Integrating Computational Science into Research in Biological Networks. Start date: July 1, 2007. Expires: June 30, 2009. Awarded amount to date: $1,249,285. Principal investigator: Gary Benson. Sponsor: Trustees of Boston University.
Supports the study of biological networks at the Integrative Graduate Education and Research Traineeship program in Bioinformatics at Boston University. The project will model networks in terms of their component interactions, regulatory properties, sub-networks or pathways, and system dynamics.
Development of Computational Tools and Experimental Verifications for Protein Design. Start date: July 15, 2007. Expires: June 30, 2010. Awarded amount to date: $375,000. Principal investigator: Costas Maranas. Sponsor: Pennsylvania State University, University Park.
Supports the development of customized computational frameworks to guide protein design. “Hypotheses generated by the modeling/optimization base are used to guide the experiment and experimental results serve to assess and correct the computational frameworks,” according to the grant abstract.
Developing Computer Simulations Integrating Biomedical Research Techniques with Bioinformatics Tools for Case-Based Learning in Introductory Biology Courses. Start date: July 15, 2007. Expires: June 30, 2011. Awarded amount to date: $447,381. Principal investigator: Mark Bergland. Sponsor: University of Wisconsin-River Falls.
Supports the development of computer simulations of laboratory procedures such as DNA microarray experiments, real-time PCR, and pulsed field gel electrophoresis, along with “a series of cases for investigative, problem-based learning involving bioinformatics,” according to the grant abstract.
Acquisition of a Linux Cluster for Bioinformatics Research and Education. Start date: Aug. 1, 2007. Expires: July 31, 2009. Awarded amount to date: $325,000. Principal investigator: Zhiping Weng. Sponsor: Trustees of Boston University.
Funds computing infrastructure to support research in biological networks at Boston University. “The algorithms, software, and data sets produced with the computing cluster will directly enhance the infrastructure for research in biological networks,” according to the grant abstract.
Any unused CPU cycles will be made available to other researchers at Boston University and all tools resulting from the project will be made freely available to the research community through a webserver.
Tools and Databases for Enzyme Function Prediction and Active Site Identification: Evolutionary Matching of Protein Surfaces. Start date: Aug. 1, 2007. Expires: July 31, 2008. Awarded amount to date: $285,848. Principal investigator: Jie Liang. Sponsor: University of Illinois at Chicago.
Funds development of computational methods for identifying surfaces on protein structures that are likely to be functionally important, for identification of key residues, and for predicting multi-functional enzymes. The investigators will develop models and methods for constructing substitution rate matrices of local binding surfaces and will build a resource database of annotated protein functional surfaces of enzymes.
Coordinated Computing in Structural Biology. Start date: Aug. 1, 2007. Expires: July 31, 2008. Awarded amount to date: $99,992. Principal investigator: Piotr Sliz. Sponsor: Harvard University.
Supports the SBGrid Research Coordination Network, an effort to provide “a uniform level of computing grid access and software availability to all structural biology groups, including those in geographically underrepresented communities and smaller universities,” according to the grant abstract. The network will adapt a number of structural biology applications to take advantage of grid resources and contemporary hardware technologies and will encourage development of parallelized, grid-compatible software in affiliated laboratories.
Collaborative Research: Integrated Modeling of Biological Nanomachines. Start date: Aug. 1, 2007. Expires: July 31, 2009. This grant was awarded to five investigative teams:
- University of Washington. Principal investigator: David Baker. Awarded amount to date: $165,000.
- Baylor College of Medicine. Principal investigator: Wah Chiu. Awarded amount to date: $165,000.
- Washington University. Principal investigator: Tao Ju. Awarded amount to date: $165,000.
- Baylor College of Medicine. Principal investigator: Matthew Baker. Awarded amount to date: $165,000.
- University of California-San Francisco. Principal investigator: Andrej Sali. Awarded amount to date: $165,000.
Funds the development of information discovery and integration methodologies for deriving atomic models of biological nanomachines — the assemblies that carry out all the basic biological processes in a living organism. These models will be derived from three-dimensional cryo-electron microscopy mass density function in conjunction with physics of protein folding and informatics data. Research goals involve information discovery, information integration, and validation of the proposed algorithms.
A Collaborative Information Repository Model Organism Database. Start date: Aug. 1, 2007. Expires: July 31, 2008. Awarded amount to date: $97,126. Principal investigator: Roy Welch. Sponsor: Syracuse University.
Supports further development of the model organism database for Myxococcus xanthus, called xanthusBase. The investigators intend to incorporate “lessons learned in the business community and by public Internet databases into the design and implementation of a novel MOD for M. xanthus that employs editing principles from Wikipedia … to function as a voluntary collaborative information repository.”
