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Funding Update: Oct 1, 2010

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NSF Bioinformatics Grants Awarded Aug. 20 — Sept. 29, 2010

Haplotype Phasing Algorithms and Clark Consistency Graphs
Start Date: Jan. 1, 2011
Expires: Dec. 31, 2012
Awarded Amount to Date: $199,999
Principal Investigator: Sorin Istrail
Sponsor: Brown University

Supports the development of long-range phasing algorithms based on the combinatorial structure of Clark consistency graphs that will be used to detect disease haplotypes in large population samples. "The primary output of this project will be new long-range phasing software, documentation, and source code, all to be immediately and continually available to the scientific community as open source for research and education," the grant abstract states.


Phenotype Ontology Research Coordination Network
Start Date: Oct. 1, 2010
Expires: Sept. 30, 2015
Awarded Amount to Date: $498,652
Principal Investigator: Paula Mabee
Sponsor: University of South Dakota Main Campus

The funds will support a network of scientists that will "develop standards and best practices for accurate phenotype representations, build key reference ontologies for plants, vertebrates, and arthropods, and cross-reference these ontologies so that key data can be easily shared and accessed," according to the grant abstract.


A Mixture Modeling Framework for Statistical Identification of Multiple Genomes in a Metagenomics Sample
Start Date: Oct. 1, 2010
Expires: Sept. 30, 2013
Awarded Amount to Date: $725,009
Principal Investigator: Hongmei Jiang
Sponsor: Northwestern University

The funds for this proposal will support the development of algorithms and methods that can be used in metagenomics studies in areas such as human health, environment, agriculture, and identification of viruses related to biological threats and infectious diseases. The statistical models and computational algorithms will be integrated into the open-source R software package and made available to the scientific community.


Statistical Methods and Software for Analyzing Massively Parallel Epigenomic Sequencing Data
Start Date: Oct. 1, 2010
Expires: Sept. 30, 2013
Awarded Amount to Date: $486,370
Principal Investigator: Shili Lin
Sponsor: Ohio State University

Funds efforts to develop likelihood-based and Bayesian statistical methods and computational algorithms to analyze epigenetic data generated by genomic sequencing technologies and to detect mutant cells that may have undergone epigenetic changes, which are expected to "contribute to early detection of exposure to potential biowarfare pathogens," according to the grant abstract.


Stochastic Modeling of Post-Transcriptional Regulation of Gene Expression in Bacteria
Start Date: Oct. 1, 2010
Expires: Sept. 30, 2011
Awarded Amount to Date: $124,956
Principal Investigator: Rahul Kulkarni
Sponsor: Virginia Polytechnic Institute and State University

According to the grant abstract, the funds will support the development of "quantitative stochastic models for modulation of gene expression by post-transcriptional regulation." The researchers will develop "an analytical framework for modeling intrinsic noise in gene expression; analytical and computational models for post-transcriptional regulation of gene expression by small RNAs; and model post-transcriptional regulation of gene expression by the quorum sensing and carbon storage regulator pathways." The tools developed during the project will be made available to the scientific community via web interfaces.


Collaborative Research: Spatial Model-based Methods for RNA-seq Analysis
Start Date: Oct. 1, 2010
Expires: Sept. 30, 2011
This grant was awarded to two investigative teams:
• $76,743, Yu Michael Zhu, Purdue University
• $119,243, Zhaohui Qin, Emory University

Supports the development of advanced statistical models based in spatial statistics to analyze RNA-seq data for prostate cancer and psoriasis transcriptomic studies. The investigators aim to develop "spatial Poisson mixed effects models including a hierarchical model and a mixture model to accommodate biases, variations, and correlations present in RNA-seq data." This will make it possible "to accurately estimate gene/isoform expression levels and to facilitate gene/isoform expression comparison and novel transcript structure or activities discovery" according to the grant abstract.


Reducing the Complexity of Comparative Genomics with Online Analytical Processing
Start Date: Sept. 15, 2010
Expires: Aug. 31, 2013
Awarded Amount to Date: $448,253
Principal Investigator: Robert Kosara
Sponsor: University of North Carolina, Charlotte

Supports the development of a "data warehouse-type database system optimized for comparative genomics," which will store sequence-linked biological data in a way that supports online analytical processing and complex set-based queries, according to the grant abstract. The investigators plan to develop a workflow tool to guide users through core operations and an interactive query tool. When it is complete, users will be able to browse, compare, and export set-based and individual record results.


