XIST plays a key role in X-chromosome inactivation (XCI) and thought to be transcribed exclusively from the inactive X in female (XX). In this new study led by Kevin O’Leary, a talented MSTP student, we find both views need to be updated. @genomeresearch.bsky.social doi.org/10.1101/gr.2...

Don’t know what to make of this. The temp is below 20F, but this spring flower??

In prep for a talk, I asked DALL•E to make an image of “mouse developing heart”. It became more creative than I expected and got me this 😂

This week, we published in @science.org an article outlining the current ethical and societal implications of research involving human neural #organoids and #assembloids, their transplantation, and highlighted potential next steps.

New work by @gleesonlab.bsky.social & colleagues in @cp-cellstemcell.bsky.social “A phenotypic brain organoid atlas and biobank for neurodevelopmental disorders” 🧪🧠🧫🧬 www.cell.com/cell-stem-ce...

🚨To celebrate #WorldMentalHealthDay, our October issue includes a Focus that examines the advances in computational psychiatry and the challenges of developing computational models to address mental health disorders. #mentalhealthresearch #Psychiatry ➡️ nature.com/collections/... 🧵(1/8)

Excited to have Mark from Yale visit us and speak in our AI seminar series tomorrow, co-sponsored by the new Data Science Institute at @einsteinmededu.bsky.social lots of to learn and catch up

🚀 NY-CURES Launch — Championing State-Wide Investment in Science! 🚀 Our new coalition advocates for sustained public support of New York’s vibrant biomedical research ecosystem — creating cures, economic gains & strengthening communities. Sign up. Stay informed. Join the movement: www.nycures.org/

🚨 Excited to share the latest preprint form the lab ➡️https://tinyurl.com/32d3be9f Here we tackle a long-standing chicken-or-egg 🐣🥚question in #autism and developmental neuroscience ➡️ Is excitation–inhibition (E:I) imbalance a "cause" or a "consequence" of #autism? Check out what we found! 🧵1/n

Still like UMAP? Why stop at one when you can make lots of them. Then you may learn something new from them and if they represent your data well.

PSA: if you're not a mouse person you may enjoy knowing that mouse Sca1 (the hematopoiesis marker) is not encoded by Sca1 (spinocerebellar ataxia 1) but rather Ly6a. I mean, OF COURSE it is. What else could it be? I'm an hg38 person and below is a self-portrait while I was figuring this out.

“With these considerations, we expect to fund through the 4th percentile.” There it is, in black and white, the destruction of cancer research in the US.

As we have learned, genes have dose-dependent effects on psychiatric traits. DOSAGE, it turns out, is a key element that helps unravel mechanisms of gene → pathway → cell type → brain region → diagnosis. Here we developed a framework to characterize cellular processes that mediate genetic effects.

Neuron programming! Pro-neural TFs + 480 morphogen conditions + scRNA-seq --> Diverse iN subtypes of forebrain, midbrain, hindbrain, spinal cord, and PNS. @hsiuchuanlin.bsky.social‬ @jasperjanssens.bsky.social‬ and Treutlein Lab! @science.org www.science.org/doi/10.1126/... #NGN2 #ASCL1

Since reading the first scATAC-seq paper, I had been wondering if the reported difference from scRNA-seq results is due to bioinformatic algorithms or biology. Finally we got a chance to look into this, by applying the same algorithm to both data types and their direct integration.

Great to see this collaboration work finally out. Congratulations to Wong, Chi and all authors!

Now online! Digital reconstruction of full embryos during early mouse organogenesis

Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice. https://www.biorxiv.org/content/10.1101/2025.06.04.657776v1

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

Yesterday we cheered the #EinsteinClassof2025 at David Geffen Hall at Lincoln Center as they marked the start of their careers and their contributions to medicine, science, and human health! And congratulations to the families and loved ones who have supported these students!

Yesterday, the Graduate Programs in the Biomedical Sciences honored the connection between graduating Ph.D. students and their mentors during its 6th annual Ph.D. Convocation. The event featured a video in which mentors and students shared reflections and paid tribute to each other. #Classof2025

Very nice new work to advance our understanding of the link between CHD8 mutations and ASD. Add to weekend reading

Today in @nature.com , we report a spatial single-cell atlas of human cortical development, revealing surprisingly early specification of human cortical layers and areas. We built an interactive browser to explore the spatial data: walshlab.org/research/cor... Paper link below 👇

We introduce POPARI -- an interpretable, spatially-aware factor-based model for multi-sample spatial transcriptomics, capturing spatial patterns of gene programs and how they vary across samples and conditions.

