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» Definable encodings in the computably enumerable sets
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BMCBI
2010
149views more  BMCBI 2010»
13 years 6 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
BMCBI
2008
145views more  BMCBI 2008»
13 years 6 months ago
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Background: Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are ...
Jonathan R. Manning, Emily R. Jefferson, Geoffrey ...
GECCO
2010
Springer
191views Optimization» more  GECCO 2010»
13 years 10 months ago
Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of sma
Recent advances in genotyping technology have led to the generation of an enormous quantity of genetic data. Traditional methods of statistical analysis have proved insufficient i...
Emily Rose Holzinger, Carrie C. Buchanan, Scott M....
VIS
2006
IEEE
157views Visualization» more  VIS 2006»
14 years 7 months ago
Analyzing Complex FTMS Simulations: a Case Study in High-Level Visualization of Ion Motions
Current practice in particle visualization renders particle position data directly onto the screen as points or glyphs. Using a camera placed at a fixed position, particle motions...
Wojciech Burakiewicz, Robert van Liere
BMCBI
2004
131views more  BMCBI 2004»
13 years 5 months ago
A web services choreography scenario for interoperating bioinformatics applications
Background: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applic...
Remko de Knikker, Youjun Guo, Jin-long Li, Albert ...