Impact of Genomic Variation on Function
@igvfconsortium.bsky.social
Reposted by Impact of Genomic Variation on Function
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
November 5, 2025 at 3:09 PM
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Incredible work from the IGVF community!
A major step forward for scalable CRT discovery, and a significant contribution to understanding gene regulation in human neurons.
A major step forward for scalable CRT discovery, and a significant contribution to understanding gene regulation in human neurons.
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
November 14, 2025 at 7:04 PM
Incredible work from the IGVF community!
A major step forward for scalable CRT discovery, and a significant contribution to understanding gene regulation in human neurons.
A major step forward for scalable CRT discovery, and a significant contribution to understanding gene regulation in human neurons.
🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data.
Learn more & access the tool here: github.com/EngreitzLab/...
Learn more & access the tool here: github.com/EngreitzLab/...
GitHub - EngreitzLab/scE2G: Pipeline to run scE2G
Pipeline to run scE2G. Contribute to EngreitzLab/scE2G development by creating an account on GitHub.
github.com
November 13, 2025 at 7:27 PM
🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data.
Learn more & access the tool here: github.com/EngreitzLab/...
Learn more & access the tool here: github.com/EngreitzLab/...
From data to discovery, IGVF is working to understand how genomic variation influences genome function and phenotype.
Learn more about our work at www.igvf.org
Learn more about our work at www.igvf.org
Impact of Genomic Variation on Function (IGVF) Consortium
IGVF, Impact of Genomic Variation on Function, IGVF Consortium, Understanding how genomic variation affects genome function to influence phenotypes
www.igvf.org
November 5, 2025 at 8:14 PM
From data to discovery, IGVF is working to understand how genomic variation influences genome function and phenotype.
Learn more about our work at www.igvf.org
Learn more about our work at www.igvf.org
Wishing everyone a spook-tacular Halloween! 👻
Whether you’re celebrating or just enjoying a well-earned weekend, we hope it’s a wickedly wonderful one!
Whether you’re celebrating or just enjoying a well-earned weekend, we hope it’s a wickedly wonderful one!
October 31, 2025 at 4:10 PM
Wishing everyone a spook-tacular Halloween! 👻
Whether you’re celebrating or just enjoying a well-earned weekend, we hope it’s a wickedly wonderful one!
Whether you’re celebrating or just enjoying a well-earned weekend, we hope it’s a wickedly wonderful one!
RSV remains a global health challenge.
Using CRISPR knockout screens and single-cell RNA-seq, researchers identified key host factors and responses that drive infection.
Read more: pmc.ncbi.nlm.nih.gov
Using CRISPR knockout screens and single-cell RNA-seq, researchers identified key host factors and responses that drive infection.
Read more: pmc.ncbi.nlm.nih.gov
Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation
Respiratory syncytial virus (RSV) is a globally prevalent pathogen, causes severe disease in older adults, and is the leading cause of bronchiolitis and pneumonia in the United States for children during their first year of life [1]. Despite its ...
pmc.ncbi.nlm.nih.gov
October 29, 2025 at 7:36 PM
RSV remains a global health challenge.
Using CRISPR knockout screens and single-cell RNA-seq, researchers identified key host factors and responses that drive infection.
Read more: pmc.ncbi.nlm.nih.gov
Using CRISPR knockout screens and single-cell RNA-seq, researchers identified key host factors and responses that drive infection.
Read more: pmc.ncbi.nlm.nih.gov
From all fields and corners of the map, IGVF members came together in Durham, NC. United by one mission, to understand how genomic variation influences function.
A huge thank you to the Durham Bulls Athletic Park for welcoming us and hosting a fantastic night of food, fun, and practice home runs! ⚾
A huge thank you to the Durham Bulls Athletic Park for welcoming us and hosting a fantastic night of food, fun, and practice home runs! ⚾
October 22, 2025 at 4:58 PM
From all fields and corners of the map, IGVF members came together in Durham, NC. United by one mission, to understand how genomic variation influences function.
