Synthetic Regeneration Laboratory at Columbia

#SyntheticRegeneration & Systems Physiology Laboratory @Columbia | Engineering Tissue Healing through Systems Physiology

[Synthetic Regeneration Laboratory at Columbia @SynRegLab]

Check out our latest study on wound healing!
#SyntheticRegeneration

[Yvon Woappi @DrWoappi]

To regenerate organs, we must 1st decode how they heal. Mammals have repaired tissues for millions of years, yet the instruction manual for organ-scale coordination remained a mystery.

📢We constructed OWHA, a 4D multimodal healing atlas to study this!📢
#SyntheticRegeneration

[Arjun Raj @arjunrajlab]

NimbusImage has a Zenodo integration now! Store your images in a project, then push all the images and analysis to Zenodo to be compliant with data management policies! (You can also just make your images publicly accessible in NimbusImage directly, no account required.)

[Caleb Ellington @probablybots]

Virtual cells are supposed to help drug discovery. Why aren't they evaluated on drug discovery tasks? In our new preprint "Cell-Level Virtual Screening," we investigate this and other fundamental questions about practical applications of virtual cells for drug discovery.

[ZhuangLab @ZhuangLab]

What is the global structure of cell-state space—and how do perturbations drive transitions within it?

Excited to share our new preprint (https://t.co/ZTlAY4eaJf), a work in collaboration with @JswLab.

[Jerzy Szablowski @JerzySzablowski]

qPCR allowed us to measure transcripts, but just once, destructively, and only in post-mortem tissues. Here, we show we can record transcript level history in vivo and recover this information with a blood test to make a "noninvasive qPCR". https://t.co/fe6yjsrdGr

[Arc Institute @arcinstitute]

Listen to a preview of PerturbSpace from first author @alexnevue:
https://t.co/C80g5gkhL1

Or go behind the scenes of the paper in this blog post: https://t.co/KGb8qZQrzl

[Arc Institute @arcinstitute]

Most spatial CRISPR screens require trade-offs in throughput or readout depth. A new preprint from @alexnevue, @Inna_Averbukh, @Davidlarastiaso & team introduces PerturbSpace: spatially resolved, multimodal, whole-transcriptome on standard single-cell workflows.

[Kyle Farh MD PhD - Illumina AI Lab @KyleFarh]

One limitation of single-cell CRISPR screens is losing spatial context after tissue dissociation. This new paper introduces Spatial Perturb-seq to study gene knockouts in intact tissue. 🧠🧬

In mouse brain, it captures both cell-intrinsic effects and how perturbations alter ajacentd cell networks.

https://t.co/NNfWgwKD8F

[Association for Single Cell Analysis @ascanet]

Zhang et al. developed spatial CRISPR screen sequencing, coupled with a statistical spatial perturbation analysis toolkit, TARDIS, to leverage the single-cell-resolution spatial whole transcriptome:
https://t.co/LBS9UXSXOx

#SingleCell #SpatialBiology

[STOmics @ST_Omics]

Imagine trying to reverse-engineer a beating heart or a developing nervous system from scratch. To do that, you need the ultimate 3D molecular blueprint.
Today, we finally have it. 🧵👇

[Cancer Research @CR_AACR]

New in Computational Cancer Biology and Technology from the May 15 issue—In Silico Reconstruction of Primary and Metastatic Tumor Architecture Using Geographic Information System–Augmented Spatial Transcriptomics https://t.co/hrcbV0UxjK

[David Lagares, PhD, MBA @david_lagares]

Our latest paper is out @ScienceTM! Natural killer cell immunotherapy reverses lung fibrosis by eliminating senescent fibroblasts | Science Translational Medicine https://t.co/YPwY048I3I #Immunotherapy #Fibrosis #Aging #Senescence #NKcell

[Le Cong@Stanford, AI+Bio+Gene-Editing @lecong]

Can we program cells like computers — using RNA?

Two years ago, our group trained the first language model to decode the regulatory grammar of 5′ UTRs in mRNA, published in Nature Machine Intelligence.

Today, we’re excited to share the next step, also in Nature Machine Intelligence:
“Programmable RNA translation through deep learning-driven IRES discovery and de novo generation.”
We built an AI engine to discover, predict, optimize, and generate IRES elements — RNA control modules that regulate translation initiation.

This brings us closer to programmable RNA systems that control when, where, and how strongly proteins are produced inside cells.

AI is no longer just helping us read biology.
It is beginning to help us write it and harness it.

The future of computing may not only run on silicon — it may also run inside living cells.
#AIForBiology #LLM #AI4S #AI #RNA #MachineLearning #Bioengineering

[AbdulAbdul @Abdul_Squared]

Spatial genomics has existed for many years, but it has often been limited by complex imaging systems, specialized equipment, and $$$.

With IRISeq, we wanted to simplify this to a simple PCR rxn. https://t.co/jmS3N6PRu2

[Rahul Satija @satijalab]

Interested in single cell and spatial genomics? Check out the agenda for our 10th Single Cell Genomics Day on Friday 6/12.

Speakers: Aviv Regev @anshulkundaje @junyue_cao @xinjin + many more! All talks are free and live-streamed at https://t.co/KJpeGwWLIr

[Fabian Theis @fabian_theis]

Excited to share our RegVelo paper in Cell
https://t.co/ZAnQphaXsg

We unify RNA velocity + GRNs into one model → better OOD prediction of perturbations (e.g. gene KOs), with examples incl. neural crest KO predictions 🔬

Big thanks to W Wang, Z Hu & T Sauka-Spengler 🙏

[Dilum Sanjaya @DilumSanjaya]

Fun interactive science app ideas | Part 3

Played around with generating 3D biological structures and made an app to explore them interactively

UI Design
GPT Images 2

Code
Gemini 3.1 Pro

More demos ↓

[Kai Mesa @KaiMesaLab]

🎉 First preprint from our lab! Regulatory T cells are selectively recruited to regenerating but not scarring mouse digit tips, driving macrophage-mediated bone remodeling essential for regrowth. #immunology #regeneration https://t.co/booG4e2H6A

[Eytan Ruppin, MD, PhD @EytanRuppin]

🚨 Out today in Cell! @CellCellPress

Path2Space: #AI that predicts spatial transcriptomics (ST) from H&E pathology, enabling spatial biomarker discovery in #BreastCancer at scale.

📄 https://t.co/GtrmH9zIDs

🧵1/8

[Ron Alfa @Ronalfa]

What if we could use a foundation model to simulate human biology from mouse data?

Today, we're sharing Perturb-MARS, a platform for genetics and drug treatment in vivo at SCALE.

... and we HUMANIZE the read-outs using TARIO-2.

[bianca dumitrascu @bidumit]

Excited for the chance to present our framework for interpretable disentanglement in multi condition data at ICML' 26 https://t.co/rEOujV3ekd . While useful for different types of data, we think it's particularly useful if you have omics collected across distinct covariates!