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» Modeling and Verifying Workflow-based Regulations
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BMCBI
2011
13 years 4 days ago
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities
Background: Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes. Un...
Yao Fu, Laura R. Jarboe, Julie A. Dickerson
IFM
2010
Springer
142views Formal Methods» more  IFM 2010»
13 years 7 months ago
An Event-B Approach to Data Sharing Agreements
A Data Sharing Agreement (DSA) is a contract among two or more principals regulating how they share data. Agreements are usually represented as a set of clauses expressed using the...
Alvaro E. Arenas, Benjamin Aziz, Juan Bicarregui, ...
RECOMB
2003
Springer
14 years 8 months ago
Physical network models and multi-source data integration
We develop a new framework for inferring models of transcriptional regulation. The models in this approach, which we call physical models, are constructed on the basis of verifiab...
Chen-Hsiang Yeang, Tommi Jaakkola
BMCBI
2004
323views more  BMCBI 2004»
13 years 8 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
BMCBI
2005
126views more  BMCBI 2005»
13 years 8 months ago
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
Background: The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some ...
Maria Persico, Arnaud Ceol, Caius Gavrila, Robert ...