to see you there! genotech.ucsf.edu

In this collaboration with the Gokcumen lab, @alberaqil.bsky.social developed a method based on interchromosomal linkage disequilibrium to detect false positive trans-eQTLs, showcased on GTEx and MAGE. The approach could be used to filter other trans molecular QTLs, which may be similarly impacted.

Gokcumen Lab@gokcumenlab.bsky.social · last wk.

New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social. Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives. authors.elsevier.com/c/1nWChgeXHnOF

The prestigious Miller Research Postdoctoral Fellowship is open! University of California, Berkeley This is a postdoc fellowship with substantial support and independence to be hosted at a lab at Berkeley, reach out with interests! miller.berkeley.edu/nominate-app...

Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...

biorxiv.org

Come and join our dream team! We’re recruiting a PhD candidate with a strong background in statistics, machine learning and (human) genetics to work at the interface of biological sequence foundational models and scores polygenic score methods.

The first articles for the new society-owned journal Population Biology Modeling & Theory are underway! We're accepting research articles and beyond - get in touch with us to discuss your ideas for submissions. pbmt.journals.sup.org/index.php/pbmt

Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/

An encyclopedia of human enhancer–gene regulatory interactions - Nature

An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...

nature.com

Had a great time at the #SIAM2026 in #Cleveland . Met colleagues, heard great talks, & gave a talk about "bounded environmental stochasticity drives secondary allee thresholds" based on recent JTB paper (see bsky.app/profile/seba...) Main conclusions shown below. More details in this thread. 1/n

Sebastian Schreiber @sebastianschreiber.bsky.social · 4mo ago

A paper plagiarizing my JTB article www.sciencedirect.com/science/arti... has been officially retracted in Physica A www.sciencedirect.com/science/arti... Grateful to the editors for taking this seriously. 1/3

How should we apply linear mixed models to populations under stabilizing selection? The first paper I wrote with my grad school advisor is published in Genetics. academic.oup.com/genetics/adv... 1/n

Save the date! The next SMTPB conference will take place May 3-6, 2027, at Stanford University. Make sure you're on the mailing list to stay in the loop for updates - reach out to info@smtpb.org.

I just followed this advice to comment on the OMB rule changes. There are about 3 hours left before the deadline (tonight at 11:59p EDT). If you benefit from US Government-funded research make sure to get your comments in. elizabethginexi.substack.com/p/what-we-ne...

What We Need to do NEXT: OMB’s Proposed Federal Financial Assistance Rule (OMB-2026-0034)

What OMB’s Proposed Federal Financial Assistance Rule Means in Practice

elizabethginexi.substack.com

For the last 5 years, my lab has focused on developing mutational scanning methods and learning how to answer specific questions in protein biology. @matthewkhoward.bsky.social and I wrote a review on experimental decisions and future directions for our nascent field! doi.org/10.1146/annu...

Mechanistic Mutational Scanning to Uncover the Secret Life of Proteins

Deep mutational scanning (DMS) has emerged as a transformative tool for dissecting individual protein function and broader cell biology. DMS methods enable comprehensive interrogation of sequence–func...

annualreviews.org

It was a lot of fun working with @nikhilmilind.dev and @jeffspence.github.io on this paper about how gene dosage relates to traits (and resolving a nice paradox along the way). Thanks Craig Smail for a great Preview article!

Jeff Spence@jeffspence.github.io · 4w ago

Craig Smail wrote up a really nice Preview of @nikhilmilind.dev's paper where we try to explain why large effect variants tend to affect traits in the same direction on average, which we think about in terms of the non-linearity of gene dosage response curves. www.cell.com/cell-genomic...

Craig Smail wrote up a really nice Preview of @nikhilmilind.dev's paper where we try to explain why large effect variants tend to affect traits in the same direction on average, which we think about in terms of the non-linearity of gene dosage response curves. www.cell.com/cell-genomic...

Gene dosage differences and non-linear impacts on complex traits

Large differences in gene dosage are usually associated with opposite phenotypic effects but show a bias toward one direction in aggregate genome wide. Milind et al. suggest that this is explained by ...

cell.com

I think this work really underscores that we are at a turning point in human genetics. There is a growing consensus that doing good research in human genetics requires an expanded skillset (including, e.g., one that can navigate the relationship between genetics, ancestry, and pop descriptors) (1/)

Jayati Sharma, PhD, ScM@jayatirsharma.bsky.social · 4w ago

In what has been a labor of love & joyful collaboration, we are super excited to share our preprint on recommendations towards the ethical and accurate use of population descriptors generated from a survey by trainees, for trainees. www.biorxiv.org/content/10.6...

In what has been a labor of love & joyful collaboration, we are super excited to share our preprint on recommendations towards the ethical and accurate use of population descriptors generated from a survey by trainees, for trainees. www.biorxiv.org/content/10.6...

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this ...

biorxiv.org

Really incredible work from the Tcheandjieu Lab that finally helps us to decipher what is going on at the 9p21 locus and its association with coronary disease on different ancestral backgrounds. www.cell.com/ajhg/fulltex...

Linkage disequilibrium and allelic heterogeneity explain variation in coronary artery disease risk at 9p21 across populations and reduced effect in Africans

Using cross-ancestry fine-mapping across global and local ancestry groups, this study dissects the 9p21.3 coronary artery disease locus and shows how ancestry-specific haplotype structure shapes assoc...

cell.com

I know it seems like a heretical idea, but one way to figure out if a preprint is really interesting (to you) is... to read the preprint. Then, in the spirit of sharing, send a note to authors: a simple kudos or a more detailed question. I do this a dozen times a year. It's awesome. Try it.

Genoio has a v0.2.0 release. Performance is better across the board, beating most other libraries or matching highly performance ones (but with a single interface in Python now). Check it out mancusolab.github.io/genoio/

Super interesting work by @jonj-udd.bsky.social and @jeffspence.github.io is now out in Genetics!

Jeff Spence@jeffspence.github.io · last mo.

Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...

Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes

Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred

doi.org

JIT 4 summer, the latest preprint from our lab, brilliantly led by @kaitezhang.bsky.social w/ support from Collepardo lab (@juliamaristany.bsky.social / @janhuemar.bsky.social). www.biorxiv.org/content/10.6... describes a new single-molecule epigenomic method, & discoveries it enables ... (1/n)

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

Nucleosome spacing influences higher-order chromatin fiber organization in vitro but how this relates to cellular chromosome structure remains contentious. To address this, we developed Ligation Analy...

biorxiv.org

Come see my poster tn! For 3 yrs, populations evolved at 43 sites worldwide. I built kMate, an alignment-free, pangenome k-mer method to track SNP & SV frequencies across space & time, opening the door to accurately and efficiently mapping climate-adaptive variants on evolution experiments! #PEQG26

#PEQG26 folks! I will be presenting my postdoc project with @jkpritch.bsky.social and @jeffspence.github.io about inferring population structure dynamics over time with tensor decomposition on ARG. The talk will be at the James Crow Talk session on Wednesday. Look forward to seeing everyone there!

got my concluding slide on challenges with estimating ancestral recombination graphs ready for PEQG