New in @nature.com! “GREGoR: Accelerating Genomics for Rare Diseases” highlights how the GREGoR Consortium is advancing rare disease discovery through data sharing, multi-omics, and next-gen sequencing across 7,500+ individuals in 3,000+ families. 🧬 www.nature.com/articles/s41...

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...

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...

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.

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!

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! 🧬💻🧪

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

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”? 🧵 ⬇️

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... 🧬💻🧪

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.

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...

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...

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 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 😊🧪

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 💻🧬

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

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...

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!!

Our team identified a new putative disease-gene using a transcriptome-first approach! 💻🧬

🚨 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! 🧬

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...

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...

It was so fun to chat with the amazing @jpflores.bsky.social about our class, incentives in science, and some of our favorite food!

This is now published! www.cell.com/cell-genomic...

It's been a minute since I've been on here, wanted to update that this is now published! www.cell.com/ajhg/fulltex... We saw genome build choice impacting RNA-seq results for ~4% of all genes, and ~39% of all quantified genes from six biospecimen types.

Congratulations to my mentee Maggie Maurer, an ASHG Trainee Research Excellence Pre-Doctoral Winner. She discovered a new disease gene in her rotation project last year! The critical method for this project was shared with us by collaborator Vijay Ganesh and clinical work was done by Rodrigo Mendez.

Great online course material, Stanford's GENE 220: Introduction to Genetics, Ethics, and Society from @roshnipatel.bsky.social and @raungar.bsky.social h/t @jpflores.bsky.social stanford-genethics.github.io/index.html

Have you ever wondered how genome build is impacting your RNA-seq results? I am excited to share our new paper on medRxiv investigating the impact of hg19, hg38, and chm13 on six routinely-collected biospecimens: www.medrxiv.org/content/10.1... (1/8) 🧬💻👩‍💻🧪

Thread of some really great works out this week in the world of countering naive genetic thinking (e.g. hereditarianism, genetic determinism, scientific racism)

Roshni Patel and I are thrilled to share our paper on the trainee-led course on genetics, ethics, and society that was developed at Stanford: www.biorxiv.org/content/10.1... (1/9) 🧬💻🧪