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Stephen Montgomery

@sbmontgom.bsky.social
567 followers 122 following 29 posts

Stephen Montgomery. Stanford Medicine Professor of Pathology, Genetics, Biomedical Data Science and, by courtesy, Computer Science. Sporadic on social media.

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Stephen Montgomery @sbmontgom.bsky.social · 15/04/2026
Also, I am chairing the committee and if you have frustrations, you can always send me an email.
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Stephen Montgomery @sbmontgom.bsky.social · 15/04/2026
I hope you consider nominating a colleague this year for the ASHG awards apply.ashg.org/a/page/awards Deadline is April 17, 2026 There is a new system this year that aims to standardize the information the Awards committee collects. Please keep that in mind
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David A Knowles @davidaknowles.bsky.social · 02/04/2026
@nygenome.org is hiring Genomic AI Fellows! (fancy postdoc positions) If you're interested in working at the interface of AI and genomics in a great environment please apply at: jobs.silkroad.com/NYGenome/Car...
jobs.silkroad.com
NYGC Genomic AI Fellows - 101 Avenue of the Americas, 7th Floor, New York, New York - New York Genome Center
Find a career with New York Genome Center
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Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · 23/03/2026
It's out! I hope this work encourages folks to move beyond a standard "one variant, one gene" QTL paradigm and consider proxitropic variant effects. Big thanks to the reviewers and editors at @ajhgnews.bsky.social for their help! @sbmontgom.bsky.social www.sciencedirect.com/science/arti...
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Stephen Montgomery @sbmontgom.bsky.social · 01/04/2026
I agree with your take. At first I had the expected reaction. But this is actually probably more realistic and fair. Since now it isn't just standing members that can get an extension, 2 weeks is probably realistic in terms of impact, and it looks like more application types are considered.
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Stephen Montgomery @sbmontgom.bsky.social · 11/01/2026
Further, as a regular grant reviewer, I am always looking for the thing that is paradigm changing and new too. As are my colleagues.
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Stephen Montgomery @sbmontgom.bsky.social · 11/01/2026
I get your larger point that "science" shouldn't go all in on any one area. But to have this criticism and suggest it "causes harm" at this particular point in time is missing another environment.
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Stephen Montgomery @sbmontgom.bsky.social · 11/01/2026
I think the rare disease community might disagree here. Sure there are teratogens. But there are 1000s of congenital, genetic disorders that have and continue to be solved by advances derived from the human genome project.
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Nicolas Robine 🇪🇺🇫🇷🇺🇸 @nicorobine.bsky.social · 08/01/2026
"Illumina Appoints Former NHGRI Director Eric Green as Chief Medical Officer" www.genomeweb.com/sequencing/i...
genomeweb.com
Illumina Appoints Former NHGRI Director Eric Green as Chief Medical Officer
Green, whose tenure as NHGRI director was terminated earlier this year, will take up his new post on Feb. 2.
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Stephen Montgomery @sbmontgom.bsky.social · 08/01/2026
I was reviewer 3. I can send you my review.
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Stephen Montgomery @sbmontgom.bsky.social · 08/01/2026
I almost get hit by a car every other week. Last night some guy went through a stop sign while I was crossing on my bike. I didn't know I could murder them..
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GREGoR Consortium @gregor-research.bsky.social · 12/11/2025
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...
nature.com
GREGoR: accelerating genomics for rare diseases - Nature
The GREGoR consortium provides foundational resources and substrates for the future of rare disease genomics.
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Stephen Montgomery @sbmontgom.bsky.social · 12/11/2025
Read about our efforts in the NHGRI's GREGoR Consortium to tackle some of the hardest-to-solve rare disease diagnoses. Online now www.nature.com/articles/s41...
nature.com
GREGoR: accelerating genomics for rare diseases - Nature
The GREGoR consortium provides foundational resources and substrates for the future of rare disease genomics.
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Ben Strober @bennystrobes.bsky.social · 07/10/2025
Exciting updates!! (1) I just opened my lab at Boston Children’s Hospital (Harvard-affiliated) (2) I’m hiring a postdoc focused on integrating GWAS and functional genomic data. Reach out if you’re interested or connect at ASHG next week! (3) Learn more at stroberlab.com
stroberlab.com
Strober Lab
The Strober lab is a computational group at Boston Children's Hospital (a Harvard Medical School affiliated hospital) focused on developing statistical and machine learning tools applied to human gene...
