Jonathan Pritchard

Good work (and good luck)

Wildlife group sues to protect rare bird in coastal Virginia, North Carolina The population of Wayne’s warblers, which rely on wetland forests, has precipitously declined in recent years.

Based on genetic work from our lab .. let’s go! 🦉🧪

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

Stanford researchers help trace ancestry for African Americans A group of Stanford researchers is offering a mathematical model to help link family connections up to 410 years ago.

Excited that our work was featured on the local (Bay Area) news for their Black History month series. Interview with Noah and clips from my interview with @dornsife.usc.edu and CGSI talk in the article below

www.nbcbayarea.com/discover-bla...

Up to what degree of interspecific genetic distance is it possible to form viable and fertile hybrids? A strange species of paramecium breaks the record:

www.biorxiv.org/content/10.6...

Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King Abstract. The Human Genome Diversity Project (HGDP) began in 1991 as an initiative to study genetic variation from human populations worldwide. In 2002, th

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

Ancestry and somatic profile indicate acral melanoma origin and prognosis - Nature Analysis of the somatic and transcriptomic profile of 123 acral melanoma samples from Mexican patients helps understand tumour origins and prognosis, and highlights the importance of including samples...

We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️

www.nature.com/articles/s41...

Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n

What's your sense of how many genes are affected by this mechanism? It seems this could in principle act on heterozygous LoF mutations to upregulate the second copy of the *same* gene. But I don't think that can be a strong & widespread effect, based on LoF analyses that we have done over the years.

Thanks for sharing. Very cool paper!

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

that is so awesome!

I am excited to share our latest preprint showing that systemic hypoxia suppresses solid tumor growth: www.biorxiv.org/content/10.6...

This has been a tremendous collaborative effort in the labs of Isha Jain @ishahjain.bsky.social and Hani Goodarzi @genophoria.bsky.social.

🧬 New preprint alert! After years of collaborative work across 52 datasets we are presenting eQTLGen phase 2: a genome-wide eQTL meta-analysis covering 43,301 blood samples: www.medrxiv.org/content/10.6... (1/8)

This promises to be a fantastic new meeting at the intersection of human genetics and modern high-throughput functional genomics.

I'm thrilled to be heading back to the always-wonderful Biology of Genomes conference this year. Hope to see many of you there!

A figure depicting continental drift from when Gondwana existed to present day, with continents and countries colored according to the ratite species that occur or occurred on them. Next to that is a cartoon of a phylogeny that we would expect support for if continental drift explained patterns of species occurrence and relatedness. And next to that is a cartoon of the phylogeny supported by the genetic data presented in this paper, which demonstrates that closely related species must have traveled great distances after Gondwana broke up, after which flightlessness evolved, and that this happened more than once.

This paper is a great for teaching phylogenetic trees.

"Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution"

Clearly written. It discusses hypotheses of relatedness among species via continental drift vs genetic data. 🧪

www.science.org/doi/10.1126/...

Preprint: Genome-Scale Perturb-Seq in Primary Human CD4+ T Cells Maps Context-Specific Regulators of T Cell Programs and Human Immune Traits
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social

Plot of modeling new NIH grants after a switch to 100% MYF. There is a large drop in grants in the first year with a gradual recovery over 5 years.

There is a lot of talk lately about multi-year funding (MYF) at NIH. This is mostly a paperwork issue, but it can have a dramatic impact on the number of grants that get funded. I was curious how this would impact grant numbers over time, so I did some simple modeling. 1/n

Three years ago, we showed ~70% of lifespan variation in yeast traces to rDNA copy number. Ribosomal DNA, encoded as 5S and 45S subunits in hundreds of copies, vary substantially across humans. Does this copy number variation, and sequence variation within these paralogs, matter for humans?

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

Pentatomidae - Wikipedia

Looks like some kind of shield bug. Stick it on iNaturalist.
en.wikipedia.org/wiki/Pentato...

Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.

Congratulations!

A cat holds a passerine bird between its teeth. Source: https://www.sgeseller.shop/?path=page/ggitem&ggpid=97865

Chu et al. (urls.fr/Yeo6-K) estimate that cats kill ~60 million birds per year in Canada (possibly up to 197 M). Outdoor cats pose a serious risk to native birds. Potential responses include bylaws, education, social engagement, and trap-neuter-release programs. Think about it if you own a cat 🧪🌿🌎🦉🦊

Thanks for pointing us to your paper! cc: @nikhilmilind.dev @peter-gerlach.bsky.social

Clever use of proteomic data to stress-test TWAS and QTL colocalization methods, revealing a high false sign rate. This hypothesis about high-LD and cross-tissue confounding is particularly interesting:

thanks, that's very kind of you to say!

New preprint alert: we use sign errors as a test of how well TWAS works.

Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...

Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025