This $324,118 National Science Foundation project grant supports research to decipher RNA-based regulatory logic through interpretable machine learning models. Funded under the Mathematical and Physical Sciences program (CFDA 47.049), the three-year award to New York University will develop and apply interpretable neural networks to massive parallel reporter assay datasets. Specifically, the models aim to elucidate the splicing code that determines exon skipping and the 5'UTR code regulating...
This $750,000 Project Grant award from the National Science Foundation's (NSF) Mathematical and Physical Sciences (CFDA 47.049) program supports the development of a novel platform to enable rapid and robust identification of functional RNA molecules directly within mammalian cellular environments. The research aims to solve the challenge of RNA structure sensitivity to local environments that has hindered progress in the field of functional RNA discovery. The project will deliver a customized...
The National Science Foundation (NSF) awarded a $1,199,997 Project Grant under its Biological Sciences program (CFDA 47.074) to the University of Colorado-Denver. The grant will fund research to improve understanding of the mechanisms underlying messenger RNA (mRNA) localization and translation, and develop machine learning models to better predict protein production from mRNA. The project will apply recent advancements in RNA sequencing technology to study how factors like tRNA abundance and...
This National Science Foundation (NSF) Project Grant, awarded under the Biological Sciences program (CFDA 47.074), provides $750,000 to Stanford University to develop new technologies for studying RNA, the essential molecules that carry genetic information and play crucial roles in cell functions. The key products and services to be delivered under this 3-year award include: Creating non-destructive methods to directly study RNA localization and interactions within living cells, achieving...
This National Science Foundation (NSF) Project Grant award under the Biological Sciences program (CFDA 47.074) provides $522,131.00 to New York University (NYU) from August 1, 2023 to July 31, 2026. The funded research aims to understand the relationship between RNA sequence features and splicing outcomes, as well as the role that nuclear speckles play in RNA splicing decisions. The project will leverage high-throughput assays and interpretable machine learning to identify sequence-encoded...
This Project Grant award from the National Science Foundation (NSF) Division of Molecular and Cellular Biosciences under the agency's Biological Sciences program (CFDA 47.074) provides $680,000 from August 1, 2023 to July 31, 2026 to the University of Chicago. The project aims to understand the sequences in pre-mRNA that determine which exons are removed during RNA splicing, a critical process in eukaryotic cells for generating mature messenger RNAs. The research will use high-throughput...
The National Science Foundation (NSF) Division of Chemistry awarded a $1,500,000 Project Grant to Stanford University under the Mathematical and Physical Sciences (MPS) program (CFDA 47.049). The grant, awarded on March 1, 2024, supports a 3-year research project titled "Evaluating and Advancing Cryo-EM for RNA Conformational Ensembles." The project aims to: (1) design, model, and experimentally probe RNA systems with discrete conformational states, and (2) characterize and challenge...
The National Science Foundation (NSF) Division of Molecular and Cellular Biosciences awarded a $750,000 Project Grant titled "TRANSITIONS: EVOLVING OUR UNDERSTANDING OF DYNAMIC RNA FOLDING AND FUNCTION" to Northwestern University under the Biological Sciences grant program (CFDA 47.074). The objective of this 3-year award is to uncover fundamental principles linking RNA sequence to dynamic RNA folding processes and function in biological systems. The research aims to enhance the...
Cornell University was awarded a $486,205 project grant from the National Science Foundation to develop sequence programmable triazine-thymine synthetic ligands. The grant is part of NSF's Mathematical and Physical Sciences program (CFDA 47.049), which aims to strengthen the nation's scientific enterprise through advancing knowledge and understanding of major problems. Under the three-year award beginning August 2021, Cornell researchers will design and test synthetic ligands that can be...
This $299,999 National Science Foundation project grant under the Biological Sciences program (CFDA 47.074) will support research exploring the RNA world and RNA-peptide world hypotheses using a novel dynamic combinatorial chemistry system at the University of Houston, a minority-serving institution. The two-year project beginning August 1, 2022 aims to advance understanding of the role of RNA and peptides in the origins of life. Investigators will employ a system using benzonuclease to cleave...
This three-year, $275,000 National Science Foundation Division of Chemistry Project Grant will support research into deciphering RNA-based regulatory logic using interpretable machine learning approaches. The awardee, Cornell University, will collaborate with researchers to design and deploy interpretable neural networks trained on massively parallel reporter assays. This will provide insights into splicing codes that determine exon skipping and the role of 5'UTR sequences in translation initiation and RNA stability. Experimental RNA binding protein data will be incorporated to model non-additive effects among sequence features and secondary structure. The results aim to demonstrate that interpretable machine learning can decode RNA regulatory systems, advancing the basic understanding needed for rational transcript design in biotechnology. This award is part of the NSF's $47.049 million Mathematical and Physical Sciences program to strengthen the nation's scientific enterprise through increased knowledge and major problem insights.