Recently enjoyed creating an illustration about @yulinzhang.bsky.social’s and @aabiddanda.github.io’s exciting work in Science, out this week. Check out the write up from UC Berkeley News featuring my drawing and detailing the research! news.berkeley.edu/2026/07/30/n...

New technique pinpoints human DNA inherited from ‘ghost’ ancestors - Berkeley News

Neanderthals and Denisovans interbred with modern human ancestors, leaving behind telltale DNA in our genomes. Now we have evidence of modern human interbreeding with two much older but unknown ancest...

news.berkeley.edu

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...

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

New preprint on the effect of ancient admixture / structure on genealogical trees. I introduce a new way of summarising reconstructed genealogies that captures a clear signal of ancient gene flow into the ancestors of modern humans. Feedback welcome!

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 3w ago

The distribution of integer partitions in human genome-wide genealogies reflects gene flow from a super-archaic lineage https://www.biorxiv.org/content/10.64898/2026.07.14.738421v1

1/ The world's songbirds sing in just 8 basic sounds. And where a bird lives decides which ones it uses. My first PhD paper is out now in @science.org (www.science.org/doi/10.1126/science.aee6239) Here is what we found:

A fundamental question in disease ecology remains unresolved: How can an acute, immunizing virus persist in nature? Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer. www.biorxiv.org/content/10.6...

Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus

Canine distemper\---|a measles-like disease with high mortality and presently without a cure\---|poses a major threat to wild and domestic carnivores globally. Domestic dogs are generally considered t...

biorxiv.org

Wow! A fourth class of transmissible cancers. CONTAGIOUS FISH MELANOMA, discovered in Lake Memphremagog (Vermont / Quebec) 🎣 🧬 😷 www.nature.com/articles/s41... @uvmvermont.bsky.social

Brown bullhead catfish melanoma represents a novel transmissible cancer - Nature

Whole-genome sequencing analysis of tumour and matched non-tumour host tissues of the brown bullhead catfish reveals a type of naturally occurring transmissible cancer.

nature.com

How do transposons jump when they’re released from host control? I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs. Here’s what we found & excited to share my 1st postdoc paper: “piRNA loss unleashes episodic transposition bursts” www.biorxiv.org/content/10.6...

piRNA loss unleashes episodic transposition bursts

In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...

biorxiv.org

Scaling genetic clustering (ADMIXTURE/STRUCTURE-style unsupervised clustering) is now easy. Out in Bioinformatics, our ADAMIXTURE method clusters all of UK Biobank (500k genomes) in just over a hour with likelihoods as good as ADMIXTURE, which would take weeks. doi.org/10.1093/bioi...

ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering

AbstractMotivation. Estimating genetic clusters from sequencing data is a fundamental task in population and medical genetics, enabling demographic inferen

doi.org

The Bhangale Lab at Genentech is looking for a postdoc to investigate the genetic basis of neurodegenerative diseases (Parkinson's, ALS). This is an exciting opening for scientists wanting to work at the intersection of human genetics and machine learning: careers.gene.com/us/en/job/20...

Postdoctoral Fellow - Human Genetics, Bhangale Lab in South San Francisco, California, United States of America | Students & Graduates at Genentech

Apply for Postdoctoral Fellow - Human Genetics, Bhangale Lab job with Genentech in South San Francisco, California, United States of America. Students & Graduates at Genentech

careers.gene.com

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.

Just added a couple more job apps (thanks Rachel and Arun!) but if you've gotten a job in industry, academia (R1, PUI, whatever!) in the last 5 years or so, please consider submitting your job app materials to help other folks! github.com/RILAB/statem...

GitHub - RILAB/statements: Successful Job Applications and Grants

Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

github.com

Zero-shot predictions of mutational effects seem to work well in benchmarks but frequently fail in targeted protein engineering campaigns. Why is that? blog.genesmindsmachines.com/p/how-useful...

How useful are zero-shot predictions of mutational effects?

Zero-shot predictions are great, except for when it matters

blog.genesmindsmachines.com

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 am thrilled to share that UC Berkeley and UCSF have launched a joint initiative in Computational Biomedicine! cdss.berkeley.edu/news/uc-berk... We will soon be recruiting new faculty and postdoctoral fellows. Please repost to help spread the word.

UC Berkeley and UCSF Launch Computational Biomedicine Initiative

UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...

cdss.berkeley.edu

I talked about this at PEQG a few weeks ago. In addition to github.com/RILAB/argprep (preps your genome assemblies for SINGER), argtest github.com/RILAB/argtest does some QC to clean up an ARG estimated with SINGER.

I am incredibly thrilled to announce that I will be starting as an Assistant Prof at Yale EEB in January 2027!! 🎉🎊 Stay tuned for student and postdoc openings, and please feel free to reach out to me if you are interested in eco-evo, range dynamics, species interactions, and global change! 🌐🌱🦠🧬

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

biorxiv.org

The evolution of structural variation across 500 million years of vertebrate evolution https://www.biorxiv.org/content/10.64898/2026.06.26.733778v1

Just in time for #SMBE2026! Here's DEEP for detecting ghost/superarchaic introgression: scalable, robust, and no ARG! We find ~0.5% genome with superarchaic ancestry in East Asians and Oceanians, plus a notable signal at HLA Come find our poster tonight (#241)! www.biorxiv.org/content/10.6...

Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations

Ghost introgression from unsampled hominin lineages has emerged as an increasingly important component of human evolutionary history. Recent studies suggest that deeply divergent hominin lineages may ...

biorxiv.org

Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...

biorxiv.org

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

Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...

A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them

Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi

academic.oup.com

New preprint from the last portion of my PhD! Despite low masked load, we found evidence for strong inbreeding depression in Devils Hole pupfish. The reason? A recessive lethal haplotype that causes a heart defect among developing embryos. www.biorxiv.org/content/10.6...

Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis)

As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations a...

biorxiv.org

Great talk! Loved the elegant solution to trace and visualize population structure dynamics

Yun Deng@yundeng.bsky.social · 2mo ago

#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!