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GREGoR Consortium @gregor-research.bsky.social · 19/09/2025
Thank you to all our members and collaborators for an inspiring and productive @gregor-research.bsky.social meeting last week in San Diego! ☀️🧬 #RareDisease #Research
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Stephen Montgomery @sbmontgom.bsky.social · 18/08/2025
I'd reckon that a good amount of news articles would benefit from a few scientists doing peer and editorial review.
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Michael Love @mikelove.bsky.social · 18/08/2025
Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS. www.biorxiv.org/content/10.1...
biorxiv.org
Higher eQTL power reveals signals that boost GWAS colocalization
Expression quantitative trait locus (eQTL) studies in human cohorts typically detect at least one regulatory signal per gene, and have been proposed as a way to explain mechanisms of genetic liability...
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 29/07/2025
🚨Just Announced: The 2025 ASHG Professional Award Winners! Meet the innovators shaping the future of human genetics. 💥Full list & details: www.ashg.org/membership/a... #ASHG #HumanGenetics
Announcing 2025 Awardees
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Tim Coorens @timcoorens.bsky.social · 03/07/2025
The cells in our bodies constantly acquire mutations. But what are the patterns of mutations across tissues? How do mutations in normal cells lead to cancer and disease? These are questions we will tackle within the Somatic Mosaicism across Human Tissues (SMaHT) Network, now described in @nature.com
nature.com
The Somatic Mosaicism across Human Tissues Network - Nature
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
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Yoav Gilad @ygilad.bsky.social · 10/06/2025
People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.
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Stephen Montgomery @sbmontgom.bsky.social · 10/06/2025
In general, there are settings where (1) there are independent-acting variants in partial LD or (2) a single variant acting on multiple genes or (3) multiple variants on multiple neighboring genes. There are prior examples of CTCF variants with proxitropic effects. Some SVs are clear examples.
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Tami Gjorgjieva @tamigj.bsky.social · 09/06/2025
What a joy to work on exciting science AND do it with a great friend like @itskatelawrence.bsky.social! Check out her 🧵 on our recent preprint with @sbmontgom.bsky.social:
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Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · 08/06/2025
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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Cedric Boeckx @cedricboeckx.bsky.social · 07/06/2025
“Focus on single gene effects limits discovery and interpretation of complex trait-associated variants” Very interesting preprint by Kathryn Lawrence @tamigj.bsky.social @sbmontgom.bsky.social good arguments to move beyond single-gene-at-a-time approaches 🧪🧬 www.biorxiv.org/content/10.1...
biorxiv.org
Focus on single gene effects limits discovery and interpretation of complex trait-associated variants
Standard QTL mapping approaches consider variant effects on a single gene at a time, despite abundant evidence for allelic pleiotropy, where a single variant can affect multiple genes simultaneously. ...
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Stephen Montgomery @sbmontgom.bsky.social · 03/06/2025
huge congrats Ben!
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Stephen Montgomery @sbmontgom.bsky.social · 03/06/2025
huge congrats!!
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Human Genetics and Genomics Advances @hggadvances.bsky.social · 02/06/2025
📣Online now! 📄Transcriptomic signatures of rare variant impacts across sex and the X-chromosome 🧑‍🤝‍🧑 @raungar.bsky.social @sbmontgom.bsky.social & co 👉https://bit.ly/4kmWc8Z
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Michel Nivard @michelnivard.bsky.social · 19/05/2025
This is VERY big genetics & health news, Regeneron (Pharmaceutical company with v strong genetics in medicine arm) is going to buy 23andme. investor.regeneron.com/news-release...
investor.regeneron.com
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Stephen Montgomery @sbmontgom.bsky.social · 15/05/2025
Huge congrats @soumyakundu.bsky.social !!
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Ben Lehner @benlehner.bsky.social · 06/05/2025
Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social Building AI models or the data to train them? Core funding of >$130M a year for a faculty of ~30. www.nature.com/naturecareer... acrobat.adobe.com/id/urn:aaid:... pls RT!
