This two-year project grant from the National Science Foundation's Computer and Information Science and Engineering program aims to develop deep learning methods for high-resolution three-dimensional genome structure spatial reconstruction. With a total funding amount of $175,000, the award was issued on May 1, 2022 to the University of Colorado Colorado Springs to complete the project by April 30, 2024. The grantee will apply sophisticated and automated deep learning approaches to infer...
The National Human Genome Research Institute (NHGRI) awarded a $420,379 Project Grant (CFDA 93.172 - Human Genome Research) to The Leland Stanford Junior University (Stanford University) to develop advanced imaging-based platforms, termed 3D SL-LIVEFISH and LIVEFISH PAINT. These platforms will enable tracking the dynamics of any genomic locus, including repetitive and non-repetitive regions, across different cell types including primary cells. The goal is to provide an integrated single...
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 University of Washington was awarded a $504,949 Project Grant from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) to develop a series of machine learning models that integrate Hi-C data with other genomic data types such as RNA-seq, genome sequence, and ATAC-seq. The goal is to advance the analysis of chromatin structure and its relationship to gene expression and other cellular processes. Key objectives include: Extending the SAGITTARIUS model to...
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...
This $653,880 project grant was awarded by the National Human Genome Research Institute (NHGRI) under the Human Genome Research program (CFDA 93.172) to Yale University. The grant will fund the development of a high-content, image-based CRISPR screening platform to discover the molecular regulators of 3D genome, nucleome, and transcriptome spatial organization. The project aims to advance screening technologies compatible with in situ spatial omics techniques, enable multimodal detection and...
This $131,338 Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) supports research at the University of Washington 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. The project aims to: 1) use deep learning models to predict Hi-C contacts from DNA sequence across 80 human tissues, 2) learn the...
The National Science Foundation (NSF) awarded a 5-year, $399,835 CAREER grant under the Biological Sciences program (CFDA 47.074) to the Massachusetts Institute of Technology (MIT) to investigate how transcription and loop extrusion regulate 3D genome structure. The project aims to improve the understanding of how a single genome gives rise to diverse cell types by studying the dynamics of CTCF-mediated DNA loops and topologically associating domains (TADs). The work will integrate advanced...
This Project Grant award from the National Science Foundation's (NSF) Mathematical and Physical Sciences (CFDA 47.049) program provides $200,000 in funding to The Trustees of the University of Pennsylvania to conduct collaborative research that aims to understand genomic organization in the cell nucleus. The research team will employ an integrated approach leveraging biophysical modeling, super-resolution imaging, and machine learning to develop predictive models of how chromatin structure and...
This $120,227 project grant awarded by the National Science Foundation (NSF) under the Mathematical and Physical Sciences (CFDA 47.049) program supports research at Northeastern University to develop a new theoretical approach for studying the three-dimensional architecture and conformational ensembles of genes and gene clusters. The project aims to: (i) model the mechanics of chromatin at the gene scale, (ii) investigate how genomic conformations are affected by factors like supercoiling and...