Rachel Ungar
@raungar.bsky.social
Postdoc at @StanfordBioethx
Genetics PhD @StanfordMed, BS @UArkansas
elsi / rna-seq / rare disease / multi-omics / chronic illness / x-chromosome
Genetics PhD @StanfordMed, BS @UArkansas
elsi / rna-seq / rare disease / multi-omics / chronic illness / x-chromosome
Pinned
Rachel Ungar
@raungar.bsky.social
· Jun 12
@raungar.bsky.social, @sbmontgom.bsky.social, & co. examine the impact of rare variants & sex on gene expression across the X-chromosome & autosomes, identifying 700+ rare variants w/ predicted functional differences in males & females: www.cell.com/hgg-advances... #ASHG @hggadvances.bsky.social
It's officially online, learn more about the interplay between the X-chromosome, rare variants, sex, and gene expression! 🧬💻🧪
Reposted by Rachel Ungar
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 12:05 AM
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...
Reposted by Rachel Ungar
I am super proud to present our new manuscript “Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores”
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores
Background: SpliceAI is a deep learning algorithm that predicts whether genetic variants are likely to affect splicing. Precomputed spliceAI predictions for all theoretical SNVs and small indels were ...
www.medrxiv.org
August 29, 2025 at 8:57 AM
I am super proud to present our new manuscript “Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores”
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Rachel Ungar
Happy to see this online!
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
📣Online now!
📄 #PheWAS of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
@finngen.bsky.social @ukbiobank.bsky.social
📄 #PheWAS of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
@finngen.bsky.social @ukbiobank.bsky.social
Phenome-wide association study of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
We examined disease associations for sex chromosome trisomies (SCTs) by performing
a phenome-wide association study in 2,769 individuals with SCT (47,XXY: 1,319; 47,XYY:
1,108; and 47,XXX: 342). Many ...
www.cell.com
August 22, 2025 at 8:59 AM
Happy to see this online!
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Reposted by Rachel Ungar
Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪
Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪
June 26, 2025 at 4:15 PM
Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪
Roshni is one of the best people to work with, academia is so lucky to have her as a professor!
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
August 7, 2025 at 2:04 PM
Roshni is one of the best people to work with, academia is so lucky to have her as a professor!
Reposted by Rachel Ungar
You've never seen anything like this before. Come see for yourself! mitnano.mit.edu/events/studi...
July 23, 2025 at 12:51 AM
You've never seen anything like this before. Come see for yourself! mitnano.mit.edu/events/studi...
Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪
Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪
June 26, 2025 at 4:15 PM
Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪
It's officially online, learn more about the interplay between the X-chromosome, rare variants, sex, and gene expression! 🧬💻🧪
@raungar.bsky.social, @sbmontgom.bsky.social, & co. examine the impact of rare variants & sex on gene expression across the X-chromosome & autosomes, identifying 700+ rare variants w/ predicted functional differences in males & females: www.cell.com/hgg-advances... #ASHG @hggadvances.bsky.social
June 12, 2025 at 9:17 PM
It's officially online, learn more about the interplay between the X-chromosome, rare variants, sex, and gene expression! 🧬💻🧪
Reposted by Rachel Ungar
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
June 8, 2025 at 5:39 PM
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
Reposted by Rachel Ungar
This survey was put together by several fellow trainees and friends who are dedicated to the ethical conduct of human genetics research. Tagging some below! @christacaggiano.bsky.social @roshnipatel.bsky.social @raungar.bsky.social @dianexue.bsky.social @jpflores.rbind.io
June 2, 2025 at 5:37 PM
This survey was put together by several fellow trainees and friends who are dedicated to the ethical conduct of human genetics research. Tagging some below! @christacaggiano.bsky.social @roshnipatel.bsky.social @raungar.bsky.social @dianexue.bsky.social @jpflores.rbind.io
Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪
June 2, 2025 at 10:02 PM
Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪
Reposted by Rachel Ungar
I wrote a thing.
I am eternally grateful for my editor, who took the original draft and helped me narrow down my key points into a more effective piece with a broader reach.
Also, thanks to the editorial & legal teams, who maintained the message while protecting us in this fraught moment.
I am eternally grateful for my editor, who took the original draft and helped me narrow down my key points into a more effective piece with a broader reach.
Also, thanks to the editorial & legal teams, who maintained the message while protecting us in this fraught moment.
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics
https://go.nature.com/4jGqiUc
https://go.nature.com/4jGqiUc
Eugenics is on the rise again: human geneticists must take a stand
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics.
go.nature.com
April 24, 2025 at 2:25 PM
I wrote a thing.
I am eternally grateful for my editor, who took the original draft and helped me narrow down my key points into a more effective piece with a broader reach.
