Francisco De La Vega

Maybe a fitting place for it - next to the historical collection of eugenic journals and books that originated from this building.

You can still find it - inside the Carnegie building back staircase.

James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97

James Watson has died.
#giftarticle

www.nytimes.com/2025/11/07/s...

And in the meantime China is stating to block for some application purchase of foreign chips to bolster their home brew industry - at some time in the not too far future they will match capabilities and these controls will do more harm than good.

Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests.

We describe a critical concept that we call *specificity*.

Led by Jeff Spence and Hakhamanesh Mostafavi:

The elimination of USAID was an unforgivable moral atrocity that should haunt Trump, Elon Musk and Marco Rubio for the rest of their days and beyond

🤣

Very well put. However, how often most coding tasks require truly novel algorithm development outside of the academic arena? Often, the value of having a team member with a CS PhD is their ability to recognize that a problem being tackled has already being solved and applying the proper algorithm?

LLMs excel at programming—how can they be so bad at it? My explanation for the mystery of why LLMs can be both exceptionally good and quite terrible at programming.

I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them.
blog.genesmindsmachines.com/p/llms-excel...

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database - Nature Communications Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD),…

New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...

UnitedHealthcare Pays Optum Providers More Than Non-Optum Providers | Health Affairs Journal During the past several decades, physicians have transitioned from small, physician-owned practices to larger practices owned by corporations such as hospitals, private equity firms, and health insure...

UnitedHealthcare Pays Optum Providers More Than Non-Optum Providers www.healthaffairs.org/doi/abs/10.1...

I’ve spent many years explaining/defending biorxiv’s “no reviews” policy.

The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.

LLMs mean it makes even more sense 1/2

We’ve put up summary statistics for over 3,000 traits in the All of Us resource, and a shiny new browser alongside it! Explore your favorite gene or phenotype here: allbyall.researchallofus.org #ASHG24

Registration for BAPG 2025, Stanford Dec 6 2025

Bay Area Pop Gen conference Dec 6! One of my favorite conferences. Registration is free! Only controversy is how to pronounce BAPG (bap-guh is the right answer). docs.google.com/forms/d/e/1F...

PRSformer: Disease Prediction from Million-Scale Individual Genotypes Predicting disease risk from DNA presents an unprecedented emerging challenge as biobanks approach population scale sizes (N>106 individuals) with ultra-high-dimensional features (L>105 genotypes). Cu...

Delighted to see our method, PRSformer, at #NeurIPS2025! PRSformer is AI model for population-scale disease-risk prediction from individual genomes. It lays the groundwork for phenome-wide risk prediction.

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

Improving the Reliability, Quality and Maintainability of Bioinformatics Pipelines with nf-test. #NextFlow #Unitest #CodeTesting #Bioinformatics #Pipelines @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...

Three schematic diagrams. The first illustrates selective publishing of internal resection, the second selective causal focus, and the third selective access and funding for researchers.

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv.

There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

The Risks of Industry Influence in Tech Research Emerging information technologies like social media, search engines, and AI can have a broad impact on public health, political institutions, social dynamics, and the natural world. It is critical to ...

2. Here's the paper itself: arxiv.org/abs/2510.19894

And there was no abstract search tool this time.

The White House is asking people not to share pictures of the East Wing because it’s even worse today.

US PhD admissions shrink as fears over Trump’s cuts take hold Some doctoral programmes are admitting no students at all amid uncertainty about federal science funding.

Many US universities are reducing or pausing PhD admissions for 2026 due to uncertainty over federal science funding. This threatens to throttle the pipeline of future experts and may ultimately shrink the scientific workforce.
#AcademicSky

People with some cancers live longer after a COVID vaccine mRNA vaccines seem to boost the effectiveness of an immune therapy for skin and lung cancer ― in an unexpected way.

People with some cancers live longer after COVID vaccination 😮

mRNA vaccines can augment immune checkpoint inhibition efficacy for patients with skin or lung cancers - by globally boosting immune responses 💉🧪⚕️

www.nature.com/articles/d41...

Grippen et al study:
www.nature.com/articles/s41...

People with some cancers live longer after a COVID vaccine mRNA vaccines seem to boost the effectiveness of an immune therapy for skin and lung cancer ― in an unexpected way.

People being treated for certain deadly cancers lived longer if they had received an mRNA-based vaccine against COVID-19 than if they hadn’t

go.nature.com/4hkqZma

Autism diagnoses are on the rise – but autism itself may not be Autism is better known and diagnosed than ever before, leading to misconceptions that cases are skyrocketing.

Autism diagnoses are on the rise – but autism itself may not be bbc.com/future/artic...

Done!

So much for Catholic and Christian values

Images of the @nanoporetech.com party at #ASHG25 - going until 1AM!

Should they at least pay one cent to be compliant and not indenture?

My lightning talk on “Uncovering Genomic Diversity in the African Diaspora via Long-Read Nanopore Sequencing” will be presented at 1:45 PM in Room 206AB (Level 2). #ASHG25

#ASHG25 Short talks, instant gratification! Come and listen to the lightning talks today starting at 1:30 PM in Room 206AB (Level 2), “Scaling Precision Medicine” session.