Synthetic Regeneration Laboratory at Columbia @SynRegLab
#SyntheticRegeneration & Systems Physiology Laboratory @Columbia | Engineering Tissue Healing through Systems Physiology WoappiLab.com Manhattan, NY Joined April 2022-
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Our 10th Single Cell Genomics Day is next Friday (6/12)! Thanks to amazing speakers Aviv Regev @xinjin @anshulkundaje @junyue_cao and many more! Talks are live-streamed on YouTube and are free (no registration required) at satijalab.org/scgd
Evaluating AI agents for biology is hard: data is noisy and often not cleanly verifiable. This paper constructs 100 synthetic tasks across genomics, transcriptomics, epigenomics, single-cell, and genetics. Agents start from a minimal environment and must fetch data/tools, write code, and solve the task end-to-end. Agents can already handle many well-scoped comp bio workflows: Codex CLI reaches 83% and Claude Code 81% overall, but performance drops on harder tasks. biorxiv.org/content/10.648…
A multimodal perturbation atlas of 1,000 pooled CRISPR knockouts in A549 cells, profiled by fluorescence microscopy (39 live, 13 fixed markers), label-free phase imaging of the same live cells, and single-cell RNA sequencing (scRNA-seq) Totaling ~57 million single-cell profiles Preprint: biorxiv.org/content/10.648…
Combining gene regulatory networks and RNA velocity improves perturbation prediction across systems, highlighting a path toward more mechanistic “virtual cell” models. RegVelo: Gene-regulatory-informed dynamics of single cells cell.com/cell/fulltext/…
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.)
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.
What is the global structure of cell-state space—and how do perturbations drive transitions within it? Excited to share our new preprint (biorxiv.org/content/10.648…), a work in collaboration with @JswLab.
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". nature.com/articles/s4146…
Listen to a preview of PerturbSpace from first author @alexnevue: youtube.com/watch?v=SNzdo8… Or go behind the scenes of the paper in this blog post: arcinstitute.org/news/perturbsp…
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.
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. nature.com/articles/s4146…
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: cell.com/cell/fulltext/… #SingleCell #SpatialBiology
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. 🧵👇
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 brnw.ch/21x2MHz
Our latest paper is out @ScienceTM! Natural killer cell immunotherapy reverses lung fibrosis by eliminating senescent fibroblasts | Science Translational Medicine science.org/doi/10.1126/sc… #Immunotherapy #Fibrosis #Aging #Senescence #NKcell
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
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. nature.com/articles/s4159…
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 satijalab.org/scgd
Excited to share our RegVelo paper in Cell cell.com/cell/fulltext/… 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 🙏
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 ↓
Yvon Woappi @DrWoappi
2K Followers 589 Following Husband and dad, at times professor @Columbia | Proud member of @SynRegLab #SyntheticRegeneration
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Ajay Labade @ajaylabade31
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Yvon Woappi @DrWoappi
2K Followers 589 Following Husband and dad, at times professor @Columbia | Proud member of @SynRegLab #SyntheticRegeneration
Dr. Chrystal Ama Star... @drstarbird
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Denis Wirtz @deniswirtz
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Santiago Correa 🏳�... @SantiCorreaPhD
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Ishmail Abdus-Saboor @IshmailSaboor
21K Followers 2K Following We study how the skin-brain axis drives somatosensory behaviors | Associate Professor @Zuckermanbrain @Columbia_Bio | Freeman Hrabowski Scholar @HHMINEWS
Columbia BME @ColumbiaBME
5K Followers 2K Following Columbia University's Department of Biomedical Engineering is at the Forefront of Converging Health and Engineering
Joel Boerckel @jboerckel
8K Followers 4K Following Mechanobiology of development & regeneration. Assc Prof: @PennMedicine @PennBioeng. Co-Dir: @McKayLaboratory. Dir: @Penn_PCMD Biomechanics Core. Prov. 25:2. 🦛
Oded Rechavi @OdedRechavi
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Harmit S. Malik @HarmitMalik
43K Followers 7K Following Study genetic conflicts professionally. Try to avoid conflicts in personal life (with mixed results). @HutchBasicSci @fredhutch @HHMINEWS He/him
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Dr. Melanie McReynold... @dr_ohsopretty
4K Followers 2K Following Who needs a twitter? I have followers in real life. Assistant Professor at Penn State. Aging, Metabolism, and Faith-Based Science. #BlackandSTEM
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eLife - the journal @eLife
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392 Followers 1K Following Head of Illumina AI Lab. Deep Learning. Human Genetics. Perturb-seq.
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535 Followers 95 Following Stereo-seq technology offers unprecedented field-of-view & nanoscale resolution, providing researchers with a novel tool to explore spatial biology.
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601 Followers 640 Following PI, Associate Professor at Karolinska Institutet. X-chromosome regulation, development, single-cell omics & RNA detection
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806 Followers 803 Following Dermatologist / dermatopathologist-scientist, translational skin cancer researcher, @MoffittNews, Father, Husband
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333 Followers 235 Following HHMI HG Fellow/K00 DSPAN/UNCF E.E. Just/BWF PDEP Fellow. Postdoc in the Abdus-Saboor Lab at Columbia University. Former Ph.D. Student in the Maze lab at ISMMS.
Waggoner Lab @LabWaggoner
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787 Followers 5K Following Machine learning for biology. @ELLISforEurope PhD student @fabian_theis lab. prev. @genentech & @Novartis, MSc @EPFL_en. Opinions stated here are my own.
Valentin Hofmann @vjhofmann
1K Followers 285 Following Assistant Professor @CisLMU @LMU_Muenchen | Formerly @allen_ai @uwnlp @UniofOxford @stanfordnlp @GoogleDeepMind
Moustafa Gabr @MT_Gabr
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AmericanSkinAssociati... @american_skin1
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3K Followers 3K Following Software & AI | Founder, @DAISEA_AfricaBP @EuglenaNetwork & @Gleanloop | PhD, @Cambridge_Uni | Global EM @emblebi DS | former Contractor, @wellcometrust
Sanju Sinha @Sanjusinha7
4K Followers 242 Following Assistant Prof @sbpdiscovery Aging Reserach | PhD in ML→cancer therapies| ex-NCI, UMD, IITG, Max Delbruck, NCL
Sendoel Lab @SendoelLab
234 Followers 216 Following Sendoel lab at @UZH_en, alumnus of the @RockefellerUniv, we are excited about mRNA translation, stem cells and cancer.
Peter F. Renz @PeterFRenz3
97 Followers 156 Following Constantly Curious. Mostly about Single Cells, Signaling, CRISPR and Cancer
Segun Fatumo @SFatumo
5K Followers 1K Following Professor and Chair of Genomic Diversity @QMUL ; Head, NCD Genomics at MRC/UVRI and LSHTM Uganda. Genomics | GWAS | Africa | Capacity Building | Global HealthYou might like