A huge thank you to the Durham Bulls Athletic Park for welcoming us and hosting a fantastic night of food, fun, and practice home runs! ⚾
A huge thank you to the Durham Bulls Athletic Park for welcoming us and hosting a fantastic night of food, fun, and practice home runs! ⚾
How do genetic variants in brain vascular cells shape neurological disease risk?
With MultiVINE-seq, researchers mapped thousands of risk variants, revealing distinct mechanisms for cerebrovascular vs. neurodegenerative disorders—including Alzheimer’s.
www.cell.com/neuron/fullt...
With MultiVINE-seq, researchers mapped thousands of risk variants, revealing distinct mechanisms for cerebrovascular vs. neurodegenerative disorders—including Alzheimer’s.
www.cell.com/neuron/fullt...
Human brain vascular multi-omics elucidates disease-risk associations
Reid et al. develop MultiVINE-seq to map thousands of non-coding disease variants
to genes in human brain vascular cells. Cerebrovascular disease variants compromise
vessel integrity, whereas Alzheime...
www.cell.com
October 3, 2025 at 5:54 PM
How do genetic variants in brain vascular cells shape neurological disease risk?
With MultiVINE-seq, researchers mapped thousands of risk variants, revealing distinct mechanisms for cerebrovascular vs. neurodegenerative disorders—including Alzheimer’s.
www.cell.com/neuron/fullt...
With MultiVINE-seq, researchers mapped thousands of risk variants, revealing distinct mechanisms for cerebrovascular vs. neurodegenerative disorders—including Alzheimer’s.
www.cell.com/neuron/fullt...
How do cells respond to chemical and genetic perturbations?
A recent study introduces PerturbNet, a deep generative model that predicts how unseen drugs, CRISPR edits, or even missense mutations alter single-cell gene expression.
Read the full publication:
pmc.ncbi.nlm.nih.gov/articles/PMC...
A recent study introduces PerturbNet, a deep generative model that predicts how unseen drugs, CRISPR edits, or even missense mutations alter single-cell gene expression.
Read the full publication:
pmc.ncbi.nlm.nih.gov/articles/PMC...
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations
Chemical and genetic perturbations, such as those induced by small molecules and CRISPR, effect complex changes in the molecular states of cells. Despite advances in high-throughput single-cell pertur...
pmc.ncbi.nlm.nih.gov
September 26, 2025 at 8:20 PM
How do cells respond to chemical and genetic perturbations?
A recent study introduces PerturbNet, a deep generative model that predicts how unseen drugs, CRISPR edits, or even missense mutations alter single-cell gene expression.
Read the full publication:
pmc.ncbi.nlm.nih.gov/articles/PMC...
A recent study introduces PerturbNet, a deep generative model that predicts how unseen drugs, CRISPR edits, or even missense mutations alter single-cell gene expression.
Read the full publication:
pmc.ncbi.nlm.nih.gov/articles/PMC...
ASHG 2025 is coming up! 🎉
Keep an eye out for IGVF talks and posters throughout the meeting.
We'll see you in Boston!
Keep an eye out for IGVF talks and posters throughout the meeting.
We'll see you in Boston!
September 25, 2025 at 8:22 PM
ASHG 2025 is coming up! 🎉
Keep an eye out for IGVF talks and posters throughout the meeting.
We'll see you in Boston!
Keep an eye out for IGVF talks and posters throughout the meeting.
We'll see you in Boston!
scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or multiome data.
Explore the tool here: github.com/EngreitzLab/...
Explore the tool here: github.com/EngreitzLab/...
GitHub - EngreitzLab/scE2G: Pipeline to run scE2G
Pipeline to run scE2G. Contribute to EngreitzLab/scE2G development by creating an account on GitHub.
github.com
September 19, 2025 at 6:43 PM
scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or multiome data.
Explore the tool here: github.com/EngreitzLab/...
Explore the tool here: github.com/EngreitzLab/...
