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...

ASHG 2025 is coming up! 🎉 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/...

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

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...

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.

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...

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

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...

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...

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

🔍 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/...

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

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...

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...

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

Process 30M reads in minutes with high performance and efficiency. Kallisto is a fast, accurate tool for quantifying transcript abundances from RNA-seq data using pseudoalignment; no full alignment needed. Explore it here: github.com/pachterlab/k...

A recent study demonstrates how biophysical modeling of high-throughput perturbation data can reveal transcriptional dynamics, like bursting and splicing, that shape cell fate and disease response. Explore the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

Part of the IGVF single-cell analysis workflow - the IGVF-chromap tool offers a command-line interface for indexing and aligning single-cell ATAC-seq data using the Chromap pipeline. Explore the tool: github.com/IGVF/atomic-...

Click editing is a recently developed platform that combines RNA-guided nickases and DNA-dependent polymerases to install precise genome edits, including substitutions, insertions, and deletions, with high efficiency and minimal indels. Here’s how… pmc.ncbi.nlm.nih.gov/articles/PMC...

🎉 Big milestone for our sister consortium, SMaHT! Congrats on the paper in Nature, this is a huge step in mapping somatic variation!

🛠️ Topyfic is a Python library for applying reproducible LDA (rLDA) to single-cell and bulk RNA-seq data, helping identify consistent gene expression programs and key regulators like transcription factors across conditions. Explore the tool: github.com/mortazavilab...

IGVF is uncovering how genomic variation impacts genome function and phenotype through mapping, modeling, and resource generation to advance research across the community. Learn more: igvf.org

Catch up on the latest research from the IGVF Catalog Working Group during our upcoming Knowledge Portal Webinar, featuring Michael Love, PhD. Tune in Thursday, June 12th from 12–1 PM ET. Details: hugeamp.org/news.html?ni...

New collection available from the ‪@igvfconsortium.bsky.social‬! Developed through the National Human Genome Research Institute (NHGRI), this growing collection of plasmids will power a better understanding of genomic variants’ impact on genome function and phenotypes. www.addgene.org/depo...

IGVF teams across the U.S. are working together to advance understanding of how genomic variation impacts genome function and human health. From mapping and predictive modeling to characterization and coordination, IGVF unites varied expertise toward a shared mission. Learn more: igvf.org/about/

A recent study shows that complete human & plant genomes can be assembled using only Oxford Nanopore reads, offering a single-platform path to high-accuracy, telomere-to-telomere assemblies. Explore the findings: pmc.ncbi.nlm.nih.gov/articles/PMC...

BIRD is a powerful tool for identifying regulatory variants from STARR-seq and other MPRAs. It improves detection of rare, disease-relevant variants by modeling replicate variability and integrating prior information. Read the full article & access BIRD: pmc.ncbi.nlm.nih.gov/articles/PMC...

This upcoming #WorldEnvironmentDay, we reflect on how IGVF’s mission supports a more sustainable future. By enabling more precise, efficient healthcare, we can reduce waste, streamline treatments, and advance environmental responsibility in biomedicine. 🌱🌍

CellSpace: a scalable, sequence-informed tool for scATAC-seq that captures cell states, TF activity & mitigates batch effects across datasets. Explore the full publication for details and Cellspace tool access: www.nature.com/articles/s41...

IGVF is advancing our understanding of how genomic variation affects genome function to influence phenotypes. 1️⃣ study, 1️⃣ collaboration, 1️⃣ discovery at a time.

🎉 Big news from our sister consortium! Release 2 is now live. Find the latest insights in the HPRC data explorer!👇🏼

A recent study demonstrates how CRISPRa Perturb-seq can model in vivo cell states in vitro by activating thousands of transcription factors. This scalable approach reveals key regulators and therapeutic potential of fibroblast states. Uncover the findings: www.biorxiv.org/content/10.1...