Also, thanks to the editorial & legal teams, who maintained the message while protecting us in this fraught moment.
I am eternally grateful for my editor, who took the original draft and helped me narrow down my key points into a more effective piece with a broader reach.
Also, thanks to the editorial & legal teams, who maintained the message while protecting us in this fraught moment.
Reposted by Rachel Ungar
Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
March 26, 2025 at 2:30 PM
Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...
Reposted by Rachel Ungar
New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social !
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart
Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...
www.biorxiv.org
February 19, 2025 at 1:32 PM
New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social !
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
The Stanford Center for Biomedical Ethics was asked to be the Montgomery Lab's valentine this year via an IRB, and we delightfully approved their request!
February 14, 2025 at 9:32 PM
The Stanford Center for Biomedical Ethics was asked to be the Montgomery Lab's valentine this year via an IRB, and we delightfully approved their request!
Reposted by Rachel Ungar
Are you a scientist interested in science communication but don’t know where to start? Ever wonder how a graduate student has time for outreach projects?
Check out SCOPE! An org @vangeliqueallen.bsky.social and I created! First panel on creating children’s books and podcasts is today at 1pm ET 😊🧪
Check out SCOPE! An org @vangeliqueallen.bsky.social and I created! First panel on creating children’s books and podcasts is today at 1pm ET 😊🧪
January 31, 2025 at 5:29 PM
Are you a scientist interested in science communication but don’t know where to start? Ever wonder how a graduate student has time for outreach projects?
Check out SCOPE! An org @vangeliqueallen.bsky.social and I created! First panel on creating children’s books and podcasts is today at 1pm ET 😊🧪
Check out SCOPE! An org @vangeliqueallen.bsky.social and I created! First panel on creating children’s books and podcasts is today at 1pm ET 😊🧪
Interested in rare variants, the X-chromosome, sex-differences, pharmacogenetics, or transcription factors? You might be interested in our new manuscript where we identified >700 functional rare variants with a difference in effect by sex in GTEx! bit.ly/x_rv_sex #genomics #multiomics 💻🧬
Functional impact of rare variants and sex across the X-chromosome and autosomes
The human X-chromosome contains hundreds of genes and has well-established impacts on sex differences and traits. However, the X-chromosome is often excluded from many genetic analyses, limiting broad...
www.biorxiv.org
January 24, 2025 at 3:58 PM
Interested in rare variants, the X-chromosome, sex-differences, pharmacogenetics, or transcription factors? You might be interested in our new manuscript where we identified >700 functional rare variants with a difference in effect by sex in GTEx! bit.ly/x_rv_sex #genomics #multiomics 💻🧬
Reposted by Rachel Ungar
What do you mean when you say that you've #shared your #data broadly? @jonathanmoreno.bsky.social and I published a new data sharing framework in @naturegenet.bsky.social along with #bioethics challenges for #genomics in the #ai era. www.nature.com/articles/s41... @pennmedresearch.bsky.social
Overcoming challenges associated with broad sharing of human genomic data - Nature Genetics
This Perspective discusses the definitions of ‘broad’ that have been used in the context of sharing of human genomic data and proposes a clarified and reformed terminology for describing genomic data ...
www.nature.com
January 22, 2025 at 3:51 PM
What do you mean when you say that you've #shared your #data broadly? @jonathanmoreno.bsky.social and I published a new data sharing framework in @naturegenet.bsky.social along with #bioethics challenges for #genomics in the #ai era. www.nature.com/articles/s41... @pennmedresearch.bsky.social
Reposted by Rachel Ungar
If anyone happens to need it this week for...reasons...this is the best graphic on the complexity of human sex determination I've ever seen. I use it in an undergrad course on gene regulatory mechanisms. Shoutout to @unamandita.bsky.social!
www.scientificamerican.com/article/beyo...
www.scientificamerican.com/article/beyo...
Beyond XX and XY: The Extraordinary Complexity of Sex Determination
A host of factors figure into whether someone is female, male or somewhere in between
www.scientificamerican.com
January 21, 2025 at 8:58 PM
If anyone happens to need it this week for...reasons...this is the best graphic on the complexity of human sex determination I've ever seen. I use it in an undergrad course on gene regulatory mechanisms. Shoutout to @unamandita.bsky.social!
www.scientificamerican.com/article/beyo...
www.scientificamerican.com/article/beyo...
Reposted by Rachel Ungar
So excited to read this preprint after Maggie's amazing plenary at ASHG. Congrats @maggie-arriaga.bsky.social and team 🥳
A transcriptome first approach identifies pathogenic variants in RNU4ATAC and highlights the RNU6ATAC as a putative new disease gene 🧬🖥️
A 💪 day for snRNA preprints!!
