I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...

My Peer Review of The 1%

I wanted to like QED's new 1% ranking. I don't.

open.substack.com

geneticcounseling.bsd.uchicago.edu

Hey @genomeresearch.bsky.social, second time I decline a review assignment (sorry, just really busy this month), but your system still sends reminders of the request. Something seems to be wrong in recording the response. Promise to accept assignments as soon as have some bandwidth!

We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes; however, population-scale pang...

biorxiv.org

Single Cell Genomics Day: A (Virtual) Practical Workshop. June 12, 2026, organized by @nygenome.org's Rahul Satija Free, livestreamed, no registration.

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

journals.plos.org

Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago. Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia open.substack.com/pub/blekhman...

Seven points on the current state of AI in genomics

A grounded take from the messy middle of an AI revolution

open.substack.com

Had an amazing time at #BOG26 — and even got to give my first talk 🥳

Happy to share our new preprint on non-coding genetic variation in the human brain and Parkinson's disease. Great team effort with @alexanrna.bsky.social, @juliedeman.bsky.social, Koen Theunis, and all co-authors, supervised by @steinaerts.bsky.social and @jdemeul.bsky.social. Thread below:

Alexandra P@alexanrna.bsky.social · 4mo ago

1/ 🧬 Happy to share our new preprint on modeling cis-regulatory variation in human brain enhancers across a large Parkinson’s disease cohort: www.biorxiv.org/content/10.6... Details in the thread below:

New paper alert: Our latest shows how maternal diet impacts ribosome levels and early growth intergenerationally in #Celegans Led by Sigma Pradhan and in collab with @nstroustrup.bsky.social journals.plos.org/plosbiology/... @plosbiology.org @izb-unibern.bsky.social @unibe.ch

📣 New preprint 🧵: we profiled post-mortem human BA22 (speech cortex) in autism across 100 donors using single-nucleus multiomics (~500,000 nuclei), integrating RNA + chromatin accessibility. Shout-out to my co-first authors Varun Suresh and Yuhan Hao: www.biorxiv.org/content/10.6...

Our latest publication is now out at Genome Biology! link.springer.com/article/10.1... We uncover a unique association between a H3K27me3 reader complex and active transcription. A thread with our key findings: (1/8) #TEsky #Polycomb #transcription #smallRNAs

A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium - Genome Biology

Background The ability to deposit histone H3K27-trimethyl (me3) marks is essential for transcriptional repression by Polycomb Repressive Complex 2 (PRC2). This is largely attributed to Polycomb repres...

link.springer.com

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

Beyond the mean: genetic control of gene expression fidelity and dispersion www.biorxiv.org/content/10.6...

@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...

"Beyond the baseline: mapping the context-specific regulatory landscape of disease" by Yoav Gilad and Alexis Battle authors.elsevier.com/sd/article/S...

New review on context-specificity and disease genetics from @ygilad.bsky.social and me: authors.elsevier.com/sd/article/S...

www.sciencedirect.com/science/arti...

Beyond the baseline: mapping the context-specific regulatory landscape of disease

Genome-wide association studies have identified thousands of intergenic variants associated with disease, most of which are presumed to act by affecti…

sciencedirect.com

UAB is recruiting neuroscience faculty at two different levels - come join our vibrant neuroscience community!

UAB Comprehensive Neuroscience Center@uabneuro.bsky.social · 5mo ago

The UAB Heersink School of Medicine is seeking to recruit up to 16 new research-intensive faculty as part of a major strategic investment in neurosciences. Faculty will be housed in a brand new research facility at the heart of campus, which is scheduled for completion this summer.

Finally, today's offering! www.biorxiv.org/content/10.6... This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social

Pre-print on cardiomyocyte response to novel anti-cancer drug CX-5461 now published! Includes new gene expression response data at higher CX doses. Response to micromolar CX doses starts to mimic DOX responses, suggesting that off-target effects on the heart should be considered for this drug.

CX-5461 and doxorubicin activate a shared DNA damage-associated transcriptional response in human cardiomyocytes

Abstract. CX-5461 (CX) is under investigation for the treatment of late-stage cancers. While CX was first described as an RNA polymerase I inhibitor, it ha

academic.oup.com

I can hardly find science posts here. I don't know how to change that. Yes, I know a lot is going on (obviously), but I get all the other things everywhere... this was where I used to get the science 😞

Recommended

Luisa F. Pallares@luisapallares.bsky.social · 5mo ago

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥 www.biorxiv.org/content/10.6...

My daughter Maya, who had to wear a scoliosis brace for 2 years, wants to connect with other teens who live with invisible diseases. www.under-the-iceberg.com/about

About | Who We Are — Under the Iceberg

Learn about Under the Iceberg, a youth organization dedicated to nurturing future leaders through education and growth. Contact us to join or collaborate.

under-the-iceberg.com

This action could not be completed, please try again later. What a joke

We're hiring for multiple open rank positions in the broad areas of biochemistry, molecular biology, and computational biology. With the recruitment of a new chair our Departmental strengths now include nuclear architecture, genomics and ancient DNA. jobs.sciencecareers.org/job/676677/b...

Biology Faculty Opportunities (Open Rank) - Galveston, Texas job with University of Texas Medical Branch | 676677

The Department of Biochemistry and Molecular Biology at UTMB Health invites applications for multiple tenure-track positions at all ranks; assistant,

jobs.sciencecareers.org

Faculty position at the department of medicine, University of Chicago. Please share.

Yoav Gilad@ygilad.bsky.social · 8mo ago

academicjobs.uchicago.edu/positions/16...

I’ve been wondering more and more if TADs are about limiting recombination search and less about gene expression?

Alejandro Montenegro@aemonten.bsky.social · 8mo ago

"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD. (...) These results suggest that TAD boundary architecture and gene activity are largely uncoupled"