Completed Funding since 2001
NSF ABI: 1458652
- New methods for multiple sequence alignment with improved accuracy and scalability
PI: Tandy Warnow
August 2015 - July 2021.
This project developed
new methods for multiple sequence alignment,
building on our SATé, PASTA, and UPP methods.
NSF CCF: 1535977
Graph-Theoretic Algorithms to Improve Phylogenomic Analyses
Lead Institution: Illinois (PI: Warnow, Co-PI: Chandra Chekuri)
Collaborative Institution: Berkeley (PI: Satish Rao)
NSF IIS: 1513629
Scalable and Highly Accurate Methods for Metagenomics.
Lead Institution: Illinois (PI: Tandy Warnow)
Collaborative Institution: University Maryland (PI: Mihai Pop)
Novel Methodologies for Genome-scale Evolutionary
Analysis of Multi-locus data
PI: Luay Nakhleh (Rice University), Co-PIs Noah Rosenberg (Stanford)
and Tandy Warnow (Illinois)
Collaborators: Rice University (Luay Nakhleh, PI) and Stanford University (Noah Rosenberg, PI),
2011-2014 (no-cost extensions to 2016).
Rice University, Stanford University, and the University of Texas at Austin
were awarded collaborative grants to develop and implement algorithms and
software tools for the analysis of gene genealogies and
inference of species phylogenies from them.
A gene genealogy, also known as a gene tree, models how genes replicate and get
transmitted from one generation to the next during evolution.
A species phylogeny models how species arise and diverge.
A species phylogeny is traditionally inferred by a three-step process: (1) a genomic region
from the set of species under study is sequenced; (2) a "gene tree" is inferred for the genomic region; and,
(3) the gene tree is declared to be the species tree.
However, recent evolutionary genomic analyses of various groups of organisms have
demonstrated that different genomic regions may have evolutionary histories
that disagree with each other as well as with that of the species.
Further, evolutionary processes such as horizontal gene transfer, result in
network-like, rather than tree-like, species phylogenies.
This joint project will develop accurate computational methods for determining the causes of
gene tree discordance, and inferring species phylogenies (trees as well as networks)
from gene trees despite their discordance.
Special emphasis will be put on the efficiency of the methods
so that they allow for analysis of genome-scale data sets.
All methods will be implemented and extensively tested for performance.
John Simon Guggenheim Memorial Foundation Fellowship
The fellowship (2010-2011) was awarded for the Computer Science field of study,
three problems in evolutionary tree estimation:
whole genome phylogeny, co-estimation of sequence alignments
and phylogenetic trees, and metagenomic phylogenetic placement
(see this page).
NSF DEB 0733029
Large-Scale Simultaneous Multiple Alignment and Phylogeny Estimation
PI: Warnow. Co-PI: Linder.
Collaborators: University of Georgia, University of Kansas, University of Nebraska
2007-2012, $1.7 Million
NSF ITR 0331453
Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics
Collaborators: Florida State University, UC Berkeley, UC San Diego, University of New Mexico
2003-2010, $11.6 Million
NSF ITR BCS 0312830
Algorithms for Inferring Reticulate Evolution in Historical Linguistics
PI: Warnow, PI at the University of Pennsylvania (collaborating institution) Donald Ringe
Collaborators: Rice University, UC Berkeley, University of Pennsylvania
Computational Phylogenetics for Historical Linguistics webpage
NSF IGERT DGE 0114387
- Computational Phylogenetics and Applications to Biology
PI: Hillis, Co-PIs Warnow, Jansen, and Gutell, 2001-2007. Total amount $2,741,575.
NSF DEB 0120709
- Comparative Chloroplast Genomics: Integrating
Computational Methods, Molecular Evolution, and Phylogeny.
PI: Robert Jansen, Co-PIs Warnow and Raubeson, 2001-2007.
Total amount: $1,350,000.
NSF ITR/AP 0121680