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Impact of Genomic Variation on Function

@igvfconsortium.bsky.social
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 24/09/2026
SEEK-VEC is a new framework for finding hidden patterns in count-based data. By combining multiple topic models, it helps identify key terms, uncover relationships, and assess results, especially when signals are weak. www.biorxiv.org/content/10.6...
biorxiv.org
SEEK-VEC: Augmenting topic modeling with spectral ensemble learning
Count data are ubiquitous across many applications in which understanding latent patterns is of interest. Topic modeling is a powerful tool for detecting latent structure in count data. However, stand...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 09/09/2026
The Integrative Analysis Working Group brings together multimodal IGVF data to define variant function, resolve assay discrepancies, characterize pleiotropic effects, and develop models to predict and interpret variant function.  Explore this and other IGVF working groups: igvf.org/working-grou...
igvf.org
IGVF Working Groups
Code of Conduct of Impact of Genomic Variation on Function (IGVF) Consortium
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 01/09/2026
How specific is a gene to a cell type, tissue, or condition? This preprint introduces ember, a principled approach to measuring gene specificity, with applications across mouse tissues and human PBMCs. Uncover the science behind it: www.biorxiv.org/content/10.1...
biorxiv.org
Determining gene specificity from multivariate single-cell RNA sequencing data
An important application of single-cell genomics experiments is to identify genes specific to biological categories or experimental conditions. Although numerous approaches have been proposed to ident...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 28/08/2026
MPRAsnakeflow enables standardized, reproducible processing and analysis of MPRA data. Developed by the IGVF Consortium, the tool and community standards support robust integration of diverse datasets for regulatory genomics. genome.cshlp.org/content/earl...
genome.cshlp.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 26/08/2026
How do genetic variants affect secreted proteins? A new study introduces MultiSTEP, a scalable method for measuring variant effects in coagulation factor IX. The approach assessed >8,500 F9 missense variants and helped reclassify 63.1% of VUSs. pubmed.ncbi.nlm.nih.gov/40514537/
pubmed.ncbi.nlm.nih.gov
Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP - PubMed
Despite widespread advances in DNA sequencing, the functional consequences of most genetic variants remain poorly understood. Multiplexed assays of variant effect can measure the function of variants at scale but cannot readily be applied to the ~10% of human genes encoding secreted proteins. Here w …
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 20/08/2026
Explore pySpade, a computational tool for whole-transcriptome analysis of single-cell perturbation datasets. Using Cell Ranger output, pySpade identifies differential expression and generates hit tables and Manhattan plots. github.com/Hon-lab/pySp...
github.com
GitHub - Hon-lab/pySpade: Single cell Perturbations - Analysis of Differential gene Expression
Single cell Perturbations - Analysis of Differential gene Expression - Hon-lab/pySpade
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 13/08/2026
Our interactive high-level consortium map lets you explore the experiments, teams, and technologies that make up IGVF.  Explore the map to see the connections between experiments, teams, and technologies.  igvf.org/high-level-c...
igvf.org
IGVF High-level Consortium Map
IGVF High-level Consortium Map
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 07/08/2026
Demuxafy streamlines demultiplexing and doublet detection for droplet-based scRNA-seq, giving users the flexibility to choose and efficiently run methods best suited to their dataset. Explore the tool:  demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/
demultiplexing-doublet-detecting-docs.readthedocs.io
Demuxafy — Demuxafy 3.0.0 documentation
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 06/08/2026
An open-source framework for exploring functional genomic regions through an interactive web app or command-line tool. Design and analyze CRISPR-Cas, CRISPRi, and CRISPRa tiling screens with CRISPR-SURF. Explore the tool: github.com/pinellolab/C...
github.com
GitHub - pinellolab/CRISPR-SURF
Contribute to pinellolab/CRISPR-SURF development by creating an account on GitHub.
