Dr. DY Zheng

A robot on a chair sits next to a patient against a backdrop of a medical report. Credit: mathisworks / DigitalVision Vectors / Getty Images

🚨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/...

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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

Fibroblast-Specific Loss of TGF-β Signaling Mediates Lipomatous Metaplasia in the Infarcted Heart | Circulation BACKGROUND: In patients surviving myocardial infarction, adipose tissue infiltration within the scar is a common pathological finding and has been suggested to contribute to dysfunction and arrhythmog...

www.ahajournals.org/doi/10.1161/...

🚀 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!
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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.

Example of how AI helps some PIs’ *productivity*😀

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

This work was led by a talented postdoc Rohan, who is on the job market, and a PhD student Alex, who has graduated. We thank the reviewers and editors for their excellent suggestions and insights.

While we didn’t fully address the original curiosity, biological context seems to have a role. Hope more studies can be done to further explore the contributions of both biology and methodology.

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!

Digital reconstruction of full embryos during early mouse organogenesis Single-cell digital embryo reconstruction during early organogenesis creates spatiotemporal atlases for mesoderm and endoderm lineages and captures the primordium determination zone (PDZ) at the E7.75 embryonic-extraembryonic interface, where cross-germ-layer signaling communication drives organogenesis.

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.

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

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...

Albert Einstein College of Medicine Launches Data Science Institute

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

Regulatory logic of human cortex evolution by combinatorial perturbations Comparative genomic studies between contemporary and extinct hominins revealed key evolutionary modifications, but their number has hampered a system level investigation of their combined roles in sca...

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...

Leading Autism Organizations Release Joint Statement on Upholding Scientific Integrity and Supporting the Autism Community - Autistic Self Advocacy Network April 17, 2025, Washington, D.C. – As national organizations dedicated to advancing the well-being of Autistic individuals, the Autistic Self Advocacy Network, Autism Society of America, Autism…

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...

These Faculty Senates Are Trying to Band Together to Stand Up to Trump The idea of a compact among institutions is based on the idea that there’s strength in numbers, and it comes amid frustration that few presidents are speaking out against the administration’s actions ...

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

Bing Ren Appointed Scientific Director and Chief Executive Officer of the New York Genome Center - March 27, 2025 Read about Bing Ren Appointed Scientific Director and Chief Executive Officer of the New York Genome Center at the New York Genome Center on March 27, 2025

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