🖥️🧬🚀 I am excited to share that our #omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130...

Single-subject Proteomic Signatures in Alzheimers Disease Reflect Clinical Phenotypes and Distinguish Asymptomatic from Symptomatic Cases https://www.biorxiv.org/content/10.64898/2026.02.06.704408v1

New pre-print is out! We combined long- and short-read RNA sequencing in iPSC-derived excitatory neurons, astrocytes, and microglia to build a cell-type resolved atlas of NMD-sensitive alternative splicing. www.biorxiv.org/content/10.6...

Please share: we're hiring a new tenure-track faculty member to our Department of Genetics at Albert Einstein College of Medicine. faculty-einstein.icims.com/jobs/17847/a...

Please share this with your network: Postdoctoral position available in my group. www.linkedin.com/jobs/view/43...

Unquestionably the result of combined effort from all current and former lab members, support from colleagues @CSU and @CU, and support from @hhmi-science.bsky.social and NIH over decades. A heartfelt 🙏 to my nominators and of course @vilcekfoundation.bsky.social. vilcek.org/prizes/prize...

Molecular features of human pathological tau distinguish tauopathy-associated dementias www.cell.com/cell/fulltex...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex... TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments. More below 👇

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis: @cellpress.bsky.social www.cell.com/cell/fulltex...

"we find that peripheral cancer inhibits amyloid pathology & rescues cognition via secretion of cystatin-c, which binds amyloid oligomers & activates triggering receptor expressed on myeloid cells 2 in microglia, enabling microglia to degrade the existing plaques in AD mice" doi.org/10.1016/j.ce...

👇 'Here, we systematically benchmark five commercial ST platforms (Visium v1, Visium v2/CytAssist, Visium HD, Xenium, and CosMx) using matched FFPE human tumor sections from six cancer types.' link.springer.com/article/10.1...

New preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.

Preprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them! www.biorxiv.org/content/10.6...

Drug discovery for nervous system disorders is really challenging. We think early/rapid in vivo testing with zebrafish will accelerate the drug development cycle for conserved targets. Check out our proof-of-principle pilot study and virtual drug discovery pipeline (tinyurl.com/3whr23hs). #Skytorial

Paper is here and preview is below. This is case where the long back and forth between authors and reviewers is illuminating and touches on the historical literature elifesciences.org/articles/105...

We are proud to announce a new ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) track for hg38 as described in Moore et al., Nature 2026. See our news for more: bit.ly/ucscENCODE4cCREs

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Most iPSC lines come from European donors. Now, two teams in Africa are studying neurodevelopment and neurodegeneration using iPSCs and organoids from African donors. By Lauren Schenkman www.thetransmitter.org/cellular-neu...

The clock is ticking—Jan 20 is the proposal deadline for Featured Symposia & Interactive Workshops! Make the most of the holiday weekend & finalize your submission for #ASHG26 in Montréal. We’re excited to receive your ideas. Submit now: https://www.ashg.org/annual-meeting-2026/ #ASHG #HumanGenetics

New online: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription

T2T zebrafish annotation drop 🐟

Whole-genome profiling of native 5-hydroxymethylation in human neurons with long-read sequencing https://www.biorxiv.org/content/10.64898/2026.01.11.695537v1

Schaepe et al, 2026. Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.cell.com/cell/fulltex...

Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10.... Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

New Year, New Paper!🎊 Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system www.biorxiv.org/content/10.6... Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵

🔬 pertpy: a unified, scalable framework for single-cell perturbation analysis, now out in Nature Methods Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions. 👉 www.nature.com/articles/s41...

Our paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉 www.nature.com/articles/s41... To celebrate, here’s a "meme-torial" walkthrough of the science. Let’s get started 🧵 1/11

Why do some individuals defy their polygenic score? In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference? www.medrxiv.org/content/10.6...

The countdown is on—3 weeks left! Submit your proposal for Featured Symposia or Interactive Workshop by Jan 20! Need help with your submission? Join our LIVE Q&A on Jan 13 for tips & answers. 📝Submit: https://www.ashg.org/annual-meeting-2026/ 🗣️Live Q&A: https://learning.ashg.org/p/ashg2026-qa #ASHG

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

See this recent paper by @andersshansen.bsky.social that discovers similar microcompartmentalization during mitotic exit: www.nature.com/articles/s41...

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...

Our Science paper is out! Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group News: bit.ly/4avnkAr and bit.ly/3XBGVHS Great perspective by @vram142.bsky.social +K Zhang

CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample? Yes, one can. with CUT&ID ✂️🪪 Spearheaded — singlehandedly — by @annanordin.bsky.social No need of transgenesis, cloning and overexpression. Check it out, it's fast and its works.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

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...

First paper from the lab is now online @natneuro.nature.com ! We mapped injury induced enhancers in the mouse CNS and decoded their sequence architecture. Little 🧵 rdcu.be/eSQi1

Pls Repost: I am putting together an edition of “Methods in Molecular Biology” focused on early development, encompassing gastrulation. I am making a list of potential authors for chapters. If interested, please contact me - An excellent opportunity for trainees to co-author with their advisors.

Proteomic Analysis in Alzheimer's Disease with Psychosis Reveals Separate Molecular Signatures for Core AD Proteinopathy and Postsynaptic Density Disruption https://www.biorxiv.org/content/10.1101/2025.11.26.690872v1

Longitudinal Proteomic Profiling Defines Robust Molecular Subtypes Underlying the Heterogeneity of Parkinson's Disease https://www.biorxiv.org/content/10.1101/2025.11.27.691036v1

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social www.cell.com/cell/fulltex... Key findings in a thread (1/6):

Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...

Looking for some Thanksgiving reading? 🦃🦃🦃 🚨Check out our new preprint on CRISPore-seq!🚨 Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

We are excited to announce our most recent preprint “Single-cell long-read sequencing of the experience-induced transcriptome” (www.biorxiv.org/content/10.1...) led by @sheridan in collaboration with Richard Huganir. A few highlights: