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Funding Update: NSF Bioinformatics Grants Awarded Oct. 19 — Dec. 21. 2011

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Exact and Approximate Algorithms for 3D Structure Modeling of Protein-Protein Interactions
Start Date: July 1, 2012
Expires: June 30, 2017
Awarded Amount to Date: $95,431
Principal Investigator: Jinbo Xu
Sponsor: Toyota Technological Institute at Chicago

Supports research efforts focused on creating algorithms for 3D structure modeling of protein-protein interactions that will be used to enrich large-scale PPI networks as well as to verify experimental PPIs and predict novel ones. The abstract states that the investigator will use a number of techniques, including graph minor theory, probabilistic graphical models, dual relaxation, and decomposition, to "understand the mathematical structure of the problem" and design efficient algorithms.


Models and Algorithms for Comparative Analysis of Biological Networks
Start Date: Feb. 1, 2012
Expires: Jan. 31, 2017
Awarded Amount to Date: $69,640
Principal Investigator: Byung-Jun Yoon
Sponsor: Texas Engineering Experiment Station

This award supports the development of a mathematical framework and methods for comparative analysis of genome-scale biological networks that could be used to identify novel pathways as well as explore their functions and mechanisms. According to the abstract, the investigator will develop a multi-state semi-Markov random walk model for probabilistic comparison of large-scale networks as well as algorithms for querying and aligning them.


Building a Comprehensive Catalog of Conserved Alternative Splicing Events from Heterogeneous Data
Start Date: Aug. 1, 2011
Expires: July 31, 2014
Awarded Amount to Date: $574,124
Principal Investigator: Liliana Florea
Sponsor: Johns Hopkins University

Supports efforts to build catalogs of conserved alternative splicing events from heterogeneous sequence data. The investigator intends to produce novel software tools that can align various types of sequence data to a target genome as well as construct models of genes and their splice variants and map them between species.


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The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.