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 30/07/2026
Utilize the IGVF Data Portal to access research data, software, predictive models, and genomic resources generated by the IGVF Consortium. From raw sequencing data to analyzed results, discover data driving functional genomics: data.igvf.org
data.igvf.org
IGVF
Portal for the Impact of Genomic Variation on Function consortium
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 24/07/2026
FastGxC enables fast, powerful mapping of context-specific eQTLs from bulk and single-cell RNA-seq data, improving trait interpretation while expanding candidate causal genes.  Explore the study: www.cell.com/cell-genomic...
cell.com
FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data
Krockenberger, Lu, et al. introduce FastGxC, a method that identifies how genetic variants regulate gene activity in specific tissues and cell types more efficiently than existing approaches. Applied ...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 22/07/2026
Explore the IGVF YouTube channel for workshops, Q&A sessions, presentations, and more. Hear directly from consortium members and discover resources that support functional genomics research. Watch here: www.youtube.com/@igvf
youtube.com
Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 14/07/2026
Understanding sequencing library structure is essential for accurate genomics data processing. seqspec provides a machine-readable specification that standardizes library descriptions, improving preprocessing, reproducibility, and assay comparisons.  Learn more: academic.oup.com/bioinformati...
academic.oup.com
Validate User
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 09/07/2026
IGVF is building resources to better understand how genomic variation influences genome function and human health through predictive modeling, functional characterization, mapping, networking, and shared data resources. Learn more about our initiative: www.igvf.org/about/
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 02/07/2026
FastGxC is a tool for identifying context-specific genetic effects from single-cell and bulk RNA-seq data. By modeling repeated samples from the same individual, it improves detection power and remains robust even with missing data. Explore the tool: github.com/BalliuLab/Fa...
github.com
GitHub - BalliuLab/FastGxC
Contribute to BalliuLab/FastGxC development by creating an account on GitHub.
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 25/06/2026
New preprint! 📢 PerturbPlan introduces an analytical framework for designing Perturb-seq and TAP-seq experiments, reducing power calculation runtimes by up to seven orders of magnitude and enabling interactive experimental design. www.biorxiv.org/content/10.6...
biorxiv.org
PerturbPlan: An analytical framework for designing Perturb-seq experiments
CRISPR screens with single-cell RNA-seq readouts provide a powerful tool for characterizing the functions of noncoding elements and genes. However, designing these experiments to balance statistical p...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 19/06/2026
A recent preprint presents an MPRA framework that assays cis-regulatory elements alongside their target promoter, providing a functional map of 1,214 CYP3A4 regulatory variants and insights into gene regulation, drug response, and disease. Read more: www.biorxiv.org/content/10.6...
biorxiv.org
Massively parallel reporter assays for CYP3A4 enhancer variants alongside their native promoter
Massively parallel reporter assays (MPRAs) enable high-throughput functional testing of thousands of cis -regulatory elements (CREs). However, conventional MPRAs typically use short CRE fragments comb...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 16/06/2026
Explore the IGVF YouTube channel for workshop recordings, research presentations, consortium updates, and insights from scientists working to understand how genomic variation impacts genome function. www.youtube.com/@igvf
youtube.com
Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 09/06/2026
MPRA is an R package that provides tools for the differential analysis of Massively Parallel Reporter Assay (MPRA) data, helping researchers investigate regulatory element activity at scale. Explore MPRA: github.com/hansenlab/mpra
github.com
GitHub - hansenlab/mpra
Contribute to hansenlab/mpra development by creating an account on GitHub.
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 03/06/2026
Looking for information on a gene, variant, or genomic region? The IGVF catalog brings together experimental data and computational predictions from the IGVF Consortium and other resources on a single searchable platform. catalog.igvf.org
catalog.igvf.org
IGVF Catalog
Browse the IGVF Catalog
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 28/05/2026
Hear from Andreas Gschwind, PhD, as he highlights enhancer-gene mapping, CRISPR perturbation data, predictive models, and tools within the IGVF catalog.  youtu.be/jVxcwRXZYMc
youtu.be
Using the IGVF Catalog to Study Noncoding Variant Function
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 22/05/2026
How can researchers access and build on IGVF resources?  In this workshop presentation, Michael Love, PhD, highlights the IGVF data portal, catalog, APIs, and computational tools supporting reproducible functional genomics research. youtu.be/W6Mr7O7gUNY
youtu.be
Accessing and Building on the IGVF Data Portal and Catalog
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 19/05/2026
IGVF has adopted seqspec, a machine-readable standard helping improve reproducibility, transparency, and interoperability across functional genomics datasets. Learn how seqspec is supporting scalable data sharing and QC across IGVF: igvf.org/news/seqspec/
igvf.org
IGVF Adopts 'seqspec' to Advance Reproducibility and Data Standards in Functional Genomics
IGVF Adopts 'seqspec' to Advance Reproducibility and Data Standards in Functional Genomics
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 14/05/2026
Roulette is a basepair-resolution model for predicting germline de novo mutation rates across the human genome, helping uncover mechanisms that shape mutagenesis, including the impact of Polymerase III transcription.  Explore the tool: github.com/vseplyarskiy...
