This National Science Foundation project grant of $638,016 awarded to Claremont McKenna College on May 1, 2022 under the Computer and Information Science and Engineering program (CFDA 47.070) will support the development of new algorithms and software tools to analyze phylogenetic tree reconciliations. Specifically, the award will fund research to design efficient algorithms for identifying best representative reconciliations of pairs of phylogenetic trees, such as those depicting hosts and...
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 $457,904 Project Grant from the National Science Foundation's Biological Sciences program (CFDA 47.074) will fund the development of novel computational frameworks for biomolecular sequence analysis at Michigan State University from March 2022 through February 2027. The university will create new statistical resampling algorithms and mathematical models to move beyond traditional assumptions in phylogenetic analysis, such as treating sequences as independent and identically distributed or...
This $1,205,737.49 Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) will fund the development of scalable computational methods and software tools to enable better analysis and interpretation of large genomic datasets. The key products and services to be delivered under this 4-year project (Sep 2024 - Jun 2028) include: Developing novel maximum likelihood estimation (MLE) frameworks and optimization techniques to enable significantly...
This Project Grant award from the National Science Foundation (NSF) Biological Sciences program (CFDA 47.074) will support research by the University of California, Berkeley to characterize the evolutionary history and legacy of archaic ancestry in diverse human populations. The $193,608 award, effective August 1, 2024, will enable the development of novel statistical methods to analyze archaic introgression across large-scale, multiethnic genomic datasets. The research aims to generate the...
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 $249,000 federal Project Grant award from the National Science Foundation (NSF) Biological Sciences (CFDA 47.074) program supports a phylogenetic investigation into the genetic basis of life history trait variation across eucalyptus trees. The project aims to leverage the diversity of wild eucalyptus species to gain insights into the genetic architecture underlying traits like overall size, growth, and reproduction in these economically important plants. The research will develop and...
This $741,002 federal Project Grant award from the National Science Foundation's Biological Sciences program supports the development of a novel machine learning framework for analyzing large-scale, multi-modal single-cell biological data. The project aims to construct advanced computational tools and user-friendly software to enable more effective extraction of insights and knowledge from complex single-cell datasets spanning genomics, transcriptomics, epigenomics, and proteomics. The...
The National Science Foundation (NSF) awarded a $299,868 project grant under the NSF Technology, Innovation, and Partnerships (CFDA 47.084) program to Iowa State University of Science and Technology. This 12-month grant, which began on June 15, 2024, aims to assess strategies for transitioning the open-source RevBayes phylogenetic software community into a self-sustaining and self-governing ecosystem. The project will investigate ways to improve the experiences of RevBayes users, contributors,...
The National Science Foundation (NSF) awarded a $162,510 Project Grant under the Computer and Information Science and Engineering (CFDA 47.070) program to the University of Oklahoma to develop algorithms for scalable inference and phylodynamic analysis of tumor haplotypes using low-coverage single-cell sequencing data. The goal is to create a phylodynamic framework to jointly infer cancer phylogenetic trees and evolutionary parameters from single-cell DNA sequencing data. This will enable cancer...