J. K. Wickiser Lab

Posts Tagged ‘Network Science’

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Enzymatic networks

Monday, October 17, 2011

This group analyzes enzyme networks for robustness and dynamics.

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A network analysis approach to prediabetes

Friday, October 14, 2011

The molecular, cellular, and evironemental factors of diabetes makes for a complex problem that this group attacks using a network analysis approach.

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The essential genome of a bacterium: wants versus needs.

Tuesday, October 11, 2011

Lucy Shaprio and colleagues have identifed the minimal set of genes required for caulobacter to thrive on rich media. This work will help others bioengineer the organism to function in a variety of roles involving the production of small molecule metabolites and the generation of biosensor systems.

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Microbial Bioinfomatics tools

Friday, October 7, 2011

Cool tools for microbial bioinformatics from Berkeley Lab.

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Network Science – making even Slime Molds sexy

Thursday, October 6, 2011

Slime molds don’t sound very exciting but researchers are using them to optimize networks ranging from highway systems to disasters emergency response procedures. In this recent NYT Science Times piece, the research of several prominent labs is showcased.

In short, these organisms live as individual soil-dwelling cells and are content to survive on their basic food source: bacteria. But when food becomes scarce, these individuals send a chemical signal out to each other and a major change in physiology and strategy takes place. Some cells will sacrifice themselves for the great good of the group by filling themselves up with a carbohydrate that stiffens them (causing death). These cells serve as a scaffold support so that other cells can use this stalk as a structure to form spores, or cellular life rafts, that are capable of weathering the starvation conditions. Only when food becomes plentiful do the spores change back into individual cells to form a new colony.

The Bionetworks group in the Network Science Center is currently studying the modes of communication between cells as they respond not only to starvation conditions, but chemical contaminants of military interest as well.

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Krebs Cycle Funnery

Tuesday, September 20, 2011

Here’s an interesting take on the Krebs Cycle, and more importantly, learning the Krebs Cycle.

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Distributed Computing and Structural Biology

Monday, September 19, 2011

X-box science in action.

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TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.

Thursday, September 15, 2011

The timecourse data sets are huge in systems biology. This paper details efforts to generate gene networks using microarray data. Time-course data used to create a gene network

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Protein networks in a plant model

Wednesday, September 14, 2011

Here’s a paper and press release for some recent work on the protein networks in Arabadopsis.

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Rank-based edge reconstruction for scale-free genetic regulatory networks.

Tuesday, September 13, 2011

The construction of gene networks is tricky business and this group details a Rank-based edge method: Rank-based edge reconstruction

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