Project Grant R43HG010123

The National Human Genome Research Institute (NHGRI) awarded a $1,711,422 Project Grant under the Human Genome Research program (CFDA 93.172) to the New York Genome Center, Inc. (NYGC) to develop privacy-preserving tools for transcriptomic data analysis. The tools will enable bulk and single-cell RNA-seq gene/transcript quantification and eQTL mapping on encrypted data, addressing privacy concerns around sharing human genomic and transcriptomic data. The project will involve collaboration...

This Cooperative Agreement, awarded by the National Human Genome Research Institute (NHGRI) under the Human Genome Research program (CFDA 93.172), will develop advanced sequence alignment, population genetic, and visualization tools to enable new ways of accessing and understanding the human pangenome. The $1,645,076 award will fund the creation of rapid sequence mapping and comparison methods using succinct data structures, as well as pangenome graph-based analyses for GWAS, heritability,...

This Project Grant award of $200,000.00 from the National Science Foundation (NSF) Biological Sciences program (CFDA 47.074) to Cornell University aims to improve the efficiency of whole genome sequencing (WGS) data analysis. The research focuses on two main objectives: Optimizing the Genotype Representation Graph (GRG) data structure for modern parallel computing architectures, particularly GPUs, to handle the dynamic nature of genomic computations. Additionally, a matrix abstraction of the GRG...

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...

This Project Grant award from the National Science Foundation's (NSF) Computer and Information Science and Engineering (CISE) Program (CFDA 47.070) aims to build a next-generation genomic data processing system that incorporates state-of-the-art systems design principles. The $200,000 award, effective from October 1, 2024 to September 30, 2027, focuses on three key innovations: (1) improving cluster scheduling policies based on characterization of genomic workloads, (2) developing machinery...

This $644,578 federal Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) aims to develop advanced algorithms and software tools to enable "fully realizing pangenomics alignment" - a method to improve genome sequence read alignment by utilizing a population of reference genomes rather than a single reference. The key products/services to be delivered include: 1) Algorithms to select an optimal subset of genomes from a large...

This Project Grant award from the National Human Genome Research Institute (NHGRI), under the Human Genome Research program (CFDA 93.172), aims to develop scalable computational methods and software tools to enable the biomedical research community to better analyze and interpret large genomic datasets. The $1,205,737.49 award, spanning from September 2024 to June 2028, will fund the following key activities: Developing a novel maximum likelihood estimation framework and optimization...

This federal Cooperative Agreement award, issued by the National Human Genome Research Institute (NHGRI) under the Human Genome Research program (CFDA 93.172), provides $1,696,968 in funding to the University of California, Santa Cruz (UCSC) 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 project involves five key...

This federal Cooperative Agreement award from the National Human Genome Research Institute (NHGRI), under the Human Genome Research program (CFDA 93.172), provides $1,310,799 to the University of California, San Diego (UCSD) to develop tools that leverage pangenomes to improve analysis and visualization of complex genomic regions associated with human traits and diseases. The key products and services to be delivered include: A web-based pangenome browser that integrates existing biobank...

The Project Grant award of $339,000 from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) will support the development of GFASTAR, a suite of C++ algorithms and tools for evaluating and manipulating genome assembly graphs. This will help advance telomere-to-telomere (T2T) genome assembly capabilities, enabling the generation of more complete and accurate reference genomes across multiple species. The GFASTAR software ecosystem, powered by the expanded GFALIBS...