The National Human Genome Research Institute (NHGRI) awarded a $504,949 Project Grant (CFDA 93.172 - Human Genome Research) to the University of Washington to develop advanced machine learning models that integrate Hi-C chromatin contact data with other genomics data types. The project aims to: 1) Extend the SAGITTARIUS model to analyze Hi-C time-series data and study the dynamic interplay between gene expression and chromatin structure during biological processes; 2) Develop a graph-based...
This $1,273,296 Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) supports research to develop advanced models for predicting the impact of genetic variants on mRNA stability, translation, and protein levels. The key products and services to be delivered include: High-throughput reporter assays to characterize how variants in coding and untranslated regions impact mRNA stability and translation, including across multiple cell types....
The National Human Genome Research Institute (NHGRI) awarded a $400,000 Project Grant (CFDA 93.172 - Human Genome Research) to the University of Washington to develop new single-cell multi-omic technologies for studying the relationship between three-dimensional genome organization and gene expression. Specifically, the grant will fund the development of CARE-Seq, a novel method to jointly measure whole-genome chromatin interactions and gene expression in the same single cells from complex...
The National Human Genome Research Institute (NHGRI) awarded a $1,350,896 Project Grant under the Human Genome Research program (CFDA 93.172) to the University of California, San Diego (UCSD) effective January 1, 2025 through December 31, 2028. The overarching goal of this research project is to develop novel technology based on massively parallel reporter barcoding strategies to enable simultaneous measurements of the effects of sequence perturbations on chromatin state, DNA-protein...
This $292,727 Project Grant award from the National Institutes of Health (NIH) under the Trans-NIH Research Support program (CFDA 93.310) supports a research project by The Broad Institute, Inc. to discover novel regulators of 3D genome organization. The project aims to leverage large-scale genomic datasets to predict and experimentally validate new trans-acting factors that regulate chromatin interactions and genome architecture. By applying deep neural network models to in silico genetic...
The National Human Genome Research Institute (NHGRI) awarded a $259,446 Project Grant under CFDA Program 93.172 - Human Genome Research to the University of Washington. The grant, effective September 4, 2024 through June 30, 2025, will fund the development of semi-supervised machine learning integration tools to predict undercharacterized genomic and proteomic data from single-cell profiling. The research aims to computationally fill gaps in single-cell time series data, predict the physical...
This Project Grant award, valued at $491,366, was issued by the National Human Genome Research Institute (NHGRI) under the Human Genome Research federal grant program (CFDA 93.172). The award is focused on developing new algorithms to robustly map disease-associated genetic variants to critical target genes, particularly in underrepresented populations. Key objectives include: Improving the ability to identify disease-critical genes in non-European populations where data is limited. Developing...
This $653,880 Project Grant awarded by the National Human Genome Research Institute (NHGRI) under the Human Genome Research program (CFDA 93.172) supports the development of a high-content, image-based CRISPR screening platform to discover regulators of three-dimensional (3D) genome architecture across multiple length scales. The goal is to advance screening technology to enable large-scale, multi-omic analysis of the spatial organization of the genome, nucleome, and transcriptome. Key...
The National Human Genome Research Institute (NHGRI), through the Human Genome Research program (CFDA 93.172), awarded a $444,125 Project Grant to the Rector & Visitors of the University of Virginia (UVA) to develop computational models that accurately quantify open chromatin bias and TN5 intrinsic cleavage bias in both bulk and single-cell Cleavage Under Targets & Tagmentation (CUT & TAG) data. The models will characterize how these biases affect the detection of histone...
This Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) supports research to develop new computational methods and models for integrating single-cell 3D genomics data with other single-cell modalities. The $501,191.23 award, effective from September 2, 2024 to June 30, 2027, will fund the University of Texas MD Anderson Cancer Center's work to: Create a single-cell gene-body associating domain (SCGAD) scoring system to explore 3D...
This $131,338 federal Project Grant award was provided by the National Human Genome Research Institute (CFDA 93.172 Human Genome Research) to the University of Washington. The overarching goal of this 2-year award is to identify the functional consequences of variations in nuclear architecture on transcriptional and post-transcriptional regulation, and the role of this variation in human health and disease.
Specifically, the award supports three research aims: 1) developing novel deep learning models to predict Hi-C contacts from DNA sequences across 80 human tissues, 2) learning the rules of chromatin organization shared across 100 mammalian species using a deep learning model to translate between Hi-C and ATAC-seq data, and 3) modeling the impact of nuclear organization variations on tissue-specific gene regulation in humans using machine learning, long-read RNA-seq, and Hi-C. The research outputs will provide open-source, interpretable models to enable discovery and quantification of the regulatory causes and consequences of nuclear DNA organization in healthy and diseased human tissues.