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» Mining protein networks for synthetic genetic interactions
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ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
14 years 2 months ago
Anton, a special-purpose machine for molecular dynamics simulation
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
FM
2009
Springer
138views Formal Methods» more  FM 2009»
14 years 3 months ago
What Can Formal Methods Bring to Systems Biology?
This position paper argues that the operational modelling approaches from the formal methods community can be applied fruitfully within the systems biology domain. The results can ...
Nicola Bonzanni, K. Anton Feenstra, Wan Fokkink, E...
NAR
2006
177views more  NAR 2006»
13 years 8 months ago
PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways
The PUMA2 system (available at http://compbio.mcs. 10 anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and met...
Natalia Maltsev, Elizabeth M. Glass, Dinanath Sula...
BMCBI
2010
126views more  BMCBI 2010»
13 years 6 months ago
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling
Background: Colon cancer is driven by mutations in a number of genes, the most notorious of which is Apc. Though much of Apc's signaling has been mechanistically identified o...
Gürkan Bebek, Vishal Patel, Mark R. Chance
BMCBI
2005
120views more  BMCBI 2005»
13 years 8 months ago
SpectralNET - an application for spectral graph analysis and visualization
Background: Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks ...
Joshua J. Forman, Paul A. Clemons, Stuart L. Schre...