Hi Luke, thanks so much for your careful reading!
In our experience we are finding that genome-scale promoter perturbseq are hugely helpful for understanding the overall structure of gene regulatory networks in the relevant cell types and that context has been very helpful for our interpretation.
In our experience we are finding that genome-scale promoter perturbseq are hugely helpful for understanding the overall structure of gene regulatory networks in the relevant cell types and that context has been very helpful for our interpretation.
October 17, 2026 at 3:48 PM
Hi Luke, thanks so much for your careful reading!
In our experience we are finding that genome-scale promoter perturbseq are hugely helpful for understanding the overall structure of gene regulatory networks in the relevant cell types and that context has been very helpful for our interpretation.
In our experience we are finding that genome-scale promoter perturbseq are hugely helpful for understanding the overall structure of gene regulatory networks in the relevant cell types and that context has been very helpful for our interpretation.
New Epigenome Technologies Blog! u.epigenome.us/BR72ohsu
"Characterizing Maintenance of Pluripotency with iPSC-Perturb-Seq"
New research applies Perturb-Seq to iPSCs to improve our understanding of pluripotency
#Epigenetics #Blog #PerturbSeq #iPSCs #StemCells #Pluripotency
"Characterizing Maintenance of Pluripotency with iPSC-Perturb-Seq"
New research applies Perturb-Seq to iPSCs to improve our understanding of pluripotency
#Epigenetics #Blog #PerturbSeq #iPSCs #StemCells #Pluripotency
September 2, 2026 at 7:43 PM
New Epigenome Technologies Blog! u.epigenome.us/BR72ohsu
"Characterizing Maintenance of Pluripotency with iPSC-Perturb-Seq"
New research applies Perturb-Seq to iPSCs to improve our understanding of pluripotency
#Epigenetics #Blog #PerturbSeq #iPSCs #StemCells #Pluripotency
"Characterizing Maintenance of Pluripotency with iPSC-Perturb-Seq"
New research applies Perturb-Seq to iPSCs to improve our understanding of pluripotency
#Epigenetics #Blog #PerturbSeq #iPSCs #StemCells #Pluripotency
Using interventions (PerturbSeq)
to move from
correlation (GWAS hit)
to
causation (gene -> gene program -> trait)
to
knowledge representation (graphs).
to move from
correlation (GWAS hit)
to
causation (gene -> gene program -> trait)
to
knowledge representation (graphs).
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 5:02 PM
Using interventions (PerturbSeq)
to move from
correlation (GWAS hit)
to
causation (gene -> gene program -> trait)
to
knowledge representation (graphs).
to move from
correlation (GWAS hit)
to
causation (gene -> gene program -> trait)
to
knowledge representation (graphs).
arXiv:2503.14571v1 Announce Type: new
Abstract: Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural [1/6 of https://arxiv.org/abs/2503.14571v1]
Abstract: Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural [1/6 of https://arxiv.org/abs/2503.14571v1]
March 20, 2025 at 6:16 AM
arXiv:2503.14571v1 Announce Type: new
Abstract: Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural [1/6 of https://arxiv.org/abs/2503.14571v1]
Abstract: Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural [1/6 of https://arxiv.org/abs/2503.14571v1]
33/ We'd love to get feedback from the community #neuroinflammation #multiplesclerosis #Alzheimer #microglia #iPSC #CRISPR #Perturbseq #GWAS #epigenome #neurodegeneration
June 22, 2025 at 9:51 PM
33/ We'd love to get feedback from the community #neuroinflammation #multiplesclerosis #Alzheimer #microglia #iPSC #CRISPR #Perturbseq #GWAS #epigenome #neurodegeneration
PerturbSeq and suspension preps in general keep getting cheaper. Sooner or later even stats dorks like me realize the cost per bit of information is plummeting, and give it a shot
January 24, 2025 at 1:11 PM
PerturbSeq and suspension preps in general keep getting cheaper. Sooner or later even stats dorks like me realize the cost per bit of information is plummeting, and give it a shot
HypoGeneAgent, an LLM tool, generates GO hypotheses with a score for cluster granularity; on K562 CRISPRi Perturb‑seq dataset it outperformed silhouette scores. Read more: https://getnews.me/llm-powered-hypogeneagent-improves-cluster-resolution-for-perturb-seq/ #hypogeneagent #perturbseq
September 17, 2025 at 7:27 AM
HypoGeneAgent, an LLM tool, generates GO hypotheses with a score for cluster granularity; on K562 CRISPRi Perturb‑seq dataset it outperformed silhouette scores. Read more: https://getnews.me/llm-powered-hypogeneagent-improves-cluster-resolution-for-perturb-seq/ #hypogeneagent #perturbseq
The preprint detailing the results of the #SchmidtCenter Cancer Immunotherapy Machine Learning Competition is online!