🛠️ The IGVF TAP-seq design tool enables efficient primer design for targeted single-cell RNA-seq experiments. Generate gene-specific primers with Primer3 and assess off-targets using BLAST. Uncover the tool: bioconductor.org/packages/rel...

IGVF is advancing our understanding of how genomic variation impacts genome function and phenotype. Through collaborative research, we're building a comprehensive catalog of variant effects to support the broader scientific community! Explore our work: igvf.org

A recent study highlights how chromatin reconfiguration drives X-chromosome inactivation and how noncoding RNAs like Xist help organize nuclear compartments. Uncover the science behind it: pubmed.ncbi.nlm.nih.gov/39053028/

IGVF includes 5️⃣ core components. Predictive Modeling, Characterization, Networking, Mapping, and Data Coordination. Research teams across these groups work together to uncover how genomic variants influence genome function and phenotype. Learn more: igvf.org/about/

ArchR is a scalable tool for analyzing single-cell chromatin accessibility data. This guide walks through key steps like clustering and dimensionality reduction. Start here: www.archrproject.com/bookdown/ind...

Our program goals are what drives the research. IGVF is building a public catalog of variant impacts, advancing research across biology and medicine by combining data, tools, and models to better understand how genomic variation influences genome function and phenotypes.

sc-linker integrates scRNA-seq, epigenomic maps, and GWAS data to identify cell types and processes influenced by genetic variants in disease. Analyze single-cell datasets and explore disease mechanisms. 🛠️ Find the tool here: github.com/karthikj89/s...

Collaboration is how we establish and conquer our common goals. April 1-4 in Cambridge, MA, we’re coming together to advance the GA4GH Road Map and shape the future of genomics. We look forward to next week and to fostering partnerships and advancing common goals. 🎉

Explore the CRISPRi Tiling Design Tool from the Engreitz Lab. This novel resource streamlines the design of CRISPRi and prime editing tiling screens by optimizing gRNA selection, filtering off-target effects, and assembling oligo pools. Access the tool here: github.com/broadinstitu...

🗓️ The deadline to register for in-person attendance at GA4GH Connect is Wednesday, March 18! Join us April 1-4 in Cambridge, MA to collaborate, share insights, and help shape the future of the GA4GH Roadmap. We’ll see you there! broadinstitute.swoogo.com/connect25bos/

GA4GH April Connect 2025 is 31 days away! April 1–4 in Cambridge, MA, join IGVF along with the GA4GH community in our common goal of advancing the GA4GH Road Map and shaping future developments. In-person registration closes on March 18! broadinstitute.swoogo.com/connect25bos...

IGVF is advancing genomic research by developing a framework to understand how genetic variation affects genome function and shapes phenotypes. This fundamental work lays the foundation for new discoveries in health and disease.

How are multiplexed assays of variant effect (MAVEs) transforming genetic variant curation? Dr. Douglas Fowler of IGVF joins the DNA Today podcast to discuss how MAVEs improve variant interpretation and are advancing precision medicine. 🎧 Listen now: dnatodaypodcast.podbean.com/e/325-revolu...

How can genomic variation shape genome function and influence phenotypes? IGVF tackles this question by creating innovative models, mapping genes and regulatory elements, and building a variant impact catalog. Read more about the IGVF impact: www.sciencedirect.com/science/arti...

IGVF is driving innovation by developing and testing predictive models to understand how genomic variation impacts genome function. These crucial breakthroughs bring us closer to unraveling the complexities of human biology. Learn more about our goals: igvf.org

IGVF researchers propose ALL-Sum: a faster, more precise method for polygenic risk scores. Advancing personalized medicine with GWAS data. 25% higher accuracy, 15x faster, and half the memory of current tools. Read more: pubmed.ncbi.nlm.nih.gov/39110727/

Another year in the books! 🗓️ IGVF wishes everyone a joyous start to 2025! 🎉 As we roll into a new month in a new year, we look forward to continued collaboration, innovation, and progress in genomic variation research. #happynewyear