This $138,428 project grant from the National Science Foundation's Computer and Information Science and Engineering program (CFDA 47.070) will support the development of computationally tractable structured hierarchical models to identify complex genetic associations hidden from current methods. The grantee, J. David Gladstone Institutes, will analyze genomic and clinical trait data using machine learning to build predictive models for individualized disease risk assessment and personalized...
This $900,000 Project Grant, awarded by the National Science Foundation's (NSF) Computer and Information Science and Engineering (CFDA 47.070) program, supports the development of custom hardware accelerators and software solutions to enable pervasive use of genome sequencing in precision healthcare. The three key objectives are: 1) designing domain-specific accelerators for whole genome sequencing and emerging genomics applications, 2) developing point-of-care pathogen detectors using real-time...
This $1,205,737.49 federal Project Grant award was made on September 10, 2024 by the National Human Genome Research Institute (NHGRI) under the Human Genome Research program (CFDA 93.172). The grant will support the development of scalable computational methods and software tools to enable more effective analysis and interpretation of large genomic datasets for biomedical research. Key objectives include: Improving the computational efficiency of maximum likelihood estimation methods for...
This $565,783 National Science Foundation project grant under the Computer and Information Science and Engineering program will support the development of new data structures and software for computational biology and big data storage systems at the University of Maryland, College Park. The grantee will create compact summary data structures that can represent huge datasets and fit within computer memory, enabling applications to run much more quickly and scale to larger data sets. The data...
This $400,000 Project Grant award from the National Human Genome Research Institute (NHGRI) under CFDA 93.172 "Human Genome Research" will support a research program at Brigham & Women's Hospital to develop advanced computational methods for accurately identifying and genotyping structural variants within large genetic biobank datasets. The key objectives of the work are to: 1) create haplotype-informed algorithms to improve detection sensitivity and genotyping accuracy for...
This National Science Foundation (NSF) Biological Sciences (CFDA 47.074) program grant awarded to Cornell University provides $200,000 in funding from April 15, 2025 to March 31, 2027 to develop tools and infrastructure that will enable researchers to advance the understanding of human genetics and improve the accuracy of population genetic studies. The key goals are to: 1) Optimize the Genotype Representation Graph (GRG) data structure for modern parallel computing architectures, particularly...
This five-year, $997,720 Project Grant from the National Science Foundation's Computer and Information Science and Engineering program aims to develop new mathematical models and algorithms for genetic data analysis using deep learning techniques. Funded through the NSF's statutory mission to support basic research, the award will support research at Cornell University from July 2022 through June 2027. Specifically, the principal investigator will create novel deep generative models to replace...
This $2,963,428 Project Grant award from the National Science Foundation's Biological Sciences program (CFDA 47.074) aims to develop critical infrastructure and tools for interpreting genomic data. The project will create high-quality genome assembly workflows, comprehensive documentation, and interactive training materials to make these advanced genomic analysis capabilities accessible to a wide audience of biology researchers. This will enable downstream discoveries in areas such as...
This Cooperative Agreement award from the National Human Genome Research Institute (NHGRI), under the Human Genome Research federal grant program (CFDA 93.172), provides $1,696,968 in funding from September 2024 to August 2027 to develop novel computational methods and software tools for analyzing pangenomic data, with a focus on improving the accuracy and efficiency of variant calling and genotyping, particularly for complex structural variants. The key products and services to be developed...
The National Science Foundation awarded a $397,483 Project Grant to the University of California, Davis for research titled "COMPUTATIONAL METHODS TO IMPROVE OUR UNDERSTANDING OF THE DIVERSITY OF GENOMIC STRUCTURAL VARIATION." The award period is from April 1, 2021 through March 31, 2026. The grant is funded through NSF's Biological Sciences program (CFDA 47.074), which supports basic research to increase scientific knowledge and enhance understanding of major problems confronting...
This three-year Project Grant from the National Science Foundation's Division of Information and Intelligent Systems under the Computer and Information Science and Engineering program ($600,000) will support the development of new computational methods and software for analyzing collections of genomic variants. Specifically, the grantee, Carnegie Mellon University, will create algorithms and open-source software tools to more accurately construct, compare, and assess the complexity of genome graphs - an important data structure for representing populations of genomic sequences. These new techniques are expected to increase the accuracy and efficiency of genomic analyses, enabling faster and more comprehensive study of how genetic differences affect human health and biology. The grantee will apply the new methods to improve genome alignment, cancer tumor sequencing, and modeling of cancer heterogeneity. Educational videos will also be produced to introduce key concepts to broader audiences.