definitely not AI generated

ChromSMF preprint is out!🚀
tinyurl.com/ChromSMF

We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting!

In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬

What does this unlock? ⬇️

In collab w @hdashnow.bsky.social, we have a new preprint out on tandem repeat (TR) mutagenesis! Using HiFi sequencing, we profiled nearly 8 million TR loci across four generations of a large CEPH/Utah family and identified 1,270 de novo expansions and contractions.
www.biorxiv.org/content/10.6...

More broadly, it has become clear in the past few years that long-read sequencing offers an advantage over short reads when it comes to detecting disease-causing variants (e.g. complex structural variants). Our work shows that it can also improve the *interpretation* of variation. (n/n)

It's often not feasible to collect samples from both biological parents for genetic testing. With current technologies, it is not possible to detect de novo variants in these cases, which decreases the yield and leads to missed diagnoses. We're hoping duoNovo will help address this. (2/n)

Very happy to share our work with Seth Berger and UCI-GREGoR at @ajhgnews.bsky.social .

We developed and extensively evaluated a method - duoNovo - that uses long-read sequencing to detect de novo variants using *only one* biological parent. (1/n)

R package: github.com/sbergercnmc/...

A reminder that we are actively recruiting a geneticist to the Department of Genetics at Albert Einstein College of Medicine

careers-einstein.icims.com/jobs/17847/a...

has, of course, proved correct.

May he rest in peace. (n/n)

by Aravinda Chakravarti, offering commentary and personal insight on his pioneering work on QTL mapping with Eric Lander. His belief that the future of biology is unrelentingly quantitative and as a result we need to reimagine biology education at the undergrad and graduate levels, (3/n)

imbuing the atmosphere with intensity and keeping the speakers earnest when needed. I could tell then that he was a scientific giant, but I now also recognize how unusual his commitment to education was. He was the only faculty who attended a (fantastic) workshop on trait-gene associations (2/n)

Sad to hear of David Botstein's passing. I got into Genomics after attending the famous Bar Harbor course at Jackson Labs in 2013. Botstein was the senior lecturer that year. He had an incredible presence throughout those two weeks, (1/n)

A new preprint out with Shamil Sunyaev. We talk about GWAS, gene expression, evolution, and why searching for trait-associated eQTLs is easier in cattle and pigs.
www.biorxiv.org/content/10.6...

Please share this with your network: Postdoctoral position available in my group.

www.linkedin.com/jobs/view/43...

Very important work to reconcile canonical transcription initiation structures with the promoter diversity occurring in vivo. Some explanation on how the large majority of our promoters (TATA-less) ma initiate transcription through contacts downstream of the TSS.

SET1/MLL complexes control transcription independently of H3K4me3 Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...

An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!

www.biorxiv.org/content/10.6...

Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...):
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.

Application to speak in the Fragile Nucleosome series Thank you for your interest in our seminar series! We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...

Do you have an exciting new chromatin/transcription story that you'd like to share with the #FN community?

Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...

Please repost and share!

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...

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...

It's publication day, and Cold Spring Harbor Laboratory Press is running a promotion bundling the hard cover and e-book, and other offers:
cshlpress.com/default.tpl?...

#EpigeneticsBook

A challenge faced by many families undergoing genetic testing is that it's not feasible to collect samples from both biological parents. Hoping duoNovo can help address this.

Identification of de novo variants from parent-proband duos via long-read sequencing While de novo variants cause many Mendelian disorders, their detection currently requires sequencing of the proband and both biological parents. This is not feasible when only one parent is available,...

Looking forward to presenting duoNovo at ASHG this week.

We use long-read sequencing to detect de novo variants without having to sequence both parents. It's conceptually straightforward, and performs very accurately among variants likely to be clinically relevant.

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

Thanks, John. Hope this ends up being useful!

David Baltimore YouTube video by InfiniteHistoryProject MIT

One of the greats of 20th century biology. What a life.

www.youtube.com/watch?v=v9Em...

yeah it's a very vanilla setting

That's amusing for sure. But still, the approach is imo quite interesting and there's interesting results, e.g. the lower MAE for dispersion.

Negative binomial regression and inference using a pre-trained transformer Negative binomial regression is essential for analyzing over-dispersed count data in in comparative studies, but parameter estimation becomes computationally challenging in large screens requiring mil...

This looks like a creative use of transformers. Looking forward to diving into this.
arxiv.org/abs/2508.04111

My book Epigenetics: History, Molecules and Diseases will be published in exactly one month (September 2).

Finalizing cover (looks great), probably going to printer this week.

Nervous anticipation is the mood right now.

#apaperaday is back from holiday. Yuzu is still with the birbsitter so a holiday picture it is. Today's pick is from @nejm.org by Musunuru et al on an N=1 case (patient with severe metabolic disease) treated by base editing (CRISPR therapy). DOI: 10.1056/NEJMoa2504747 Very good way to restart!

Multiple headlines about the first CRISPR 2.0 personalized genome editing and photo of the baby treated

This week's genome editing triumph is a big deal.
Here's why
erictopol.substack.com/p/the-first-...

Reminded of Ed Yong’s response to this question:

“If I cover a preprint, I talk to 2-3 experts to get their views before writing the story.

That’s exactly what I do if I cover a journal article…”