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Vincent J Lynch 🐘🦣🦥 🦇🐋🐢🐍 @devoevomed.bsky.social · 3d

Viruses, just wow...

www.biorxiv.org/content/10.1...

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life

In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...

www.biorxiv.org

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Bryan White, MS Bio, MPH 🧬 @crvscience.com · 3d

Homie got 229 pairs of chromosomes

www.sciencedaily.com/releases/202...

This tiny butterfly has the most chromosomes of any animal on Earth

Scientists have confirmed that the Atlas blue butterfly carries the most chromosomes of any animal, with 229 pairs. Unlike duplication, its chromosomes split apart, reshaping its genome in surprising ...

www.sciencedaily.com

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Yun S. Song @yun-s-song.bsky.social · 16d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Yun S. Song @yun-s-song.bsky.social · 27d

SINGER, our ARG inference method, is finally published and freely available online:

doi.org/10.1038/s415...

It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics

SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.

doi.org

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Laura K Hayward @lkhayward.bsky.social · Aug 23

Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same

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Matthew Aguirre @aguirre404.bsky.social · Aug 22

Thrilled to share the second half of my PhD work here!

We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)

doi.org/10.1101/2025...

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Roshni Patel @roshnipatel.bsky.social · Aug 6

We'll primarily work at the intersection of statistical and population genetics, and we also have active projects related to the ethical and social implications of human genetics (ELSI). Please get in touch if that's a combination that sounds interesting to you!

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Roshni Patel @roshnipatel.bsky.social · Aug 6

Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.

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Jonathan Pritchard @jkpritch.bsky.social · Jul 29

Thanks! This is amazing! So the term 'Manhattan Plot' is not originally a GWAS term at all.

Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:

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Yun S. Song @yun-s-song.bsky.social · Jun 6

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io

Please help spread the news.

Home - ProbGen 2026

Your Site Description

probgen2026.github.io

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Jonathan Pritchard @jkpritch.bsky.social · Jul 28

Does anyone know who first used the term "Manhattan Plot"?

Wikipedia links to a 2010 paper by Greg Gibson. I haven't yet found an earlier use, but Greg's phrasing suggests that he did not invent the term.
doi.org/10.1038/ng07...

Hints of hidden heritability in GWAS - Nature Genetics

Although susceptibility loci identified through genome-wide association studies (GWAS) typically explain only a small proportion of the heritability, a classical quantitative genetic analysis now argu...

doi.org

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Jonathan Pritchard @jkpritch.bsky.social · Jul 26

Can anyone point me to full resolution versions of these classic images from NHGRI that show the growth of GWAS from ~2006--2015? I'm looking for the timelapse versions.
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)

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Hakhamanesh Mostafavi @hakha.bsky.social · Jul 25

I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!

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Hanbin Lee @epigenci.bsky.social · Jul 19

My talk from this year's probgen is finally out.

Where do linear mixed models and random effects come from?

They emerge from *mutations* on Ancestral Recombination Graphs.

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 18

Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1

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Molly Przeworski @mollyprz.bsky.social · Jul 16

New paper by Luke O'Connor
@lukeoconnor.bsky.social and Guy Sella @gs2747.bsky.social

bioRxiv Genetics @biorxiv-genetic.bsky.social · Jul 16

Principled measures and estimates of trait polygenicity https://www.biorxiv.org/content/10.1101/2025.07.10.664154v1

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Jonathan Pritchard @jkpritch.bsky.social · Jul 7

Staff scientist position (computational):

I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs

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Rachel Ungar @raungar.bsky.social · Jun 26

Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪

Rachel Ungar @raungar.bsky.social · Jun 2

Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪

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Sophie Jean Walton @sophiejwalton.bsky.social · Jun 20

Super excited for #Evol2025! I will be sharing some cool work on selection in the gut microbial communities at 9:30 am on Monday in the Evolutionary Ecology I session (Parthenon 2)!! Looking forward to chatting with folks as well!

Mueller diagram of ecological and evolutionary dynamics in a gut microbiome. Species fluctuate in abundance and accumulate new mutations. New conspecific strains also colonize from the global population.

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Anastasia Lyulina @alyulina.github.io · Jun 20

Looking forward to #evolution2025! I will be talking about how time-varying demography and selection shape the site frequency spectrum — Saturday at 4:15 pm, Population Genetics Theory IV. Come say hi if you are around!

A schematic illustrating the allele frequency trajectories that contribute to a slice of the site frequency spectrum.

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Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · Jun 8

🧵4/5 But are new pcQTLs relevant? We examined associations with GWAS for complex traits and diseases and found over 500 new colocalizations – a 34% increase over single-gene-based analyses! In fact, variants with distributed effects are more likely to be GWAS hits than those affecting just one gene

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Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · Jun 8

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

Standard methods are equivalent to a flashlight, looking at each gene independently. We combine signals from multiple genes, turning a floodlight onto the genome.

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Jonathan Pritchard @jkpritch.bsky.social · Jun 3

Congratulations Jeff! It's been really wonderful to have you in the lab! I cannot wait to see all the fantastic work that will come out of your future lab.

...and trainees, Jeff is an amazing scientist and mentor! If you ever have a chance to work with him you should seize it with both hands!

Jeff Spence @jeffspence.github.io · Jun 2

I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.

We'll work at the intersection of statistical genetics, population genetics, and machine learning.

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Jeff Spence @jeffspence.github.io · Jun 2

I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.

We'll work at the intersection of statistical genetics, population genetics, and machine learning.

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Jonathan Pritchard @jkpritch.bsky.social · Jun 1

I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.

Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.

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Jeff Spence @jeffspence.github.io · May 30

In any case, it’s useful to plug mechanistic models of how we think an experiment is perturbing the cell into the inputs of deep learning models. This lets us see if our deep learning model has learned a casual relationship that’s consistent with our understanding of the experimental perturbation.

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