Francisco De La Vega

Notes from Beethoven’s genome Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇

RFK Jr. cuts $500 million in mRNA vaccine contracts, dealing major blow to promising area of research The cuts add to mounting evidence that Kennedy is pursuing an aggressive anti-vaccine agenda.

We need a word for someone who is beyond perverse, sadistic, sociopathic. Blocking mRNA vaccine research means that you or someone you love will die of something you could have avoided or survived. He is intentionally killing people.

“However, participation remained below cancer incidence rates for Hispanic/Latino and non-Hispanic Black patients, and was negligible among American Indian and Alaska Native populations.”

Lithium deficiency and the onset of Alzheimer’s disease - Nature Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level.

New @nature.com
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

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

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

The Platinum Pedigree offers a pedigree-derived benchmark for SNVs, indels, structural variants and tandem repeats. The resulting variant map will help validate sequencing workflows and support development of new variant callers.

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

Happy to pay twice for the excellent shows that are only available there, such as those Nova, Nature, and the Masterpiece productions.

Since this is a state school, I hope Newson goes to court to win and doesn’t fold like the private schools

one cool thing about Scandinavian countries with comprehensive public health insurance is places like Denmark can do a study on… everybody and conclude that yes COVID vaccines are safe

I just got an email informing me that my Annual Review on structural racism with @tyson-brown.bsky.social and @pahoman.bsky.social is open access. So, download away.

Faceted plot with panels for Atlanta, Pittsbrugh, and Houston. Focal counties (Dekalb, Alleghany, and Houston) are outlined. Surrounding counties are shaded by future estimated annual economic loss due to the proposed cap on indirect costs based on commuter flows that connect to a focal county (indicated by light pink outline).

#SCIMaP estimates current & future economic losses in local communities across the US (counties & Congressional Districts). We explain our approach in a new preprint: www.medrxiv.org/content/10.1...

(w @joshuasweitz.bsky.social @asinclair.bsky.social @cl10.bsky.social)

We have officially started #HitSeq track @hitseq.bsky.social at #ISMBECCB2025. Francisco de la Vega, introduces our first #keynote speaker Valentina Boeva @valboeva.bsky.social with her talk: "Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data"

We open our second day at #Hitseq @hitseq.bsky.social with our last key note speaker Tobias Marschall and his insightful talk about the human pangenome and the challenges for structural variation analysis. His work has focused on tackling current limitations such as sample size and remaining gaps

‘Genetic Risk Effects on Psychiatric Disorders Act in Sets’, the title of our new preprint on
@medrxivpreprint.bsky.social! This huge collaborative effort advances our understanding of psychiatric genetic architecture and emphasizes the importance of looking beyond additive effects. 🧵1/n; 🧪👩🏽‍🔬🧬

Structural variation in 1,019 diverse humans based on long-read sequencing - Nature Intermediate-coverage long-read sequencing in 1,019 diverse humans from the 1000 Genomes Project, representing 26 populations, enables the generation of comprehensive population-scale structural varia...

Another taste of the future of human genetics, also in @nature.com. Long-read sequencing in >1,000 humans across 26 populations shows how the approach can accelerate biological & medical research. Work led by @bernardo-rodriguez.bsky.social @trausch.bsky.social @tobiasmar.bsky.social & Jan Korbel.🧬🧪

Meet our second sponsor Oxford Nanopore @nanoporetech.com at @hitseq.bsky.social #ISMBECCB2025. During his talk, Mike Vella @vellamike.bsky.social takes us to the latest applications of machine learning methods to tackle one the most difficult challenges for long reads sequencing: base calling

🤔

How Trump Killed Cancer Research — WIRED Attempting to eliminate funding for certain kinds of “woke” studies, the Trump administration erased hundreds of millions of dollars being used for cancer research.

How Trump Killed Cancer Research apple.news/AGy9h5YrORry...

Having your dangerous, unscientific ideas heard and then rejected by the mainstream of public health does not equate to censorship of those ideas.

I have come across people unaware that people are still being hospitalised or even dying in the ongoing COVID pandemic, just as a century after the Spanish flu pandemic, people still die of influenza. Infections often exacerbate intercurrent illness. Get vaccinated

Long-read sequencing of trios reveals increased germline and postzygotic mutation rates in repetitive DNA https://www.biorxiv.org/content/10.1101/2025.07.18.665621v1

Polls are open! ISCB Members, cast your vote for President and Vice President by July 27. Sign in to your MyISCB account and hit “Vote Now”!

Imidazole propionate is a driver and therapeutic target in atherosclerosis - Nature Imidazole propionate produced by gut microbiota is associated with atherosclerosis in mouse models and in humans, and causes the development of atherosclerosis through activation of the imidazoline-1 receptor in myeloid cells.

Nature research paper: Imidazole propionate is a driver and therapeutic target in atherosclerosis

go.nature.com/44Te0SA

In challenging times for science, as we experience now, it’s more important than ever to come together, share advances across academia and industry, and advocate for the value of our work by showing its impact on society.

I want to thank our industry sponsors, Pacbio and Oxford Nanopore, who will be presenting talks on the latest applications and tools for their technologies. Their support helps fund travel fellowships for early career researchers.

On my way to #ISMB25 - @iscb.bsky.social We have a set of excellent keynotes, talks, and posters at @hitseq.bsky.social this year. See you at Liverpool!

YouTube video by PharmGKB PSB 2025 TERI Talk - Francisco De La Vega

🎥 Video of the talk available at YouTube: youtu.be/Hf5sZMZlcf0?...

These explorations run in parallel to my industry work—where we “eat our own dog food” to show how our tech helps customers and, hopefully, contributes to science. 3/4