Learning from Graph-Structured Data: New Algorithms for Modeling Physical Interactions in Cellular Networks. Start date: Aug. 15, 2007. Expires: July 31, 2008. Awarded amount to date: $253,905. Principal investigator: Christina Leslie. Sponsor: Columbia University.
Supports development of new machine-learning learning algorithms for analyzing graph-structured data. The algorithms include boosting with efficient graph mining; graph kernels based on subgraph histogramming; and information-based graph partitioning. The algorithms will be used to integrate physical interaction network data into models of gene regulation, and the focus will be two modeling problems: inferring signal transduction pathways and modeling cis regulatory modules at the level of DNA sequence and interacting regulatory proteins.
Genomic Data. Start date: Aug. 15, 2007. Expires: July 31, 2008. This grant was awarded to two investigative teams:
- Arizona State University. Principal investigator: Shu-Chuan Chen. Awarded amount to date: $162,335.
- Pennsylvania State University, University Park. Principal investigator: Bruce Lindsay. Awarded amount to date: $43,908.
Supports the development of statistical methods and algorithms for SNP analysis “that are designed to enhance the biological realism of the underlying models,” according to the grant abstract. The project plans to extend the development of a new method for constructing hierarchical trees from sequence data using maximum likelihood and modal inference. A second project aim is to “enhance the biological realism of the ancestral mixture model” to include multi-state characters, advanced models of sequence evolution, and recombination. Another goal is the development of a new method for reconstructing haplotype sequences from genotype data without knowing the parental information.
Development of Bioinformatic Methods for Studying Gene Expression Network Inflammation and Neuronal Regeneration. Start date: Aug. 15, 2007. Expires: July 31, 2008. This grant was awarded to two investigative teams:
- Rutgers University New Brunswick. Principal investigator: Yi Ren. Awarded amount to date: $207,591.
- Princeton University. Principal investigator: Jianqing Fan. Awarded amount to date: $141088
Funds development of new bioinformatic and statistical methods to study traumatic central nervous system including spinal cord injury, which provokes an inflammatory response that generates substantial secondary tissue damage and inhibits neuronal regeneration. The investigators will use microarrays to study expression profiles for microglia and macrophages in different time points and will develop new statistical techniques to analyze the data. These techniques include “removing intensity effects of the Affymetrix data, identifying significant genes and determining gene expressions patterns over time, [and] identifying a small group of genes that differentiate invading macrophages from activated microglia in the spinal cord,” according to the grant abstract.
Large-Scale Analysis of Collections of Phylogenetic Trees. Start date: Aug. 15, 2007. Expires: July 31, 2008. Awarded amount to date: $140,152. Principal investigator: Tiffani Williams. Sponsor: Texas Engineering Experiment Station.
Proposal to develop methods for analyzing the large collection of trees encountered during a phylogenetic search. “A better understanding of search behavior can drive the design of better heuristics, which ultimately lead to more accurate reconstructions of phylogenetic trees,” the investigators state in the grant abstract. Goals include: developing a search history repository that contains all of the trees examined by a phylogenetic heuristic; designing algorithms for exploiting informative patterns in a search history repository; and developing visualization tools that provide informative views of the data residing in the repository.
Structure Comparison and Mining for RNA Genomics. Start date: Aug. 15, 2007. Expires: July 31, 2009. Awarded amount to date: $123,310. Principal investigator: Jason Wang. Sponsor: New Jersey Institute of Technology.
Supports development of a new tool for motif discovery using “algorithmically efficient” alignment methods, according to the grant abstract. The proposal is based on an extension of the loop model commonly used in RNA structure prediction. The extended model “achieves better efficiency than current algorithms and allows a biologist to annotate conserved regions and incorporate these into the process, thereby obtaining more meaningful results.”
Bioinformatics: Learning by Doing. Start date: Sept. 1, 2007. Expires: Aug. 31, 2009. Awarded amount to date: $826,268. Principal investigator: William Sofer. Sponsor: Rutgers University New Brunswick
Supports a four-year project called the DNA Sequencing Analysis Program, or DSAP, which will educate high school students about genomics via web-based bioinformatics tools. DSAP will include a student DNA sequence analysis scaffolding program; an administrative program that allows teachers to view student work, students to evaluate peers, and teachers to communicate with their students; a staff administrative program; an embedded assessment tool; and a series of tutorials that will guide students through DNA sequence analysis.
Science Research at Kean University. Start date: Sept. 1, 2007. Expires: Aug. 31, 2009. Awarded amount to date: $420,412. Principal investigator: David Joiner. Sponsor: Kean University.
Funds a multi-teraflop compute cluster at Kean University to support a variety of research topics, including bioinformatics, meteorology, astrophysics, and nonlinear optics.