The IGVF Consortium began with one mission: to understand how genomic variation shapes genome function and influences health. Together, we’re building lasting resources for the research community.
igvf.org
igvf.org
September 17, 2025 at 7:01 PM
The IGVF Consortium began with one mission: to understand how genomic variation shapes genome function and influences health. Together, we’re building lasting resources for the research community.
igvf.org
igvf.org
Neomer-based classifiers "short DNA sequences from tumor mutations”, show high accuracy in detecting cancer, even at early stages, and distinguishing subtypes.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Leveraging sequences missing from the human genome to diagnose cancer
Cancer diagnosis using cell-free DNA (cfDNA) has the potential to improve treatment and survival but has several technical limitations. In this study, we developed a prediction model based on neomers,...
pmc.ncbi.nlm.nih.gov
September 12, 2025 at 4:47 PM
Neomer-based classifiers "short DNA sequences from tumor mutations”, show high accuracy in detecting cancer, even at early stages, and distinguishing subtypes.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
IGVF uses state-of-the-art experimental and computational approaches to model, predict, characterize, and map genome function.
Together, these efforts are building a catalog that reveals how genomic variation influences genome function and phenotypes.
Together, these efforts are building a catalog that reveals how genomic variation influences genome function and phenotypes.
September 11, 2025 at 3:41 PM
IGVF uses state-of-the-art experimental and computational approaches to model, predict, characterize, and map genome function.
Together, these efforts are building a catalog that reveals how genomic variation influences genome function and phenotypes.
Together, these efforts are building a catalog that reveals how genomic variation influences genome function and phenotypes.
Deadline extended! 🏁
The submission deadlines for TCS2 and ATP7B in CAGI7 are now September 15.
A big thanks to our collaborators in the Fowler and Roth groups for their leadership on this effort.
genomeinterpretation.org/cagi7-challe...
The submission deadlines for TCS2 and ATP7B in CAGI7 are now September 15.
A big thanks to our collaborators in the Fowler and Roth groups for their leadership on this effort.
genomeinterpretation.org/cagi7-challe...
CAGI7 Challenge
genomeinterpretation.org
September 3, 2025 at 9:02 PM
Deadline extended! 🏁
The submission deadlines for TCS2 and ATP7B in CAGI7 are now September 15.
A big thanks to our collaborators in the Fowler and Roth groups for their leadership on this effort.
genomeinterpretation.org/cagi7-challe...
The submission deadlines for TCS2 and ATP7B in CAGI7 are now September 15.
A big thanks to our collaborators in the Fowler and Roth groups for their leadership on this effort.
genomeinterpretation.org/cagi7-challe...
Scanpy is a scalable Python toolkit for analyzing single-cell gene expression data. From preprocessing & visualization to clustering, trajectory inference, and differential expression testing, Scanpy can handle datasets with over 1M cells.
Learn more & access the tool:
github.com/scverse/scanpy
Learn more & access the tool:
github.com/scverse/scanpy
GitHub - scverse/scanpy: Single-cell analysis in Python. Scales to >100M cells.
Single-cell analysis in Python. Scales to >100M cells. - scverse/scanpy
github.com
August 29, 2025 at 4:43 PM
Scanpy is a scalable Python toolkit for analyzing single-cell gene expression data. From preprocessing & visualization to clustering, trajectory inference, and differential expression testing, Scanpy can handle datasets with over 1M cells.
Learn more & access the tool:
github.com/scverse/scanpy
Learn more & access the tool:
github.com/scverse/scanpy
See how IGVF comes together 🧩
Our High-Level Consortium Map highlights the experiments, teams & technologies driving discovery on how genomic variation impacts function.
Explore the map: igvf.org/high-level-c...
Our High-Level Consortium Map highlights the experiments, teams & technologies driving discovery on how genomic variation impacts function.
Explore the map: igvf.org/high-level-c...
IGVF High-level Consortium Map
IGVF High-level Consortium Map
igvf.org
August 27, 2025 at 6:05 PM
See how IGVF comes together 🧩
Our High-Level Consortium Map highlights the experiments, teams & technologies driving discovery on how genomic variation impacts function.
Explore the map: igvf.org/high-level-c...
Our High-Level Consortium Map highlights the experiments, teams & technologies driving discovery on how genomic variation impacts function.
