Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we: 1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs bsky.app/profile/bior...

Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate https://www.biorxiv.org/content/10.1101/2025.09.23.678137v1

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

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...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Fascinating new work by @federicamosti.bsky.social @debbysilver.bsky.social on human-specific neurodevelopment, linking ‘Human Accelerated Regions’ to chromatin architecture, cortical cell fate and expansion and folding of brains 🧪🧠🧬 www.biorxiv.org/content/10.1...

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.

The Anne West lab at Duke is hiring a postdoc to work on nuclear cell biology in neurogenesis. Please help me spread the word! Applications to [email protected].

Two parallel lineage-committed progenitors contribute to the developing brain https://www.biorxiv.org/content/10.1101/2025.07.02.662771v1

🧵Excited to share our new preprint introducing iHOTT - an autologous tumor-immune co-culture model that captures patient-specific responses in #Glioblastoma 💥Now on @biorxivpreprint : biorxiv.org/content/10.1... Led by Dr. Shivani Baisiwala, Neurosurgery Resident in the lab

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...

Excited to share our latest manuscript, a collaboration with @justinperryphd.bsky.social led by Weill Cornell Neuroscience PhD student @annbaako.bsky.social. Ann developed a new, improved mouse PSC model for studying tissue-resident macrophage differentiation. www.biorxiv.org/content/10.1...

It’s out! The first paper from my postdoc – and first from the @bhadurilab.bsky.social – is now live @natneuro.nature.com . 🧠✨ Using a new meta-atlas generation strategy, we identified functional gene networks that more fully explain how cell types are formed in the human cortex. (1/13)

Preprint from @bhadurilab.bsky.social: Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Upper Layer Neurogenesis (www.biorxiv.org/content/10.1...)

What contributes to human specific neural specification? Check out these two wonderful preprints from a wonderful scientist Ava carter! 1. www.biorxiv.org/content/10.1...; 2. www.biorxiv.org/content/10.1... Stay tuned! third preprint is on its way!

💫 New preprint from the lab: Comparing great ape cerebral organoids, we found that human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution. Fantastic work from super-talented PhD student Theresa Schütze! www.biorxiv.org/content/10.1...

Delighted to share our most recent preprint led by the incredible @MilJessenya and @Jalbsoto! In this study, we generated a metabolomic atlas of human cortical development and discovered that the pentose phosphate pathway regulates radial glia cell fate. www.biorxiv.org/content/10.1...

Our collaborative project with Matthias Stadtfeld and Jason Mezey labs has now been published. We examined how genetic variation impacts regulation of DNA methylation at the control regions of imprinted genes in naive pluripotent stem cells. www.cell.com/stem-cell-re...

⚡Next #FragileNucleosome meeting is less than a week away! Three amazing ECR scientists, 🔬@anajaneva.bsky.social, 🧠@anastasiahains.bsky.social, & 🧬@martyyang.bsky.social will discuss their research next Wed! 🗓️Don't forget to register: us06web.zoom.us/webinar/regi...

Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers https://www.biorxiv.org/content/10.1101/2025.01.17.633622v1

Excited to share the second story from my post-doc in pre-print form! Many thanks to @vram142.bsky.social, lab members, and collaborators for contributions! In brief, we examine heterogeneity in (sub)nucleosome structure from in vivo long-read m6dA footprinting data. See Vijay's thread for details.

Our latest paper, led by Emmy Li, is out on Neuron today: CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions www.cell.com/neuron/fullt...

Happy to share our mouse cortical organoid system, which recapitulates in vivo tempos and cell types. We used it to identify gene expression changes across subspecies during development, which might underlie neuroanatomical differences and affect disease penetrance. www.biorxiv.org/content/10.1...

Excited to share the first story from my post-doc, co-led with Megan Ostrowski! Many thanks to @vram142.bsky.social and all our wonderful co-authors and collaborators for making this project a huge success: www.cell.com/cell/fulltex...

Very excited to share our latest @vram142 lab preprint on developing methods for long-read footprinting of protein-DNA contacts in newly replicated chromatin fibers, co-led with Megan Ostrowski. www.biorxiv.org/content/10.1... (1/x)