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Modeling Quantum Tunnel Current to Statistically Sequence Biomolecules
Start Date: Sept. 15, 2010
Expires: Aug. 31, 2013
Awarded Amount to Date: $576,001
Principal Investigator: Manjeri Anantram
Sponsor: University of Washington

Funds the development of computational approaches to change the way biomolecules are designed "by providing a synergistic combination of physical modeling, computational data, and adapted statistical learning methods that proactively account for the randomness," according to the grant abstract. The project aims to discover "whether significant performance gains can be obtained by designing learning algorithms that explicitly account for the physical variations and randomness in electronic sequencing."


Graph-Based Theoretical Models and Mining Algorithms for Bioinformatics Data Analysis
Start Date: Sept 1., 2010
Expires: Aug. 31, 2012
Awarded Amount to Date: $150,000
Principal Investigator: Xiaohua (Tony) Hu
Sponsor: Drexel University

Supports a project that aims to develop graph-based theoretical models and algorithms that will be used to analyze bioinformatics data sets that are represented as single large graphs or in a graph database. According to the grant abstract, the investigators will focus on developing structure pattern discovery methods in graph databases that are based on graph decomposition and compression and mining algorithms for large scale-free network graphs.


A Unified Computational Framework to Enhance the Ab Initio Sampling of Native-Like Protein Conformations
Start Date: Sept. 1, 2010
Expires: Aug. 31, 2013
Awarded Amount to Date: $449,998
Primary Investigator: Amarda Shehu
Sponsor: George Mason University

The funds will support a project that aims to understand protein function by designing a computational framework that combines "probabilistic exploration with the theory of statistical mechanics" to compute the spatial arrangements of proteins in their biologically active state. According to the abstract, the "broader impact" of the project will be to create a filter that "computes diverse coarse-grained conformations relevant for the protein native state that can then be further refined through detailed biophysical studies."


Model Reduction in Systems Biology: The Mori-Zwanzig Projection Method
Start Date: Sept. 1, 2010
Expires: Aug. 31, 2011
Awarded Amount to Date: $108,955
Principal Investigator: Jianhua Xing
Sponsor: Virginia Polytechnic Institute and State University

Funds a project that aims to apply the Mori-Zwanzig projection method, which is widely used for studying Hamiltonian dynamics, "to develop a general formalism and numerical algorithms" for cellular regulatory networks." According to the grant abstract, the approach will be useful in cases where "a coarse-grained model is needed, or available data prevents a more detailed model, the network under study is embedded in a larger network, and where one wants to perform multi-scale modeling."


Novel Techniques for Understanding Convergence in Large-Scale Markov Chain Monte Carlo Phylogenetic Analyses
Start Date: Sept. 1, 2010
Expires: Aug. 31, 2011
Awarded Amount to Date: $128,853
Principal Investigator: Tiffani Williams
Sponsor: Texas Engineering Experiment Station

Funds the development of a suite of convergence detection algorithms that are based on the topological structures of underlying phylogenetic trees for large-scale Markov Chain Monte Carlo phylogenetic analyses. In addition, the investigators will identify the causes of non-convergence in phylogenetic analysis, performing real-time convergence analysis, and develop data visualization tools.


Collaborative Research: Developing Genomic Tools for Integrative Biology Research
Start Date: Sept 1., 2010
Expires: Aug. 31, 2012
This grant was awarded to two investigative teams:
• $100,000, Keith Crandall, Brigham Young University
• $200,000, Todd Oakley, University of California, Santa Barbara

Supports a project that will use high-throughput sequencing technologies to explore the genetic components of eyes and vision in multiple species of invertebrate animals. The new genetic data will be made available in public databases.


Enhancing Genomic Exploration through Reality-Based Interaction
Start Date: Sept. 1, 2010
Expires: Aug. 31, 2013
Awarded Amount to Date: $268,712
Principal Investigator: Orit Shaer
Sponsor: Wellesley College

Funds research that aims to design, develop, and evaluate the benefits of a tabletop reality-based interface for exploring diverse types of genomic information.


New Tools for Characterizing Protein Dynamics
Start Date: Sept. 1, 2010
Expires: Aug. 31, 2011
Awarded Amount to Date: $207,038
Principal Investigator: Shawn Newsam
Sponsor: University of California, Merced

The grant will fund the development of tools and methods that will be used to investigate protein dynamics. The tools will be used to "determine to what extent denatured or intrinsically disordered proteins behave as random polymers or have motions constrained to lower dimensional dynamics," "elucidate whether there are differences between the dynamics of intrinsically disordered proteins and natively folded proteins in the early stages of folding," and "determine the efficiency of different molecular simulations in sampling the denatured or disordered states of proteins" according to the grant abstract.

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.