Manuel Rivas
@mrivas03.bsky.social
Stanford professor. Interested in human genetics, AI, statistical modeling, entrepreneurship.
https://rivaslab.stanford.edu
https://rivaslab.stanford.edu
🧠 Mind Reading Meets Data Science
In this post I explore how statistical learning and wavelet methods can help decode brain wave patterns to predict thoughts — turning neural waves into words, images, and videos.
mrivas.su.domains/gbe/uncatego...
In this post I explore how statistical learning and wavelet methods can help decode brain wave patterns to predict thoughts — turning neural waves into words, images, and videos.
mrivas.su.domains/gbe/uncatego...
November 9, 2025 at 6:26 PM
🧠 Mind Reading Meets Data Science
In this post I explore how statistical learning and wavelet methods can help decode brain wave patterns to predict thoughts — turning neural waves into words, images, and videos.
mrivas.su.domains/gbe/uncatego...
In this post I explore how statistical learning and wavelet methods can help decode brain wave patterns to predict thoughts — turning neural waves into words, images, and videos.
mrivas.su.domains/gbe/uncatego...
Reposted by Manuel Rivas
I’m in Oxford this Monday and Tuesday (morning). Looking forward to seeing many old friends and colleagues… and hopefully meet some new ones! talks.ox.ac.uk/talks/id/b6e...
Genetic prediction and multi-omics: Towards disease prevention
The last 10 years have seen the emergence of predictive models based on genetics which quantify an individual’s genetic predisposition for a specific trait or disease. In this talk, I will present our...
talks.ox.ac.uk
November 2, 2025 at 8:49 PM
I’m in Oxford this Monday and Tuesday (morning). Looking forward to seeing many old friends and colleagues… and hopefully meet some new ones! talks.ox.ac.uk/talks/id/b6e...
Reposted by Manuel Rivas
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 Manuel Rivas
Joint Spherical-Harmonics Regression for PheWAS: Global Maps, Residual Localization, and Spherical-Cap Enrichment https://www.biorxiv.org/content/10.1101/2025.10.27.684843v1
October 28, 2025 at 6:33 PM
Joint Spherical-Harmonics Regression for PheWAS: Global Maps, Residual Localization, and Spherical-Cap Enrichment https://www.biorxiv.org/content/10.1101/2025.10.27.684843v1
Reposted by Manuel Rivas
Eric Green is out as head of National Human Genome Research Institute
www.statnews.com/2025/03/17/t...
www.statnews.com/2025/03/17/t...
Eric Green is out as head of National Human Genome Research Institute
The longtime director of the National Human Genome Research Institute is stepping down, as the larger NIH braces for more changes.
www.statnews.com
March 18, 2025 at 7:33 PM
Eric Green is out as head of National Human Genome Research Institute
www.statnews.com/2025/03/17/t...
www.statnews.com/2025/03/17/t...
Reposted by Manuel Rivas
Inflammatory bowel disease risk gene C1ORF106 regulates actin dynamics in intestinal epithelial cells https://www.biorxiv.org/content/10.1101/2025.03.14.643205v1
March 16, 2025 at 3:33 AM
Inflammatory bowel disease risk gene C1ORF106 regulates actin dynamics in intestinal epithelial cells https://www.biorxiv.org/content/10.1101/2025.03.14.643205v1
Reposted by Manuel Rivas
Foundation models for generalizable electrocardiogram interpretation: comparison of supervised and self-supervised electrocardiogram foundation models https://www.medrxiv.org/content/10.1101/2025.03.02.25322575v1
March 6, 2025 at 4:56 AM
Foundation models for generalizable electrocardiogram interpretation: comparison of supervised and self-supervised electrocardiogram foundation models https://www.medrxiv.org/content/10.1101/2025.03.02.25322575v1
Reposted by Manuel Rivas
DNA sequencing data for over 37,000 children and parents is now available to researchers worldwide 🧬
Collected over multiple decades, these data can be combined with existing health information provided by participating families.
Read more ⤵️
www.sanger.ac.uk/news_item/la...
Collected over multiple decades, these data can be combined with existing health information provided by participating families.
Read more ⤵️
www.sanger.ac.uk/news_item/la...
March 4, 2025 at 11:14 AM
DNA sequencing data for over 37,000 children and parents is now available to researchers worldwide 🧬
Collected over multiple decades, these data can be combined with existing health information provided by participating families.
Read more ⤵️
www.sanger.ac.uk/news_item/la...
Collected over multiple decades, these data can be combined with existing health information provided by participating families.