Explore the map: igvf.org/high-level-c...
MPRAnalyze offers a powerful statistical framework for Massively Parallel Reporter Assays (MPRAs) to study enhancer activity.
From quantifying activity to comparing across conditions, it helps researchers uncover how enhancers drive gene regulation.
bioconductor.org/packages/rel...
From quantifying activity to comparing across conditions, it helps researchers uncover how enhancers drive gene regulation.
bioconductor.org/packages/rel...
MPRAnalyze
MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quant...
bioconductor.org
August 22, 2025 at 5:58 PM
MPRAnalyze offers a powerful statistical framework for Massively Parallel Reporter Assays (MPRAs) to study enhancer activity.
From quantifying activity to comparing across conditions, it helps researchers uncover how enhancers drive gene regulation.
bioconductor.org/packages/rel...
From quantifying activity to comparing across conditions, it helps researchers uncover how enhancers drive gene regulation.
bioconductor.org/packages/rel...
The IGVF Data Portal serves as the central hub for research data from the consortium, encompassing raw sequences, analyzed effects, software, and predictive models.
Explore how genomic variation impacts function and phenotype.
data.igvf.org
Explore how genomic variation impacts function and phenotype.
data.igvf.org
IGVF
Portal for the Impact of Genomic Variation on Function consortium
data.igvf.org
August 21, 2025 at 5:54 PM
The IGVF Data Portal serves as the central hub for research data from the consortium, encompassing raw sequences, analyzed effects, software, and predictive models.
Explore how genomic variation impacts function and phenotype.
data.igvf.org
Explore how genomic variation impacts function and phenotype.
data.igvf.org
🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data.
Learn more & access the tool here: github.com/EngreitzLab/...
Learn more & access the tool here: github.com/EngreitzLab/...
GitHub - EngreitzLab/scE2G: Pipeline to run scE2G
Pipeline to run scE2G. Contribute to EngreitzLab/scE2G development by creating an account on GitHub.
github.com
August 15, 2025 at 7:00 PM
🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data.
Learn more & access the tool here: github.com/EngreitzLab/...
Learn more & access the tool here: github.com/EngreitzLab/...
IGVF is bringing together discoveries from across the network into a lasting, openly available catalog of how genomic variants influence genome function and phenotypes.
A resource that will continue to power future research. Explore our goals and the impact ahead: igvf.org
A resource that will continue to power future research. Explore our goals and the impact ahead: igvf.org
Impact of Genomic Variation on Function (IGVF) Consortium
IGVF, Impact of Genomic Variation on Function, IGVF Consortium, Understanding how genomic variation affects genome function to influence phenotypes
igvf.org
August 13, 2025 at 8:37 PM
IGVF is bringing together discoveries from across the network into a lasting, openly available catalog of how genomic variants influence genome function and phenotypes.
A resource that will continue to power future research. Explore our goals and the impact ahead: igvf.org
A resource that will continue to power future research. Explore our goals and the impact ahead: igvf.org
Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Interface-guided phenotyping of coding variants in the transcription factor RUNX1
Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces o...
pmc.ncbi.nlm.nih.gov
August 8, 2025 at 8:40 PM
Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types.
Uncover the science behind it:
pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it:
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
August 8, 2025 at 8:38 PM
Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types.
Uncover the science behind it:
pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it:
pmc.ncbi.nlm.nih.gov/articles/PMC...
Thousands of genomic variants are linked to disease, but how do they actually function?
IGVF is building a catalog of experimental and computational insights to uncover the impact of variants.
🔎 We’re on the case: igvf.org
IGVF is building a catalog of experimental and computational insights to uncover the impact of variants.
🔎 We’re on the case: igvf.org
August 6, 2025 at 3:24 PM
Thousands of genomic variants are linked to disease, but how do they actually function?
IGVF is building a catalog of experimental and computational insights to uncover the impact of variants.
🔎 We’re on the case: igvf.org
IGVF is building a catalog of experimental and computational insights to uncover the impact of variants.
🔎 We’re on the case: igvf.org