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Stephen Montgomery @sbmontgom.bsky.social · 06/05/2025
Auditoriums that don't allow people to bring in coffee.
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Tuuli Lappalainen @tuuliel.bsky.social · 06/05/2025
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 05/05/2025
⏳Only 4 days left to nominate! Do you know someone who has contributed through research, mentoring, advocacy, or leadership to the field? Give them the recognition they deserve! Nominate them for our professional awards before May 9! 🏆👉 www.ashg.org/membership/a... #ASHG
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 02/05/2025
"An abstract is an incredible chance to showcase what you've accomplished so far and show where your project might go in the future," which is why you should submit to #ASHG25! Hear past presenter, Andrew Marderstein, PhD, share the benefits of submitting. ⤵️ youtube.com/shorts/BmYiS...
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Stephen Montgomery @sbmontgom.bsky.social · 25/04/2025
Huge congrats!!
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Emily Greenwald @emilymbgreenwald.bsky.social · 24/04/2025
I’m excited to share our paper in @narjournal.bsky.social on DragonRNA: DNA-primed RNA extension! We developed a fluorescence gel shift assay to detect DragonRNA activity by enzymes, & characterized this activity using gel assays, sequencing, & bioinformatics. academic.oup.com/nar/article/...
academic.oup.com
DragonRNA: Generality of DNA-primed RNA-extension activities by DNA-directed RNA polymerases
Abstract. RNA polymerases (RNAPs) transcribe DNA into RNA. Several RNAPs, including from bacteriophages Sp6 and T7, Escherichia coli, and wheat germ, had b
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 15/04/2025
Know a colleague, mentor, or early-career researcher committed to elevating the field of #humangenetics and inspiring the next generation? Nominate them for an ASHG 2025 Professional Award! 🎉 Nominations close on May 9. Visit here to apply: www.ashg.org/membership/a... #ASHG
Former ASHG President Bruce D. Gelb (left) with Gail Jarvik, MD, PhD (right), the 2024 ASHG Mentorship Awardee, during the 2024 Annual Meeting in Denver, CO.
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Stephen Montgomery @sbmontgom.bsky.social · 03/03/2025
Registration deadline coming up. It will be a great meeting.
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Stephen Montgomery @sbmontgom.bsky.social · 21/02/2025
The effort people put in to write grants is enormous and this is just terrible.
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Stephen Montgomery @sbmontgom.bsky.social · 21/02/2025
"Dear GHD Reviewer – I want to share the news that the GHD Meeting scheduled for Monday and Tuesday, February 24-25, 2025, will not occur on these dates. It is being postponed to later dates, to be determined. This is because the meeting has not yet posted in the Federal Register."
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Scott_Boyd_Lab_Stanford @scottboydlab.bsky.social · 21/02/2025
Attempting to read the language of B cell and T cell receptor sequences to diagnose immunological diseases: Our new paper, led by the outstanding Maxim Zaslavsky @maximzaslavsky.bsky.social sky.bsky.social with help from me and Anshul Kundaje @anshulkundaje.bsky.social. Link: buff.ly/3QvxSVf
A figure showing a model for using BCR and TCR sequences to classify immunological disorders.
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Stephen Montgomery @sbmontgom.bsky.social · 20/02/2025
Huge congrats!!
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Stephen Montgomery @sbmontgom.bsky.social · 20/02/2025
Too expensive to visit.
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Stephen Montgomery @sbmontgom.bsky.social · 20/02/2025
Huge congrats Andrew and Souyma!
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Andrew Marderstein @amarderstein.bsky.social · 19/02/2025
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...
biorxiv.org
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...
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Stephen Montgomery @sbmontgom.bsky.social · 14/02/2025
I hope you are ok. All of this is terrible.
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Stephen Montgomery @sbmontgom.bsky.social · 08/02/2025
@onsummertime.bsky.social what would be a reasonable mix of federal support to endowment support for a university's operating budget?
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Stephen Montgomery @sbmontgom.bsky.social · 08/02/2025
when they close labs as a stopgap, will you donate to my gofundme?
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Jacob Schreiber @jmschreiber91.bsky.social · 22/01/2025
Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41...
nature.com
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
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