Lightnews — Scholar-powered news

Reposted by Rachel Ungar

Alex Geary @alextremophile.bsky.social · Aug 29

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...

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

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Reposted by Rachel Ungar

Andrea Ganna @andganna.bsky.social · Aug 22

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.

The American Journal of Human Genetics @ajhgnews.bsky.social · Aug 20

📣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

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

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Reposted by Rachel Ungar

Rachel Ungar @raungar.bsky.social · Jun 26

Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪

Rachel Ungar @raungar.bsky.social · Jun 2

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... 🧬💻🧪

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Rachel Ungar @raungar.bsky.social · Aug 7

Roshni is one of the best people to work with, academia is so lucky to have her as a professor!

Roshni Patel @roshnipatel.bsky.social · Aug 6

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.

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Reposted by Rachel Ungar

Michal Caspi Tal, PhD @immunofever.bsky.social · Jul 23

You've never seen anything like this before. Come see for yourself! mitnano.mit.edu/events/studi...

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Rachel Ungar @raungar.bsky.social · Jun 26

Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪

Rachel Ungar @raungar.bsky.social · Jun 2

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... 🧬💻🧪

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Rachel Ungar @raungar.bsky.social · Jun 12

It's officially online, learn more about the interplay between the X-chromosome, rare variants, sex, and gene expression! 🧬💻🧪

American Society of Human Genetics (ASHG) @geneticssociety.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

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Reposted by Rachel Ungar

Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · Jun 8

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”? 🧵 ⬇️

Standard methods are equivalent to a flashlight, looking at each gene independently. We combine signals from multiple genes, turning a floodlight onto the genome.

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Reposted by Rachel Ungar

Jayati Sharma, PhD, ScM @jayatirsharma.bsky.social · Jun 2

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

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Rachel Ungar @raungar.bsky.social · Jun 2

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... 🧬💻🧪

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Reposted by Rachel Ungar

Gen Wojcik @genandgenes.bsky.social · Apr 24

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.

Nature @nature.com · Apr 24

Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics

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

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Reposted by Rachel Ungar

Bohan Ni @bohanni.bsky.social · Mar 26

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

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Reposted by Rachel Ungar

Andrew Marderstein @amarderstein.bsky.social · Feb 19

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...

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

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Rachel Ungar @raungar.bsky.social · Feb 14

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!

are you an irb cuz i want to spend the next 8 months of my life gaining your approval. it then says, will you be our lab valentine? with a fake irb below, and the choice to approve or decline.

a fake IRB form with the titel: a proposal for mutual affection and lab valentine's. this describes background and rationale, objectives, study design, potential risks, benefits, confidentiality, and consent

explaining why scbe should be the montgomery's lab valentine through the 4 principles of bioethics

there's no one elsi like you, i need some guidelines for navigating these feelings, scBE mine

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Reposted by Rachel Ungar

jp flores (he/him) @jpflores.rbind.io · Jan 31

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 😊🧪