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Funding Update: Aug 26, 2011

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NSF Bioinformatics Grants Awarded July 27 — August 24, 2011

Characterization, Modeling, Prediction, and Visualization of the Plant Transcriptome
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $1,499,996
Principal Investigators: Volker Brendel, Shailesh Lal, Karin Dorman, Shannon Schlueter
Sponsor: Iowa State University

Supports the development of algorithms that can predict the expressed protein-coding gene transcriptome from plant genome sequences. The investigators aim to develop software that implements these transcriptome prediction algorithms; create visualization and data access portals; and develop infrastructure for distributing these tools to the community.


Dimension Reduction, Model Selection and Classification in Functional Data Analysis
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2013
Awarded Amount to Date: $119,999
Principal Investigator: Yehua Li
Sponsor: University of Georgia Research Foundation

Using the data from colon cancer experiments, hypertension studies and other sources, the investigator will use the funds to develop computationally efficient dimension reduction methods for functional data based on spline approximations, and will use asymptotic theory to develop new statistical devices for model selection and inference.


Determining Feasibility and Scalability of a Life/Medical Science Hybrid-Core Based Platform
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $1,309,316
Principal Investigator: Harold Garner, Peter Athanas, Liqing Zhang, Kristy Collins
Sponsor: Virginia Polytechnic Institute and State University

The funds will be used to create an extensible field programmable gate array-based cluster that will expand the existing infrastructure at the institute and deploy a data storage system to address the needs that are typical of life/medical science applications. Specifically, the investigators will "optimize and evaluate the effectiveness of a hybrid-core based cluster relative to standard microprocessors and general purpose graphics processing units" for life and medical science applications; create a secure web-based portal through which users can analyze their data; and share their knowledge and experience via a training and internship program.


A Model Based System for the Automated Design of Synthetic Genetic Circuits by Mathematical Optimization
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2013
This grant is awarded to two investigative teams:
Ilias Tagkopoulos, Matthias Koeppe, University of California, Davis, $271,100
John Kececioglu, University of Arizona, $28,902

These funds will support the development of an optimization tool prototype that encompasses multiple biological models relevant to synthetic genetic circuit design — a collection of one or more genes and elements such as promoters, ribosome binding sites and so on that influence gene expression. The investigators aim to develop a hybrid optimization-simulation technique that captures additional effects related to cell division, noise, and evolutionary processes, and to that end they will focus on applying techniques from combinatorial optimization to find the optimal circuit for a specific task.


Developing a Multivariate Theory of Phenotypic Coevolution
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $246,717
Principal Investigator: Scott Nuismer
Sponsor: University of Idaho

The investigators aims to develop new mathematical tools that will make it possible to formulate a general theory of multivariate coevolution. The abstract notes these models will make it possible to analyze interactions involving multiple traits through which species adapt to each other.


Models for (Meta)Genome Identification from Next Generation Sequence Data with Errors
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2012
Awarded Amount to Date: $228,627
Principal Investigator: Karin Dorman, Srinivas Aluru, Aditya Ramamoorthy, Bradley Blitvich
Sponsor: Iowa State University

The funds will support the development of mathematically and statistically rigorous models and algorithms to interpret, assemble, and analyze sequence data for detecting bio-threats. Specifically, the investigators will develop hidden Markov models for sequencers and algorithms for parameter estimation; develop error correction schemes for the reads; develop methods for identifying bio-threats within a sample mixture via metagenomic analysis; and develop methods for identifying genomic variations in a bio-threat organism with respect to a reference genome.


Building and Sharing Molecular Visualizations with Molecular ViewBook
Start Date: Aug.15, 2011
Expires: July 31, 2012
Awarded Amount to Date: $510,773
Principal Investigator: Janet Iwasa, Piotr Sliz, Gael McGill
Sponsor: Harvard University

This award will support the development of software tools that researchers can use to create and share visual models of molecular processes. The project comprises two components: the first is a suite of free software tools called the 3D Molecular Toolkit that will help users create molecular animations. The second component is an online Molecular ViewBook through which users can share animations and animation source codes with others.


Statistical Modeling of Short-Read Counts in RNA-Seq
Start Date: Aug.15, 2011
Expires: July 31, 2012
This grant is awarded to three investigative teams:
Tingting Zhang, University of Virginia, $17,322
Jun Liu, Harvard University, $84,838
Wenxuan Zhong, University of Illinois, Urbana-Champaign, $92,380

With these funds, the investigators will model RNA-Seq data using sufficient dimension reduction models, a class of flexible nonlinear models. They aim to develop a software suite that can estimate gene expression levels from the data and identify marker genes that react to specific pathogens. The resulting tools will be used to detect bio-threats.


Exploring the Niche Space of Human Microbiome Functions Through Convex Geometry and Evolutionary Genomics
Start Date: Aug.15, 2011
Expires: July 31, 2013
Awarded Amount to Date: $734,964
Principal Investigator: Katherine Pollard
Sponsor: The Gladstone Institutes

Supports the development of a methodology for analyzing shotgun metagenomic data. The investigators plan to design a bioinformatics pipeline that uses hidden Markov models to describe the evolutionary profile of known microbial proteins in order to classify metagenomic sequences into protein families. They will also develop stochastic models that can predict the occurrence of protein families in a metagenomic sample. Finally, they plan to produce a medical Niche Atlas that links protein distributions to disease states.


Statistical Ensembles for the Identification of Bacterial Genomes
Start Date: Aug.15, 2011
Expires: July 31, 2012
This grant is awarded to two investigative teams:
Jennifer Clarke, Bertrand Clarke, University of Miami, $232,811
Adrian Dobra, University of Washington, $112,460

Will support the development of statistical theories and computational tools for detecting pathogens based on next-generation sequence data as part of efforts to reduce bioterrorism threats. Among other objectives, the investigators aim to perform comparisons of empirical clusterings and reference genomes as well as "shrinkage estimation and model selection in hierarchical log-linear models." The method is expected to help users identify differences in microbial genomes and classify them as harmless or potentially pathogenic.


Computational Identification of Gene Regulatory Networks in Microalgae
Start Date: Aug.15, 2011
Expires: July 31, 2013
Awarded Amount to Date: $174,654
Principal Investigator: Haiyan Hu
Sponsor: University of Central Florida

The funds will support the development of a computational framework to study gene regulation in the microalgal model organism Chlamydomonas reinhardtii and to integrate this information into in silico modeling and bioengineering applications for the organism.


Novel Methodologies for Genome-Scale Evolutionary Analysis of Multi-Locus Data
Start Date: July 1, 2011
Expires: June 30, 2014
Awarded Amount to Date: $467, 429
Principal Investigator: Noah Rosenberg
Sponsor: Stanford University

Supports the development of algorithms and software for analyzing gene genealogies and inferring species' phylogenies. Specifically, the investigators will develop 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.


The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.