Ever wondered how robust cellular identity is to external perturbations? Here we disrupt cellular environmnent in vivo and in vitro, and find cell population specific sensitivities. Environment sculpts development yes, but not all cells are made of the same wood. www.science.org/doi/10.1126/...

Thrilled to announce the upcoming Center for Epigenetic Research Symposium @mskcancercenter.bsky.social on Nov 17! 🎉 A full day of cutting-edge science featuring stellar external speakers & our outstanding trainees. Registration is now open! Join us in NYC or virtually from anywhere! link⬇️

Molecular rewiring of human induced pluripotent stem cell-derived cardiomyocytes during metabolic maturation https://www.biorxiv.org/content/10.1101/2025.09.14.676131v1

Here's a link to the paper: Beyond Mechanism—Extending Our Concepts of Causation in Neuroscience onlinelibrary.wiley.com/doi/10.1111/...

1/7 Really happy to see my PhD work published in ✨Developmental Cell✨ today! We find human endoderm is specified by two developmental trajectories 🔀, and the choice between alternate routes is dictated by the combinatorial BMP4/Activin signalling. www.cell.com/developmenta...

New review on how changes in cell type composition in and outside the brain contribute to the evolution of behavior. 🧪 authors.elsevier.com/a/1lihM,LqAZ...

Start the weekend by checking out the latest paper from the Vierbuchen lab, spearheaded by amazing @danielmedinacano.bsky.social 🎉 Congrats to all authors!!

Nice piece from our JAX Communication team outlining our efforts within the MorPhiC Consortium towards characterizing the function of all human protein coding genes: www.jax.org/news-and-ins...

Congrats to Tommy and team, especially to PhD student Veronika Petrova who led the work on our end. Great to see it out! @victorchang.edu.au

“A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro” Nice work by @danielmedinacano.bsky.social @tvierbuchen.bsky.social @em6wong.bsky.social @stadtfeldlab.bsky.social 🧪🧫🧠 www.cell.com/developmenta...

… my work with the Stadtfeld lab @stadtfeldlab.bsky.social‬ on the role of OTX2 during definitive endoderm and anterior gut development is also out (tinyurl.com/3unwh3eb)! Thank you so much to all collaborators, and I’ll be more than happy to discuss these protocols with anyone interested!

Fully integrated hybrid option available for the XII International Avian Meeting @stowersinstitute.bsky.social! Submit an abstract, present your work and participate in Q&As—remotely or in person. @biologists.bsky.social awards available for early-career researchers on-site. tinyurl.com/avian-models

I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…

A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro: Developmental Cell www.cell.com/developmenta...

Excited that the paper presenting our mouse brain in vivo CRISPR screening platform is out today in @natneuro.nature.com! Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab. www.nature.com/articles/s41...

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...

Excited to share our new study in @cp-devcell.bsky.social dissecting how the brain-associated transcription factor OTX2 drives anteriorization of the mammalian gut by enhancer remodeling using stem cell-based models. #development #enhancers #patterning #stemcells www.cell.com/developmenta...

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

Our latest preprint is out, focusing on characterizing the response of Lhx6-positive neurons of the zona incerta (ZI) to naturally-occurring and experimentally-induced changes in the need to sleep, also known as sleep pressure. www.biorxiv.org/content/10.1...

Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription https://www.biorxiv.org/content/10.1101/2025.08.01.667454v1

1/5: How does a presumably redundant microRNA contribute to mammalian brain development and neurodevelopmental disease? Check out our new work led by Dr. Santiago Fregoso now on bioRxiv! www.biorxiv.org/content/10.1... #Neurodev #miRNA #hydrocephalus #Genetics #bioRxiv.