A transcriptome first approach identifies pathogenic variants in RNU4ATAC and highlights the RNU6ATAC as a putative new disease gene 🧬🖥️
A 💪 day for snRNA preprints!!
What if one variant can cause splicing outliers transcriptome-wide? In our preprint, we show how examining transcriptome-wide patterns of splicing outliers can both diagnose individuals with rare spliceopathies and uncover novel disease-gene relationships! (www.medrxiv.org/content/10.1...)
Transcriptome-wide outlier approach identifies individuals with minor spliceopathies
RNA-sequencing has improved the diagnostic yield of individuals with rare diseases. Current analyses predominantly focus on identifying outliers in single genes that can be attributed to cis-acting va...
www.medrxiv.org
January 7, 2025 at 9:32 PM
So excited to read this preprint after Maggie's amazing plenary at ASHG. Congrats @maggie-arriaga.bsky.social and team 🥳
A transcriptome first approach identifies pathogenic variants in RNU4ATAC and highlights the RNU6ATAC as a putative new disease gene 🧬🖥️
A 💪 day for snRNA preprints!!
A transcriptome first approach identifies pathogenic variants in RNU4ATAC and highlights the RNU6ATAC as a putative new disease gene 🧬🖥️
A 💪 day for snRNA preprints!!
Our team identified a new putative disease-gene using a transcriptome-first approach! 💻🧬
What if one variant can cause splicing outliers transcriptome-wide? In our preprint, we show how examining transcriptome-wide patterns of splicing outliers can both diagnose individuals with rare spliceopathies and uncover novel disease-gene relationships! (www.medrxiv.org/content/10.1...)
Transcriptome-wide outlier approach identifies individuals with minor spliceopathies
RNA-sequencing has improved the diagnostic yield of individuals with rare diseases. Current analyses predominantly focus on identifying outliers in single genes that can be attributed to cis-acting va...
www.medrxiv.org
January 7, 2025 at 11:42 PM
Our team identified a new putative disease-gene using a transcriptome-first approach! 💻🧬
Reposted by Rachel Ungar
🚨 Excited to announce the Marker paper for the GREGoR Consortium! arxiv.org/abs/2412.14338
Accelerating #RareDisease diagnostics with cutting-edge #Genomics and global data sharing of omics and deep phenotyping from ~7500 individuals on NHGRI AnVIL and much more to come! 🧬
Accelerating #RareDisease diagnostics with cutting-edge #Genomics and global data sharing of omics and deep phenotyping from ~7500 individuals on NHGRI AnVIL and much more to come! 🧬
GREGoR: Accelerating Genomics for Rare Diseases
Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA seq...
arxiv.org
December 20, 2024 at 1:49 AM
🚨 Excited to announce the Marker paper for the GREGoR Consortium! arxiv.org/abs/2412.14338
Accelerating #RareDisease diagnostics with cutting-edge #Genomics and global data sharing of omics and deep phenotyping from ~7500 individuals on NHGRI AnVIL and much more to come! 🧬
Accelerating #RareDisease diagnostics with cutting-edge #Genomics and global data sharing of omics and deep phenotyping from ~7500 individuals on NHGRI AnVIL and much more to come! 🧬
Reposted by Rachel Ungar
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 Rachel Ungar
Paper came out this past week! Using MAVEs to reduce variant classification disparities in underrepresented populations and demonstrating AI bias in computational predictors rdcu.be/d2kCn
Previous tweetorial: x.com/MoezDawood/s...
Previous post by @ee-reh-neh.bsky.social: bsky.app/profile/ee-r...
Previous tweetorial: x.com/MoezDawood/s...
Previous post by @ee-reh-neh.bsky.social: bsky.app/profile/ee-r...
December 8, 2024 at 3:19 PM
Paper came out this past week! Using MAVEs to reduce variant classification disparities in underrepresented populations and demonstrating AI bias in computational predictors rdcu.be/d2kCn
Previous tweetorial: x.com/MoezDawood/s...
Previous post by @ee-reh-neh.bsky.social: bsky.app/profile/ee-r...
Previous tweetorial: x.com/MoezDawood/s...
Previous post by @ee-reh-neh.bsky.social: bsky.app/profile/ee-r...
It was so fun to chat with the amazing @jpflores.bsky.social about our class, incentives in science, and some of our favorite food!
In this episode, I interviewed Dr. Roshni Patel (@roshnipatel.bsky.social) & Dr. Rachel Ungar (@raungar.bsky.social), former students (now postdocs!) that developed the course "Introduction to Genetics, Ethics, & Society" @ Stanford. I'm so lucky to learn from and know them!
November 21, 2024 at 3:56 PM
It was so fun to chat with the amazing @jpflores.bsky.social about our class, incentives in science, and some of our favorite food!