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Today, Einstein announced the launch of its new Data Science Institute. The dynamic, state-of-the-art resource will strengthen researchers’ ability to harness vast amounts of data for biomedical breakthroughs and innovations in scientific discovery and patient care. #datascience #research #MedSky

Delighted to share our new preprint, the outcome of many years of collaborative work with Giuseppe Testa’s group, both at the bench & in front of the computer, probing human brain evolution using organoids. We tried something cool, and learned a lot 🧪🧫🧠🧬 [follow 🧵] www.biorxiv.org/content/10.1...

ASAN, Autistic Women & Nonbinary Network, the Autistic People of Color Fund, Autism Society of America, Autism Speaks, The Arc, and others stand united: Autistic people deserve respect, support, and science-based policy, not dangerous disinformation. autisticadvocacy.org/2025/04/lead...

Faculty senates at Rutgers University, the University of Nebraska at Lincoln, the University of Indiana at Bloomington, and the University of Massachusetts at Amherst have passed resolutions calling for the creation of a mutual-defense compact. chroni.cl/4cBFrnu

We are proud to announce Bing Ren, PhD, as the new Scientific Director & CEO of the New York Genome Center Dr. Ren brings his expertise in the fields of genomics & epigenetics to the NYGC & Columbia University, where he will hold a joint appointment. For more on Dr. Ren: bit.ly/3DJXtah

every college, corporate, and nonprofit president right now

Our genome encodes > 7000 microproteins that have been previously ignored in genome annotations. How do these microproteins impact tissue function? Here, we use an in vivo single-cell CRISPR screen to systematically explore microprotein function in the mouse epidermis. 1/9

scNET combines single-cell gene expression information with protein–protein interaction networks using a dual-view architecture to better characterize changes in cellular pathways and complexes across cellular conditions. www.nature.com/articles/s41...

Still processing what this means. www.statnews.com/2025/03/17/t...

Beyond diagnosis: Nathalie Gerstner mapped gene expression and chromatin accessibility in the orbitofrontal cortex, to explore how genetic risk for psychiatric disorders shapes brain cells and differs from clinical diagnoses. www.science.org/doi/10.1126/... #Genomics #BrainCells #SingleNucleus

A study from @sergiomarcosalas.bsky.social @nilssonlab.org and colleagues presents a comprehensive evaluation of Xenium in situ datasets and provides recommendations on analysis workflows. @scilifelab.se www.nature.com/articles/s41...

Our lifestyle and environmental exposures are the predominant influencers of healthy aging and premature mortality, compared with polygenic risk, in the first comprehensive assessment www.nature.com/articles/s41... open-access

New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social ! Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families. doi.org/10.1101/2025...

I am excited to share our latest paper @Nature where we construct a hi-res spatial map of the human hypothalamus, the brain region central in appetite control. It is a collaboration between @IMS_MRL @Cambridge_Uni & @MPI_Metabolism www.nature.com/articles/s41...

Check out the revised version of our latest study on uveal melanoma dormancy mechanisms. One year of additional work led by Rama Kadamb in my lab and in collaboration with Andrew Aplin's lab at Thomas Jefferson University. Congrats to all that worked on this paper! www.biorxiv.org/content/10.1...

New in @naturecomms.bsky.social: I'm thrilled to share with you our latest work that applies #srRNAseq to understand splicing accuracy across human introns, tissues and in the context of ageing and neurodegeneration www.nature.com/articles/s41...

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Where do the dopamine hits does from? A new reward center in the brain is discovered (yes, single cell, spatial omics at work again) @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...

New preprint 📣! Excited to share the result of several years of work, led by @ellylewerissa.bsky.social & @olivieroleonardi.bsky.social, in collaboration with friends @naelnadifkasri-lab.bsky.social & Giuseppe Testa. On CHD2, a chromatin remodeller, its role in evolution & development [🧵] 🧪🧠🧫🧬

What DNA variants alter transcription factor (TF) binding affinity? Here, we describe a new workflow baal-nf. We used it to trawl through 6017 ChIP-Seq data sets for 558 TFs and 46 genotyped cell lines, finding 298,783 allele-specific binding sites (ASBs). www.biorxiv.org/content/10.1... 1/2

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

Happy Holiday

A fantastic work from Dr. Tuomas Tammela’s lab at MSKCC (still in the other site 😀) out in @natureportfolio.bsky.social Several years in making, very grateful for the opportunity to make a small contribution from my group . www.nature.com/articles/s41...

Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!