Read more ⤵️
www.sanger.ac.uk/news_item/la...
Reposted by Manuel Rivas
Excited to finally share that our paper looking at the effect of rare non-coding variants using WGS on circulating protein levels in the UKB has been released in Nature Genetics @naturegenet.bsky.social! We now analyse the full 3,000 circulating proteins in all 50,000 individuals rdcu.be/ea16i
Whole-genome sequencing analysis identifies rare, large-effect noncoding variants and regulatory regions associated with circulating protein levels
Nature Genetics - Rare variant association analysis of plasma proteins using whole-genome sequencing data in 54,306 individuals in the UK Biobank demonstrates that combining both single-variant and...
rdcu.be
February 24, 2025 at 6:26 PM
Excited to finally share that our paper looking at the effect of rare non-coding variants using WGS on circulating protein levels in the UKB has been released in Nature Genetics @naturegenet.bsky.social! We now analyse the full 3,000 circulating proteins in all 50,000 individuals rdcu.be/ea16i
Reposted by Manuel Rivas
Check out our web tool for searching for interactors of your favorite cell surface protein, developed by undergrad Pinyu Liao and postdoc postdoc Brendan Floyd @stanford-chemh.bsky.social
cellsurfacemap.org
cellsurfacemap.org
Cell Surface Map
Cell Surface Map - Distribution and organization data on immune cell surface proteins
cellsurfacemap.org
February 21, 2025 at 1:56 AM
Check out our web tool for searching for interactors of your favorite cell surface protein, developed by undergrad Pinyu Liao and postdoc postdoc Brendan Floyd @stanford-chemh.bsky.social
cellsurfacemap.org
cellsurfacemap.org
Reposted by Manuel Rivas
Happy to share a new preprint, to which I provided a minor contribution.
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
February 18, 2025 at 12:05 PM
Happy to share a new preprint, to which I provided a minor contribution.
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Reposted by Manuel Rivas
Spatial proteomics in human carotid atherosclerotic plaques (N=118). A great weekend read❗️
👉subregions isolated with microdissection (lipid core, fibrous cap, tunica media)
👉mass-spec proteomics
👉proteome-defined subclusters across subregions
👉biological enrichment across subclusters
1/2
👉subregions isolated with microdissection (lipid core, fibrous cap, tunica media)
👉mass-spec proteomics
👉proteome-defined subclusters across subregions
👉biological enrichment across subclusters
1/2
February 15, 2025 at 1:32 PM
Spatial proteomics in human carotid atherosclerotic plaques (N=118). A great weekend read❗️
👉subregions isolated with microdissection (lipid core, fibrous cap, tunica media)
👉mass-spec proteomics
👉proteome-defined subclusters across subregions
👉biological enrichment across subclusters
1/2
👉subregions isolated with microdissection (lipid core, fibrous cap, tunica media)
👉mass-spec proteomics
👉proteome-defined subclusters across subregions
👉biological enrichment across subclusters
1/2
Indeed. Index SNP is missed with ceiling
Here's a perfect illustration of why underflow of p values is a problem
50 snps in a row all with p<1e-324.
The reported snp is the first of the 50, sitting in a random gene.
But the strongest association is 1e-1624, a missense variant in the causal gene
phenomics.va.ornl.gov/pheweb/gia/m...
50 snps in a row all with p<1e-324.
The reported snp is the first of the 50, sitting in a random gene.
But the strongest association is 1e-1624, a missense variant in the causal gene
phenomics.va.ornl.gov/pheweb/gia/m...
February 12, 2025 at 11:30 PM
Indeed. Index SNP is missed with ceiling
Our paper on Efficient regression for population-scale genome sequencing studies is published and online
1.5 minutes on a single machine
academic.oup.com/bioinformati...
1.5 minutes on a single machine
academic.oup.com/bioinformati...
Efficient storage and regression computation for population-scale genome sequencing studies
AbstractMotivation. The growing availability of large-scale population biobanks has the potential to significantly advance our understanding of human healt
academic.oup.com
February 12, 2025 at 9:50 PM
Our paper on Efficient regression for population-scale genome sequencing studies is published and online
1.5 minutes on a single machine
academic.oup.com/bioinformati...
1.5 minutes on a single machine
academic.oup.com/bioinformati...
