Aidan Winters
@aidanwinters.bsky.social
Working in functional genomics, machine learning, and single-cell with a focus on multi-perturbation modeling.
PhD Candidate in labs of Hani Goodarzi and Luke Gilbert @ UCSF and Arc Institute
Comp Bio and ML at Tahoe Therapeutics (formerly Vevo)
PhD Candidate in labs of Hani Goodarzi and Luke Gilbert @ UCSF and Arc Institute
Comp Bio and ML at Tahoe Therapeutics (formerly Vevo)
Reposted by Aidan Winters
🧬 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...
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...
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...
www.nature.com
April 19, 2025 at 9:46 PM
🧬 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...
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...
Reposted by Aidan Winters
BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences https://www.biorxiv.org/content/10.1101/2025.04.08.647863v1
April 15, 2025 at 12:47 PM
BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences https://www.biorxiv.org/content/10.1101/2025.04.08.647863v1
Reposted by Aidan Winters
Nature research paper: DNA-guided transcription factor interactions extend human gene regulatory code
https://go.nature.com/4j13XRc
https://go.nature.com/4j13XRc
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.
go.nature.com
April 9, 2025 at 5:24 PM
Nature research paper: DNA-guided transcription factor interactions extend human gene regulatory code
https://go.nature.com/4j13XRc
https://go.nature.com/4j13XRc
Reposted by Aidan Winters
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 🧵
Join us! We will select 40 participants, provide compute and a $400 travel voucher for 10 travelers. Details in 🧵
March 24, 2025 at 10:18 PM
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 🧵
Join us! We will select 40 participants, provide compute and a $400 travel voucher for 10 travelers. Details in 🧵
Reposted by Aidan Winters
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...
taggs.hhs.gov/Content/Data...
March 18, 2025 at 10:28 PM
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...
taggs.hhs.gov/Content/Data...
Reposted by Aidan Winters
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.🧪
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...
taggs.hhs.gov/Content/Data...
March 19, 2025 at 1:59 AM
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.🧪
Reposted by Aidan Winters
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)
March 6, 2025 at 11:01 PM
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)
Reposted by Aidan Winters
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!
☕️Kovalski et al. perform a genome-wide CRISPRi screen for selective MYC translation regulators and identify RBM42 as a ribosome-associated protein that modulates MYC translation and an #oncogenic mRNA program required for #PancreaticCancer growth.
👉🏼https://rdcu.be/ecb4e
bit.ly/41FKwY3
👉🏼https://rdcu.be/ecb4e
bit.ly/41FKwY3
Functional screen identifies RBM42 as a mediator of oncogenic mRNA translation specificity - Nature Cell Biology
Kovalski et al. perform a genome-wide CRISPRi screen for selective MYC mRNA translation regulators and identify RBM42 as a ribosome-associated protein that modulates translation of MYC and an oncogeni...
bit.ly
March 6, 2025 at 3:11 AM
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!
Reposted by Aidan Winters
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...
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
February 27, 2025 at 10:11 PM
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...
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Aidan Winters
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
February 25, 2025 at 5:52 PM
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!
@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...
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 ...
www.biorxiv.org
February 25, 2025 at 2:41 PM
Amazing working with this team!
Reposted by Aidan Winters
@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...
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 ...
www.biorxiv.org
February 25, 2025 at 1:25 PM
@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...
Reposted by Aidan Winters
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...
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 ...
www.biorxiv.org
January 2, 2025 at 1:10 PM
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...
Reposted by Aidan Winters
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...
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...
www.biorxiv.org
December 17, 2024 at 8:16 PM
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...
Reposted by Aidan Winters
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...
1/
www.nature.com/articles/s41...
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.
www.nature.com
December 16, 2024 at 12:02 PM
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...
1/
www.nature.com/articles/s41...
Reposted by Aidan Winters
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...
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
December 12, 2024 at 8:09 PM
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...
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
Reposted by Aidan Winters
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
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.
dbricks.co
December 11, 2024 at 7:00 PM
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
Reposted by Aidan Winters
(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
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...
arxiv.org
December 11, 2024 at 2:30 AM
(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
Reposted by Aidan Winters
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.
🌟 Enter GENOT: Generative Entropic Neural OT.
December 10, 2024 at 9:03 AM
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.
🌟 Enter GENOT: Generative Entropic Neural OT.
Reposted by Aidan Winters
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...
gist.github.com/ilan-gold/98...
December 11, 2024 at 3:48 PM
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...
gist.github.com/ilan-gold/98...
Reposted by Aidan Winters
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!)
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!)
December 3, 2024 at 3:27 AM
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!)
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!)
Reposted by Aidan Winters
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
go.bsky.app/73rcuJn
November 24, 2024 at 7:50 AM
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
go.bsky.app/73rcuJn
Reposted by Aidan Winters
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
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
www.biorxiv.org
November 24, 2024 at 10:32 AM
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
Reposted by Aidan Winters
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?
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?
November 22, 2024 at 4:45 PM
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?
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?
Reposted by Aidan Winters
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...
Check it out!
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 21, 2024 at 6:24 PM
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...
Check it out!
www.biorxiv.org/content/10.1...