Francisco De La Vega
@ribozyme.bsky.social
Geneticist & Computational Biologist. CTO at life sciences company. Adjunct Professor at Stanford DBDS. All opinions are my own.
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in
the scientific literature and popular press. Mitchell et al. critically examine influential
studies underpinning these...
www.cell.com
November 15, 2025 at 5:15 PM
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Maybe a fitting place for it - next to the historical collection of eugenic journals and books that originated from this building.
November 9, 2025 at 8:21 PM
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.
November 9, 2025 at 2:50 AM
You can still find it - inside the Carnegie building back staircase.
Reposted by Francisco De La Vega
James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97
www.nytimes.com
November 7, 2025 at 8:02 PM
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.
November 7, 2025 at 6:55 PM
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.
Reposted by Francisco De La Vega
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:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 4:08 AM
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:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
Reposted by Francisco De La Vega
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
One analytical model shows that, as of November 5th, the dismantling of U.S.A.I.D. has already caused the deaths of 600,000 people, two-thirds of them children. https://newyorkermag.visitlink.me/jUzNSc
The Shutdown of U.S.A.I.D. Has Already Killed Hundreds of Thousands
The short documentary “Rovina’s Choice” tells the story of what goes when aid goes.
newyorkermag.visitlink.me
November 7, 2025 at 2:36 AM
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?
November 6, 2025 at 4:05 PM
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?
Reposted by Francisco De La Vega
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...
blog.genesmindsmachines.com/p/llms-excel...
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.
blog.genesmindsmachines.com
November 6, 2025 at 3:43 PM
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...
blog.genesmindsmachines.com/p/llms-excel...
Reposted by Francisco De La Vega
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...
A big step for precision medicine!
www.nature.com/articles/s41...
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),…
www.nature.com
November 4, 2025 at 3:06 PM
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...
A big step for precision medicine!
www.nature.com/articles/s41...
UnitedHealthcare Pays Optum Providers More Than Non-Optum Providers www.healthaffairs.org/doi/abs/10.1...
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...
www.healthaffairs.org
November 4, 2025 at 4:40 AM
UnitedHealthcare Pays Optum Providers More Than Non-Optum Providers www.healthaffairs.org/doi/abs/10.1...
Reposted by Francisco De La Vega
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
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
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 2, 2025 at 5:33 PM
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
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
Reposted by Francisco De La Vega
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
All by All
The All by All browser maps known and novel associations between genotypes and phenotypes using data contributed by All of Us Research Program participants as of July 1, 2022. All by All encompasses a...
allbyall.researchallofus.org
November 8, 2024 at 8:32 PM
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
Reposted by Francisco De La Vega
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...
Registration for BAPG 2025, Stanford Dec 6 2025
docs.google.com
November 2, 2025 at 2:59 AM
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...
Reposted by Francisco De La Vega
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 28, 2025 at 10:23 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Francisco De La Vega
Improving the Reliability, Quality and Maintainability of Bioinformatics Pipelines with nf-test. #NextFlow #Unitest #CodeTesting #Bioinformatics #Pipelines @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
October 25, 2025 at 5:05 PM
Improving the Reliability, Quality and Maintainability of Bioinformatics Pipelines with nf-test. #NextFlow #Unitest #CodeTesting #Bioinformatics #Pipelines @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Reposted by Francisco De La Vega
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.
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.
October 24, 2025 at 12:47 AM
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.
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.
Reposted by Francisco De La Vega
2. Here's the paper itself: arxiv.org/abs/2510.19894
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 ...
arxiv.org
October 24, 2025 at 12:47 AM
2. Here's the paper itself: arxiv.org/abs/2510.19894
And there was no abstract search tool this time.
October 22, 2025 at 7:42 PM
And there was no abstract search tool this time.
Reposted by Francisco De La Vega
The White House is asking people not to share pictures of the East Wing because it’s even worse today.
October 21, 2025 at 10:54 PM
The White House is asking people not to share pictures of the East Wing because it’s even worse today.
Reposted by Francisco De La Vega
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
#AcademicSky
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.
www.nature.com
October 22, 2025 at 5:56 PM
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
#AcademicSky
Reposted by Francisco De La Vega
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...
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.
www.nature.com
October 22, 2025 at 6:08 PM
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...
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...
Reposted by Francisco De La Vega
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
go.nature.com/4hkqZma
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.
go.nature.com
October 22, 2025 at 3:38 PM
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
go.nature.com/4hkqZma
Reposted by Francisco De La Vega
Autism diagnoses are on the rise – but autism itself may not be bbc.com/future/artic...
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.
bbc.com
October 18, 2025 at 10:31 AM
Autism diagnoses are on the rise – but autism itself may not be bbc.com/future/artic...