dplyr 1.2.0 is out now and we are SO excited! - `filter_out()` for dropping rows - `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools These are huge quality of life wins for #rstats! tidyverse.org/blog/2026/02...

You can easily switch between magrittr pipe `%>%` and base pipe `|>` in the RStudio settings 🧰 #rstats #dataviz #phd

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain https://www.biorxiv.org/content/10.64898/2026.02.02.703166v1

A projection atlas of excitatory and inhibitory inputs to the preBötzinger Complex: substrates for multimodal breathing control https://www.biorxiv.org/content/10.64898/2026.02.02.703188v1

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...

A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons https://www.biorxiv.org/content/10.64898/2026.01.28.702385v1

First week where planyourscience.com had more than 1000 organic users. I know this is nothing by software standards but it is quite something by academic standards. And to everyone using it - tell me what could/should be better. And use it to export a first draft ;)

SqueakPose Studio: An end-to-end platform for pose estimation and real-time edge-AI deployment https://www.biorxiv.org/content/10.64898/2026.01.24.700912v1

Bright calcium-modulated bioluminescent indicators for activity imaging and red photon-assisted synaptic transmission https://www.biorxiv.org/content/10.64898/2026.01.20.700092v1

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.

TL;DR: Indirect costs as a percentage of total costs - like the private sector tends to calculate it - for NIH grants is typically around 30-35%.

New revolutionary hack about to change our molecular tool-box! Thanks @ioavlachos.bsky.social for sharing this! Rapid evolution of a highly efficient RNA polymerase by homologous recombination 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

Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq https://www.biorxiv.org/content/10.64898/2026.01.01.697286v1

A free, open-access library of high-quality organism illustrations for science communication

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease https://www.biorxiv.org/content/10.64898/2025.12.26.696622v1

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types https://www.biorxiv.org/content/10.64898/2025.12.22.695789v1

I love past me for developing the habit of simultaneously drafting presentation slides when I write papers and/or grant proposals. It makes things sooooo much easier when people ask me to give a talk.

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...

New paper alert!!...🤩 Led by @blogeman.bsky.social, we identify how cell type-specific hormonal responses in the hypothalamus tunes parenting behavior in males and females 🐭🧠🍼. Highlights in thread 👇 1/6 www.biorxiv.org/content/10.6...

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🧵:

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

Our latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...

Hunger increases exploration and risk-taking behavior, allowing an animal to forage for food despite risks Hunger-induced changes in exploration result from the modulation of dopamine signaling in the tail of the striatum via the following circuit: 1/2 www.cell.com/neuron/fullt...

Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...

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

Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation https://www.medrxiv.org/content/10.1101/2025.11.20.25340664v1

The architecture of allele-specific regulatory variant effects across five human genomes https://www.biorxiv.org/content/10.1101/2025.11.22.689315v1

Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia. www.biorxiv.org/content/10.1...

Nice! Whole-genome heritability estimates in the UK Biobank. Average WGS-h2 was 26%, with 21% common and 5% rare. Broadly aligns with recent sib-reg and RDR estimates.

First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....

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...

Here is another way to put the paradox. If you ask, "If I had different genes, would my personality be different?" Then the answer is, "Probably, yes." If you ask, "If I had THESE genes, what would my personality be like?", the answer is, "We don't have any idea."

Friendly reminder that there is only one official release of ChromBPNet at our lab GitHub github.com/kundajelab/chr… There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens https://www.biorxiv.org/content/10.1101/2025.10.11.681797v1

Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass... I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands) #WesternBlot #cellsky

Persistent hindrances to data re-use in single-cell genomics https://www.biorxiv.org/content/10.1101/2025.10.02.680150v1

My Own Lab at Westlake University is OPEN! We are recruiting cool people at all levels NOW! By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!

Every single one of these leaves is a bug.

It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!

mRNA-based sensors are now more modular, but still rely on overexpression of ADAR1 which interferes with endogenous biology. Seems to be a situation where enzyme engineering to make a bio-orthogonal ADAR-like protein that only deaminates the reporter should be within reach.

The great thing about Rosh Hashanah and Fat Bear Week starting the same day is apples and honey is completely appropriate for both

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

Jamie Drayton and I were fortunate to contribute some RCMC analyses to this beautiful paper from Eder, Moene...van Steensel that systematically maps the relationship between enhancer location and gene expression (and nice to see RCMC predict expression in Fig 2H-I): www.science.org/doi/10.1126/...

Very interesting paper from the group of Alistair Boettiger examining DNA contact using long-term live cell imaging. Generated ~75TB of data! www.science.org/doi/10.1126/...

New preprint from our lab! What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells? Find out here: www.biorxiv.org/content/10.1... 👇 1/