Aidan Winters

Safety and feasibility of 4-1BB co-stimulated CD19-specific CAR-NK cell therapy in refractory/relapsed large B cell lymphoma: a phase 1 trial - Nature Cancer Lei et al. develop a 4-1BB co-stimulated anti-CD19 CAR-NK cell product, show efficacy in pre-clinical models, and test safety and feasibility in a phase 1 trial in patients with refractory/relapsed la...

🧬 Promising Results from CD19 CAR-NK Cell Therapy Trial

A Phase 1 trial using CD19-specific CAR-NK cells (CD19-BBz) derived from cord blood showed encouraging safety and efficacy in patients with relapsed/refractory large B cell lymphoma.

www.nature.com/articles/s43...

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences https://www.biorxiv.org/content/10.1101/2025.04.08.647863v1

DNA-guided transcription factor interactions extend human gene regulatory code - Nature A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by complexes of TFs rather than by individual ones.

Nature research paper: DNA-guided transcription factor interactions extend human gene regulatory code

https://go.nature.com/4j13XRc

AIxBio Builders: @vevotherapeutics.bsky.social is joining forces with @hf.co & NVIDIA Healthcare to organize the 1st hackathon to build on Vevo's Tahoe-100M dataset.

Join us! We will select 40 participants, provide compute and a $400 travel voucher for 10 travelers. Details in 🧵

The NCI grant supporting the Columbia comprehensive cancer center was terminated. Tell me how terminating support for cancer research helps the economy.

taggs.hhs.gov/Content/Data...

This breaks my heart. My salary at St. Jude was paid through our comprehensive cancer center grant. My wife's oncologist is at a comprehensive cancer center. Millions of children and adults with cancer get treatment in these 57 centers around the country. These are essential locations for research.🧪

A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)

We are thrilled to share our discovery of a new factor, the RBP RBM42, which is key to fueling pancreas cancer through the deadly oncogene Myc. I look forward to what we uncover next! Thanks to the fantastic team lead by @DavideRuggero @rushika-perera.bsky.social & @genophoria.bsky.social!

Overview of evo2

Evo2: a fully open genome language model that can predict the functional effects of variation and generate large genomic segments

@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social

www.biorxiv.org/content/10.1...

It is always exciting when I have to adjust the y-axis limits of this plot, but extra special this time having been part of this project at @vevotherapeutics.bsky.social! tinyurl.com/vevo-tahoe100

Amazing working with this team!

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...

@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...

A generative framework for enhanced cell-type specificity in rationally designed mRNAs mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...

The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...

Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations Many agents that show promise in preclinical cancer models lack efficacy in patients due to patient heterogeneity that is not captured in traditional assays. To address this problem, we have developed...

Our latest from the indefatigable @thejohnnyyu.bsky.social in collaboration with Weissman and Shokat labs. Meet GENEVA, which enables simultaneous phenotyping and profiling of cancer cell drug responses at scale; both in vitro and in vivo across a variety of models: www.biorxiv.org/content/10.1...

CRISPR-StAR enables high-resolution genetic screening in complex in vivo models - Nature Biotechnology Pooled genetic CRISPR screening is improved in complex models through leveraging internal controls.

Today we published a new paradigm to do CRISPR screens in complex model systems such as in vivo but also e.g. in organoids. The publication came out in Nature Biotechnology.
1/
www.nature.com/articles/s41...

How can we build an Al virtual cell that simulates all functions and interactions of a cell? How will it transform research and drive breakthroughs in programmable biology, drug discovery and personalized medicine?

Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...

Innovators Unveiled: Announcing the Databricks Generative AI Startup Challenge Winners! Vevo Therapeutics has been selected as the Grand Prize Winner of the Databricks Generative AI Startup Challenge has selected.

To build disease-relevant models of the cell, we need perturbative data at scale + AI that can efficiently learn from that data. @vevotherapeutics.bsky.social may be the only team that is pushing the boundaries of both. This recognition from DataBricke is a testament to that dbricks.co/3DbIULQ

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

1/2 🚀 Discrete Optimal Transport (OT) has proved useful in a wide variety of tasks in single-cell genomics, see e.g. moscot-tools.org. Can we combine this powerful concept this with novel generative models? 🤔
🌟 Enter GENOT: Generative Entropic Neural OT.

scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...

Three BioML starter packs now!

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok

DM if you want to be included (or nominate people who should be!)

Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1 Mapping enhancers and their target genes in specific cell types is crucial for understanding gene re

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox:
For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the...

In collaboration with Reuben Saunders, @jswlab.bsky.social, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform for pooled multimodal genetic screens in intact mammalian tissue.

Check it out!
www.biorxiv.org/content/10.1...

Two BioML starter packs now:

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc

DM if you want to be included (or nominate people who should be!)

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️

🔄Share to help people finding its topic/field

- STRUCTURAL BIOLOGY

Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...

I made a starter pack for single cell and spatial people on BlueSky! 🧬🧪🥳

I’m certain it’s very incomplete, so please just let me know if you’d like to be included 😊

go.bsky.app/U57Mar8

A starter pack for single-cell/Spatial community!
This is work-in-progress, Please let me know if you want to added in this evolving list

go.bsky.app/RRBrEUx