Fantastic
T1D GRS: a tool for identifying children and adolescents with monogenic diabetes https://www.medrxiv.org/content/10.1101/2025.02.07.25320954v1
February 10, 2025 at 9:37 PM
Fantastic
Reposted by Manuel Rivas
🎇Our new paper in @ScienceMagazine
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and...
science.org
February 7, 2025 at 2:25 PM
🎇Our new paper in @ScienceMagazine
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
Reposted by Manuel Rivas
New in the February 6, 2025, issue of NEJM:
Iptacopan in IgA Nephropathy (APPLAUSE-IgAN phase 3 trial) nej.md/3UmrOkh
Atrasentan in Patients with IgA Nephropathy (ALIGN phase 3 trial) nej.md/3NzvISW
Liraglutide for Children with Obesity (SCALE Kids phase 3a trial) nej.md/3MBP1uc
#MedSky
Iptacopan in IgA Nephropathy (APPLAUSE-IgAN phase 3 trial) nej.md/3UmrOkh
Atrasentan in Patients with IgA Nephropathy (ALIGN phase 3 trial) nej.md/3NzvISW
Liraglutide for Children with Obesity (SCALE Kids phase 3a trial) nej.md/3MBP1uc
#MedSky
February 6, 2025 at 2:16 PM
New in the February 6, 2025, issue of NEJM:
Iptacopan in IgA Nephropathy (APPLAUSE-IgAN phase 3 trial) nej.md/3UmrOkh
Atrasentan in Patients with IgA Nephropathy (ALIGN phase 3 trial) nej.md/3NzvISW
Liraglutide for Children with Obesity (SCALE Kids phase 3a trial) nej.md/3MBP1uc
#MedSky
Iptacopan in IgA Nephropathy (APPLAUSE-IgAN phase 3 trial) nej.md/3UmrOkh
Atrasentan in Patients with IgA Nephropathy (ALIGN phase 3 trial) nej.md/3NzvISW
Liraglutide for Children with Obesity (SCALE Kids phase 3a trial) nej.md/3MBP1uc
#MedSky
Reposted by Manuel Rivas
Our paper led by J. Shin & A. Small evaluating the longitudinal penetrance of HCM alleles in the Mass General Brigham Biobank www.sciencedirect.com/science/arti... @jaccjournals.bsky.social #JACCAdv @broadinstitute.org @cgm-mgh.bsky.social @mgbresearch.bsky.social
February 5, 2025 at 3:57 PM
Our paper led by J. Shin & A. Small evaluating the longitudinal penetrance of HCM alleles in the Mass General Brigham Biobank www.sciencedirect.com/science/arti... @jaccjournals.bsky.social #JACCAdv @broadinstitute.org @cgm-mgh.bsky.social @mgbresearch.bsky.social
This is a great write up by Bob Carpenter (read the PDF document)
February 5, 2025 at 3:49 AM
This is a great write up by Bob Carpenter (read the PDF document)
Reposted by Manuel Rivas
Generalized linear neural network models
statmodeling.stat.columbia.edu/2025/02/04/g...
statmodeling.stat.columbia.edu/2025/02/04/g...
Generalized linear neural network models | Statistical Modeling, Causal Inference, and Social Science
statmodeling.stat.columbia.edu
February 4, 2025 at 9:43 PM
Generalized linear neural network models
statmodeling.stat.columbia.edu/2025/02/04/g...
statmodeling.stat.columbia.edu/2025/02/04/g...
Happy to see this online. We assess the genetic contribution to disease progression (as opposed to susceptibility). Time-to-event models are quite relevant here.
Genetics of cardiometabolic disease progression https://www.medrxiv.org/content/10.1101/2025.02.01.25321518v1
February 4, 2025 at 12:05 AM
Happy to see this online. We assess the genetic contribution to disease progression (as opposed to susceptibility). Time-to-event models are quite relevant here.
Reposted by Manuel Rivas
Prevalence and disease risks for male and female sex chromosome trisomies: a registry-based phenome-wide association study in 1.5 million participants of MVP, FinnGen, and UK Biobank https://www.medrxiv.org/content/10.1101/2025.01.31.25321488v1
February 3, 2025 at 12:40 AM
Prevalence and disease risks for male and female sex chromosome trisomies: a registry-based phenome-wide association study in 1.5 million participants of MVP, FinnGen, and UK Biobank https://www.medrxiv.org/content/10.1101/2025.01.31.25321488v1
Reposted by Manuel Rivas
Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells https://www.biorxiv.org/content/10.1101/2025.01.30.635675v1
January 31, 2025 at 3:33 AM
Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells https://www.biorxiv.org/content/10.1101/2025.01.30.635675v1