github.com
GitHub - vseplyarskiy/Roulette: A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription
A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription - vseplyarskiy/Roulette
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 12/05/2026
Hear from Karen Mohlke, PhD, as she introduces the IGVF Consortium and its efforts to build a functional genomics resource connecting genetic variation to genome function and disease.  Check out the full presentation: youtu.be/CbCILxe_eSI?...
youtu.be
Introduction to the IGVF Consortium and Functional Genomics Resource
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 06/05/2026
Why build a comprehensive variant effects catalog? Katherine Degner, PhD, explains how a trusted, centralized resource can help researchers explore how genes impact different tissues and cell types, all in one place. ▶️ youtu.be/Iof2mfE6sRM
youtu.be
Why is it important to build a comprehensive catalog of variant effects?
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 30/04/2026
Saturation genome editing of BARD1 variants resolves 95% of variants of uncertain significance, linking functional effects to cancer risk with high accuracy (AUC=0.99). Uncover the science behind it: www.medrxiv.org/content/10.1...
medrxiv.org
Saturation genome editing of BARD1 resolves VUS and provides insight into BRCA1-BARD1 tumor suppression
BARD1 variants are associated with hereditary breast cancer and neuroblastoma, yet, 98% of missense variants remain variants of uncertain significance (VUS). We applied Saturation Genome Editing (SGE)...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 24/04/2026
New preprint: Transcription factor collaboration shapes CD8+T cell states. Large-scale TF screens and single-cell profiling map regulatory programs and interactions (including RUNX–KLF2) that inform T cell exhaustion and potential cell therapy strategies. Read more: www.biorxiv.org/content/10.6...
biorxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 22/04/2026
Follow IGVF on YouTube for Q&As, research highlights, and insights from across the consortium. Subscribe and tune in: www.youtube.com/@igvf
youtube.com
Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 20/04/2026
MPRAflow is a pipeline for analyzing MPRA sequencing data, generating count tables, linking variants to barcodes, and modeling variant effects from saturation mutagenesis experiments. Explore the tool: github.com/shendurelab/...
github.com
GitHub - shendurelab/MPRAflow at 693d10bb6c6d6f821d23b350df694cd157a62e71
A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data - shendurelab/MPRAflow
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 14/04/2026
New research combines CRISPR activation, Perturb-seq, and in situ screening to uncover RNA-based mechanisms that enhance T cell–mediated killing of cancer and infected cells.  Read more: www.nature.com/articles/s41...
nature.com
High-content CRISPR activation screens identify synthetically lethal RNA-based mechanisms to sensitize cancer cells to targeted T cell cytotoxicity - Nature Genetics
A series of in vitro and in vivo CRISPR activation screens combined with in situ Perturb-seq identify regulators of T cell-dependent cytotoxicity in melanoma.
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 08/04/2026
The IGVF Data Portal brings together datasets, tools, models, and protocols from across the consortium, from raw sequencing data to analyzed variant effects. Explore the resource: data.igvf.org
data.igvf.org
IGVF
Portal for the Impact of Genomic Variation on Function consortium
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 01/04/2026
What’s one of the biggest challenges in genomics today? Lea Starita explains how variants of uncertain significance limit genetic medicine, and how IGVF is working to solve it using functional data and predictive models. ▶️ youtu.be/yEjEeIIkj9Q
youtu.be
What are the key problems in the field that IGVF is addressing?
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 25/03/2026
Looking for IGVF across social media? Visit our Linktree to find all IGVF platforms in one place and stay up to date on the latest research, tools, and consortium updates.  linktr.ee/IGVFConsortium
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 20/03/2026
New preprint: Neuron–astrocyte interactions reshape neuronal gene regulation. Co-culture and CRISPR screens reveal regulatory elements and TF networks that control neuronal maturation and link to schizophrenia and Alzheimer’s disease. Read more: www.biorxiv.org/content/10.6...
biorxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 18/03/2026
What makes the IGVF Catalog exciting? Michael Love, PhD, explains how it moves beyond genome annotation to map networks linking variants, regulatory elements, genes, and phenotypes, offering a new way to understand genome function. 🎬 youtu.be/oC7a_IJw9X8
youtu.be
What excites you most about the IGVF catalog?