@broadinstitute.org #MachineLearning #CancerImmunotherapy #ComputationalBiology #PerturbSeq #AI4Science #VirtualCell
www.biorxiv.org/content/10.6...
@broadinstitute.org #MachineLearning #CancerImmunotherapy #ComputationalBiology #PerturbSeq #AI4Science #VirtualCell
www.biorxiv.org/content/10.6...
May 22, 2026 at 10:43 PM
The preprint detailing the results of the #SchmidtCenter Cancer Immunotherapy Machine Learning Competition is online!
@broadinstitute.org #MachineLearning #CancerImmunotherapy #ComputationalBiology #PerturbSeq #AI4Science #VirtualCell
www.biorxiv.org/content/10.6...
@broadinstitute.org #MachineLearning #CancerImmunotherapy #ComputationalBiology #PerturbSeq #AI4Science #VirtualCell
www.biorxiv.org/content/10.6...
🚨 New preprint from the #EricAndWendySchmidtCenter! 🚨
"MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities"
www.biorxiv.org/content/10.1...
@broadinstitute.org #SingleCell #PerturbSeq #OpticalPooledScreen #AIinBiology #ScienceNews #CompBio
"MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities"
www.biorxiv.org/content/10.1...
@broadinstitute.org #SingleCell #PerturbSeq #OpticalPooledScreen #AIinBiology #ScienceNews #CompBio
July 3, 2025 at 3:17 PM
🚨 New preprint from the #EricAndWendySchmidtCenter! 🚨
"MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities"
www.biorxiv.org/content/10.1...
@broadinstitute.org #SingleCell #PerturbSeq #OpticalPooledScreen #AIinBiology #ScienceNews #CompBio
"MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities"
www.biorxiv.org/content/10.1...
@broadinstitute.org #SingleCell #PerturbSeq #OpticalPooledScreen #AIinBiology #ScienceNews #CompBio
One billion cell atlas project from #Illumina and collaborators AstraZeneca, Eli Lily and Merck
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
Illumina introduces Billion Cell Atlas to accelerate AI and drug discovery
www.illumina.com
January 17, 2026 at 7:16 AM
One billion cell atlas project from #Illumina and collaborators AstraZeneca, Eli Lily and Merck
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT #spatial #perturbseq
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT
Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for si...
www.biorxiv.org
November 20, 2024 at 2:49 AM
Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT #spatial #perturbseq
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
For classical scFMs, it would be an interesting test where they can actually learn generalizable perturbation prediction if they were trained on large scale Perturbseq data. That is often the claim. But maybe totally new approaches are needed to really leverage perturb data to learn effectively.
April 19, 2025 at 1:55 PM
For classical scFMs, it would be an interesting test where they can actually learn generalizable perturbation prediction if they were trained on large scale Perturbseq data. That is often the claim. But maybe totally new approaches are needed to really leverage perturb data to learn effectively.
2/TAP-seq focuses scRNA-seq on a gene panel you define upfront instead of sequencing everything.
Up to 50x reduction in sequencing costs. Better sensitivity for the genes that actually matter.
#scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #PerturbSeq #TAPseq
Up to 50x reduction in sequencing costs. Better sensitivity for the genes that actually matter.
#scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #PerturbSeq #TAPseq
May 30, 2026 at 6:10 PM
2/TAP-seq focuses scRNA-seq on a gene panel you define upfront instead of sequencing everything.
Up to 50x reduction in sequencing costs. Better sensitivity for the genes that actually matter.
#scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #PerturbSeq #TAPseq
Up to 50x reduction in sequencing costs. Better sensitivity for the genes that actually matter.
#scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #PerturbSeq #TAPseq
1/ Sequencing the entire transcriptome for every perturbation is too expensive.
