Mineto Ota
@minetoota.bsky.social
MD/PhD. Rheumatologist. Postdoc at Stanford and Gladstone.
Interested in complex trait genetics and immunology.
Interested in complex trait genetics and immunology.
Reposted by Mineto Ota
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
August 22, 2025 at 7:50 PM
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
Reposted by Mineto Ota
I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
June 2, 2025 at 5:45 PM
I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
Reposted by Mineto Ota
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
June 1, 2025 at 3:33 PM
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Reposted by Mineto Ota
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
www.biorxiv.org
March 28, 2025 at 1:22 AM
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
Reposted by Mineto Ota
Excited to share the peer-reviewed version of our paper on predicting the chromatin response to TF dosage using transfer learning
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
Naqvi et al. reveal how DNA sequence determines the chromatin response to transcription
factor (TF) dosage changes. By combining deep learning and chemical genetics, they
uncover specific sequence fea...
www.cell.com
February 27, 2025 at 8:31 PM
Excited to share the peer-reviewed version of our paper on predicting the chromatin response to TF dosage using transfer learning
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Reposted by Mineto Ota
Disease diagnostics using machine learning of B cell and T cell receptor sequences
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
www.science.org
February 21, 2025 at 1:12 AM
Disease diagnostics using machine learning of B cell and T cell receptor sequences
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
Reposted by Mineto Ota
Japan can be a science heavyweight once more — if it rethinks funding
Research leaders call for an end to substantial underfunding of interdisciplinary research in Japan.
On my current visit to 🇯🇵 I can see the country is ready for a change
#japan #academicSky 🧪
www.nature.com/articles/d41...
Research leaders call for an end to substantial underfunding of interdisciplinary research in Japan.
On my current visit to 🇯🇵 I can see the country is ready for a change
#japan #academicSky 🧪
www.nature.com/articles/d41...
Japan can be a science heavyweight once more — if it rethinks funding
The nation must lose its tight focus on individual disciplines if it is to keep pace with the evolving requirements of scientific enquiry.
www.nature.com
February 12, 2025 at 9:47 AM
Japan can be a science heavyweight once more — if it rethinks funding
Research leaders call for an end to substantial underfunding of interdisciplinary research in Japan.
On my current visit to 🇯🇵 I can see the country is ready for a change
#japan #academicSky 🧪
www.nature.com/articles/d41...
Research leaders call for an end to substantial underfunding of interdisciplinary research in Japan.
On my current visit to 🇯🇵 I can see the country is ready for a change
#japan #academicSky 🧪
www.nature.com/articles/d41...
Reposted by Mineto Ota
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq.
Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]
bsky.app/profile/jkpr...
Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]
bsky.app/profile/jkpr...
GWAS provides a unique tool in human biology as it can establish causal links from variants to trait.
But interpretation is difficult as most effects flow through (unobserved) gene regulatory networks. Can we gain insight by linking to modern Perturb-seq data?
www.biorxiv.org/content/10.1...
But interpretation is difficult as most effects flow through (unobserved) gene regulatory networks. Can we gain insight by linking to modern Perturb-seq data?
www.biorxiv.org/content/10.1...
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq
Genetic association studies provide a unique tool for identifying causal links from genes to human traits and diseases. However, it is challenging to determine the biological mechanisms underlying mos...
www.biorxiv.org
January 27, 2025 at 7:19 PM
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq.
Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]
bsky.app/profile/jkpr...
Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]
bsky.app/profile/jkpr...
Reposted by Mineto Ota
Beautifully elegant work on integrating LoF, GWAS & Perturb-seq data to build causal paths from regulators to genes / programs to phenotype. And it didn't require a foundational virtual cell model (well almost ... gene & protein embeddings r used in GeneBayes)! 😜
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 5:44 PM
Beautifully elegant work on integrating LoF, GWAS & Perturb-seq data to build causal paths from regulators to genes / programs to phenotype. And it didn't require a foundational virtual cell model (well almost ... gene & protein embeddings r used in GeneBayes)! 😜
Reposted by Mineto Ota
Great new study from @jkpritch.bsky.social’s lab, led by @minetoota.bsky.social,
combining ‘quantitative estimates of gene-trait relationships from loss-of-function burden tests with gene-regulatory connections inferred from Perturb-seq experiments in relevant cell types’ 👇
combining ‘quantitative estimates of gene-trait relationships from loss-of-function burden tests with gene-regulatory connections inferred from Perturb-seq experiments in relevant cell types’ 👇
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 8:43 AM
Great new study from @jkpritch.bsky.social’s lab, led by @minetoota.bsky.social,
combining ‘quantitative estimates of gene-trait relationships from loss-of-function burden tests with gene-regulatory connections inferred from Perturb-seq experiments in relevant cell types’ 👇
combining ‘quantitative estimates of gene-trait relationships from loss-of-function burden tests with gene-regulatory connections inferred from Perturb-seq experiments in relevant cell types’ 👇
Reposted by Mineto Ota
@minetoota.bsky.social set the groundwork for many ongoing projects in @jkpritch.bsky.social and Marson lab. Great to see this out!
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 7:29 PM
@minetoota.bsky.social set the groundwork for many ongoing projects in @jkpritch.bsky.social and Marson lab. Great to see this out!
Reposted by Mineto Ota
Really nice work. And they chose one of my favorite traits to model: mean corpuscular hemoglobin.
Allows me to reuse one of my figures from a few weeks ago on a gene as old as eukaryotes, mitoferrin, which is needed to move iron into mitochondria.
@jkpritch.bsky.social
Allows me to reuse one of my figures from a few weeks ago on a gene as old as eukaryotes, mitoferrin, which is needed to move iron into mitochondria.
@jkpritch.bsky.social
January 24, 2025 at 11:18 AM
Really nice work. And they chose one of my favorite traits to model: mean corpuscular hemoglobin.
Allows me to reuse one of my figures from a few weeks ago on a gene as old as eukaryotes, mitoferrin, which is needed to move iron into mitochondria.
@jkpritch.bsky.social
Allows me to reuse one of my figures from a few weeks ago on a gene as old as eukaryotes, mitoferrin, which is needed to move iron into mitochondria.
@jkpritch.bsky.social
Thank you Jonathan for these fantastic threads about our recent work!
We dove into how we can model the gene regulatory architecture of complex traits with 1) Gene effects from LoF burden tests and 2) Perturb-seq.
We dove into how we can model the gene regulatory architecture of complex traits with 1) Gene effects from LoF burden tests and 2) Perturb-seq.
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 1:35 AM
Thank you Jonathan for these fantastic threads about our recent work!
We dove into how we can model the gene regulatory architecture of complex traits with 1) Gene effects from LoF burden tests and 2) Perturb-seq.
We dove into how we can model the gene regulatory architecture of complex traits with 1) Gene effects from LoF burden tests and 2) Perturb-seq.
Reposted by Mineto Ota
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
December 17, 2024 at 7:04 AM
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
Reposted by Mineto Ota
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 7:05 AM
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Reposted by Mineto Ota
Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Central control of dynamic gene circuits governs T cell rest and activation - Nature
Resting and activated T cell states are established by context-specific regulators and dynamic gene circuits.
www.nature.com
December 11, 2024 at 8:46 PM
Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...
www.nature.com/articles/s41...