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 13/03/2026
The IGVF Mapping Working Group generates large-scale single-cell datasets, developing computational pipelines to help uncover how genetic variation influences human health and disease. Learn more about IGVF Working Groups: igvf.org/working-grou...
igvf.org
IGVF Working Groups
Code of Conduct of Impact of Genomic Variation on Function (IGVF) Consortium
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 12/03/2026
How do noncoding variants drive immune disease? Using large-scale Perturb-seq in primary human CD4+ T cells, researchers map the chain from variant → CRE → gene → regulatory network, linking risk loci to shared disease programs. Read the preprint: www.biorxiv.org/content/10.6...
biorxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 06/03/2026
Handling large-scale single-cell data requires efficient tools. 🛠️ anndata is a Python package designed for working with annotated data matrices, offering sparse data support, lazy operations, and integration with PyTorch. Learn more: github.com/scverse/annd...
github.com
GitHub - scverse/anndata: Annotated data.
Annotated data. Contribute to scverse/anndata development by creating an account on GitHub.
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 04/03/2026
What drives the science behind IGVF? In this IGVF Q&A, members share how the team is tackling long-standing genomics challenges and building a comprehensive catalog of variant effects to advance human health & research. Tune in: youtu.be/zPzGIjSQJ4U?...
youtu.be
Impact of Genomic Variation on Function (IGVF) Consortium Q&A
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 27/02/2026
A new preprint from IGVF introduces a scalable workflow to address variants of uncertain significance (VUS). Across 40 genes, the approach reclassified 75% of 16,115 VUS and preclassified >90K variants—moving clinical genomics forward. Read more:  www.biorxiv.org/content/10.6...
biorxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 19/02/2026
SIMBA enables joint embedding of cells and their defining features into a shared latent space. This attribute supports single-cell and multimodal analysis, batch correction, and multi-omic integration.  Learn more: simba-bio.readthedocs.io/en/latest/
simba-bio.readthedocs.io
SIMBA: SIngle-cell eMBedding Along with features — SIMBA 1.2 documentation
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 11/02/2026
IGGSy 2026 is coming! July 5 - 9, join researchers from around the world to explore genome graphs, pangenomics, and metagenomics, including a dedicated Human Pangenome Project session with keynotes from speakers of varied specializations. Registration open now! iggsy.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 06/02/2026
Recent IGVF research benchmarks Perturb-seq in human stem cells, enabling scalable analysis of gene and enhancer function during differentiation and disease. Uncover the science behind it: www.cell.com/stem-cell-re...
cell.com
Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells
Sivakumar et al. optimize steps for Perturb-seq in human pluripotent stem cells, differentiated cardiomyocytes, and neural progenitor cells. They define key QC steps during the experiment and propose ...
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 04/02/2026
How does IGVF research move us closer to understanding human health and disease? Charles Gersbach, PhD, explains how mapping the function of genetic variation is key to unlocking better treatments, from cancer and fibrosis to neurodegeneration and aging. ▶️ youtu.be/R6Q3yavjGDs
youtu.be
How will IGVF research advance our understanding of human health and disease?
YouTube video by Impact of Genomic Variation on Function
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 30/01/2026
A recent preprint introduces MaveMD, a clinical interface for MaveDB that integrates MAVE data with ClinVar and ClinGen to support variant classification and reduce VUS uncertainty. Uncover the science behind it:  www.medrxiv.org/content/10.1...
medrxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 28/01/2026
Momentum and connections is exactly right! Excited to see the impact highlighted in the 2025 Annual Report. 👏🏼
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 23/01/2026
Large-scale perturbation of transcription factors and enhancers reveals regulatory networks shaping human heart development and congenital heart disease.  A new reference map helps interpret CHD genes and variants.   Uncover the research behind it: www.biorxiv.org/content/10.6...
biorxiv.org
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 21/01/2026
Understanding how genomic variation shapes disease opens the door to entirely new therapeutic strategies. Hear from Jesse Engreitz, PhD, and other IGVF members in the full Q&A. ▶️ youtu.be/zPzGIjSQJ4U
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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 13/01/2026
Cells sense matrix stiffness through mechanoenhancers, genomic elements that tune gene activity in response to mechanical signals. Editing these enhancers can reshape cell behavior, pointing to new therapeutic possibilities. Read more: www.science.org/doi/10.1126/...
science.org
Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness
Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcript...
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