This workflow offers a solution. 🧵
#Trinobia #Bioinformatics #scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #FunctionalGenomics #PerturbSeq #TAPseq #NextGenSequencing #NGS #ComputationalBiology
This workflow offers a solution. 🧵
#Trinobia #Bioinformatics #scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #FunctionalGenomics #PerturbSeq #TAPseq #NextGenSequencing #NGS #ComputationalBiology
May 30, 2026 at 6:10 PM
1/ Sequencing the entire transcriptome for every perturbation is too expensive.
This workflow offers a solution. 🧵
#Trinobia #Bioinformatics #scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #FunctionalGenomics #PerturbSeq #TAPseq #NextGenSequencing #NGS #ComputationalBiology
This workflow offers a solution. 🧵
#Trinobia #Bioinformatics #scRNAseq #SingleCell #CRISPR #Genomics #Transcriptomics #RNAseq #FunctionalGenomics #PerturbSeq #TAPseq #NextGenSequencing #NGS #ComputationalBiology
Nice to see more mechanistic models appear in the single cell space with perturbseq & trans regulatory networks.
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq https://www.biorxiv.org/content/10.1101/2025.01.22.634424v1
January 24, 2025 at 1:01 PM
Nice to see more mechanistic models appear in the single cell space with perturbseq & trans regulatory networks.
🧠 Arc Workshop at the upcoming scverse conference 2025 🧠
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
October 8, 2025 at 2:55 PM
🧠 Arc Workshop at the upcoming scverse conference 2025 🧠
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
🧠 Arc Workshop at the upcoming scverse conference 2025 🧠
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
September 9, 2025 at 4:27 PM
🧠 Arc Workshop at the upcoming scverse conference 2025 🧠
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵
@arcinstitute.org
#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells
New Epigenome Technologies Blog! u.epigenome.us/65diB19t
"Perturb-seq Reveals a Compensation Mechanism Underpinning Resistance in AML"
Based on a Leukemia study by researchers led by Rui Lu and Changde Cheng
#Epigenetics #Blog #AML #Cancer #PerturbSeq
"Perturb-seq Reveals a Compensation Mechanism Underpinning Resistance in AML"
Based on a Leukemia study by researchers led by Rui Lu and Changde Cheng
#Epigenetics #Blog #AML #Cancer #PerturbSeq
July 8, 2026 at 3:20 PM
New Epigenome Technologies Blog! u.epigenome.us/65diB19t
"Perturb-seq Reveals a Compensation Mechanism Underpinning Resistance in AML"
Based on a Leukemia study by researchers led by Rui Lu and Changde Cheng
#Epigenetics #Blog #AML #Cancer #PerturbSeq
"Perturb-seq Reveals a Compensation Mechanism Underpinning Resistance in AML"
Based on a Leukemia study by researchers led by Rui Lu and Changde Cheng
#Epigenetics #Blog #AML #Cancer #PerturbSeq
New Epigenome Technologies Blog! u.epigenome.us/w23Xazct
"Perturb-multiome Identifies Aging and Senescence-Associated lncRNAs as Therapeutic Targets"
Based on a Nature Aging study from researchers led by Jing-Dong Jackie Han
#Epigenetics #Blog #Aging #PerturbSeq #lncRNAs #Senescence
"Perturb-multiome Identifies Aging and Senescence-Associated lncRNAs as Therapeutic Targets"
Based on a Nature Aging study from researchers led by Jing-Dong Jackie Han
#Epigenetics #Blog #Aging #PerturbSeq #lncRNAs #Senescence
July 6, 2026 at 3:40 PM
New Epigenome Technologies Blog! u.epigenome.us/w23Xazct
"Perturb-multiome Identifies Aging and Senescence-Associated lncRNAs as Therapeutic Targets"
Based on a Nature Aging study from researchers led by Jing-Dong Jackie Han
#Epigenetics #Blog #Aging #PerturbSeq #lncRNAs #Senescence
"Perturb-multiome Identifies Aging and Senescence-Associated lncRNAs as Therapeutic Targets"
Based on a Nature Aging study from researchers led by Jing-Dong Jackie Han
#Epigenetics #Blog #Aging #PerturbSeq #lncRNAs #Senescence