Our work on understanding how common genetic variants contribute to recombination and aneuploidy risk is published!

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.

First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

Check out our new preprint on STcompare for identifying spatially differential gene expression patterns at structurally matched locations across spatial transcriptomics datasets.

Preprint on bioRxiv: www.biorxiv.org/content/10.1...
R package on Github: github.com/JEFworks-Lab...

#AcademicSky

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Go Prabuddha!!! 🥳🥳

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...

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

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

Polygenic prediction of phenotypes with a neural empirical Bayes approach Polygenic risk scores (PRS) estimate the expected value of a phenotype based on individual genotypes. Although statistical approaches for calculating PRS have advanced considerably in recent years, fe...

Really excited to share our new PRS method, developed with @aprilkim.bsky.social and @alexisbattle.bsky.social ! Our approach is to use a lot of recently developed functional annotations to better estimate the weights of the SNPs.
www.medrxiv.org/content/10.1...

Idk I’ll have to ask my mum first

Delicious post!!!

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.

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.

It’s available on Amazon: tinyurl.com/mx2hewen

Heading to Minneapolis next week to share this work at STATGEN2025!

I'm defending my PhD next Friday, May 23!(!!!!). I'll be highlighting our work looking at aneuploidy in early human development. If you're interested I'd love to have you join via Zoom (DM me for info) or on the Homewood campus!

Hire him!! You won’t regret it!!!

If you are here at #bog25 please check out my poster (number 87) tonight! 😁 Showing our work on common variation associated with aneuploidy in human embryos

Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀

Amazing work by my buddy and colleague @supmerlin.bsky.social and Wenhe identifying treatment response specific and dynamic effects of genetic regulation in developmental contexts!!

Extremely hirable guy 10/10

Hello Bluesky 👋🏾

I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.

I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.

Thrilled to see this work out - its been fascinating to look at statistical genetics in these IVF embryo datasets underlying meiotic aneuploidies and recombination! Joint work led with @saracarioscia.bsky.social. See thread below, thoughts welcome!

www.medrxiv.org/content/10.1...

Aneuploidy is the leading cause of pregnancy loss. In work led by @saracarioscia.bsky.social and @aabiddanda.bsky.social, we reanalyzed genetic testing data from 139,416 IVF embryos to discover variants associated with recombination phenotypes and aneuploidy risk. www.medrxiv.org/content/10.1...

My main PhD work is up! See thread below. I would love to discuss! www.medrxiv.org/content/10.1...

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...

GitHub - vikshiv/mumemto: Mumemto: multi-MUM and MEM finding across pangenomes Mumemto: multi-MUM and MEM finding across pangenomes - vikshiv/mumemto

This is possible because we can now merge new assemblies as they are released easily without re-running Mumemto on the whole pangenome! We're just providing the non-zoomable image while we await the final HPRC publication. Preprint: www.biorxiv.org/content/10.1...
Github: github.com/vikshiv/mume...

Fortunes at the Battle lab lunar near year celebration were on brand. Love the lab. Watch out for confounders this year everyone, and happy new year.

Mumemto: efficient maximal matching across pangenomes Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.