Loss of miR-9-2 Causes Cerebral Hemorrhage and Hydrocephalus by Widespread Disruption of Cell-Type-Specific Neurodevelopmental Gene Networks. https://www.biorxiv.org/content/10.1101/2025.07.31.668014v1

Telomere-to-telomere DNA sequencing is set to transform the field of human genetics in coming years. For a flavour of what's coming, see this exciting work on nearly complete genomes of 65 individuals from diverse populations, out today in @nature.com by @glennislogsdon.bsky.social & colleagues. 👇🧬🧪

Ryan’s paper out in Neuron (bit.ly/3IICGFX). He derived bona fide parvalbumin (PV+) cortical interneurons from hPSCs, one the slowest developing neurons, and could capturing interneuron-related disease phenotypes linked to schizophrenia - including impaired gamma-oscillations - in his assembloids.

Also - Ryan is on the job market for a PI position ([email protected]), so if your department is interested in hiring someone who will be a leader in next generation human PSC-based CNS disease modeling for neuropsychiatric disorders such as SCZ, he is a brilliant choice!

Arrayed single-gene perturbations identify drivers of human anterior neural tube closure https://www.biorxiv.org/content/10.1101/2025.07.21.665862v1

Path through the woods

A discussion of the use of animals in research. www.youtube.com/watch?v=iSvk... 1/n (Warning: Rant coming)

Dear all, PLEASE add comments on the importance of model organism research at this link:

Just submitted a comment stating my strong belief that human cellular models are not sufficient to replace in vivo studies in model organisms. Please take a moment to add a comment before the deadline tomorrow.

Homozygous kinase-dead Csf1r mutation in outbred mice reveals essential and redundant functions of tissue resident macrophages https://www.biorxiv.org/content/10.1101/2025.07.08.663807v1

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

Too hot to play...

Checking out Manhattanhenge in the park

Social media has truly warped science consumption. On one hand it has massively democratized it. On the other hand, it's become extremely easy to use hype to simply amplify things that are simply not true. 1/

We are thrilled to announce a landmark alliance between The Jackson Laboratory (JAX) and The New York Stem Cell Foundation to transform disease research and accelerate the discovery of life-changing therapies and cures. 🧬🧪

I wrote down some of my thoughts down on the current race to build virtual cell models. Overall, excited and wary about the work ahead. Also, it's my first post to Substack; getting more excited about it as a replacement for X and Blue Sky. srikosuri.substack.com/p/the-elusiv...

Oh, horrible vultureism of earth! from which not the mightiest whale is free.

Genetics of growth rate in induced pluripotent stem cells https://www.biorxiv.org/content/10.1101/2025.07.02.662844v1

The human transcription factor occupancy landscape viewed using high-resolution in situ base-conversion strand-specific single-molecule chromatin accessibility mapping https://www.biorxiv.org/content/10.1101/2025.06.27.662080v1

New collaborative study out with Mark Wu’s group identifies a thalamic reuniens-zona incerta circuit as both responsive to induced sleep deprivation and essential for mediating recovery sleep. Further perspective on this work follows./1 www.science.org/doi/epdf/10....

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

Go fund a brain gain The gutting of US research funding represents a once-in-a-generation opportunity for Europe to boost world-class research deprioritized by the Trump administration go.nature.com/4jGhU6V

Our paper on gene regulatory networks controlling hypothalamic and prethalamic development is now out in Cell Reports./1 www.cell.com/cell-reports...

Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis www.cell.com/cell-genomic...

CrossFilt: A Cross-species Filtering Tool that Eliminates Alignment Bias in Comparative Genomics Studies https://www.biorxiv.org/content/10.1101/2025.06.05.654938v1

I’ve been studying gene regulation in primates for over 20 years, and using RNA-seq since 2008 to compare expression across species. We thought we were being careful. We used curated orthologous exons to minimize alignment bias and focused on biologically meaningful comparisons. We were wrong.

Delighted to have our work on Polygenic Modifiers of #TelomereBiologyDisorders, led by Michael Poeschla, @sashagusevposts.bsky.social, @mitchiela.bsky.social, @sharonsavage.bsky.social, @tummalalab.bsky.social, + co, published in @jclinical-invest.bsky.social today: www.jci.org/articles/vie...