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» On Timed Models of Gene Networks
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CSB
2005
IEEE
130views Bioinformatics» more  CSB 2005»
14 years 1 months ago
iSimBioSys: An "In Silico" Discrete Event Simulation Framework for Modeling Biological Systems
The genome projects have provided comprehensive information about the basic building blocks of life. The next challenge is to understand how biological functions emerge from compl...
Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal K. ...
COCOON
2006
Springer
13 years 11 months ago
Reconciling Gene Trees with Apparent Polytomies
We consider the problem of reconciling gene trees with a species tree based on the widely accepted Gene Duplication model from Goodman et al. Current algorithms that solve this pro...
Wen-Chieh Chang 0002, Oliver Eulenstein
BIRD
2007
Springer
14 years 2 months ago
Analysing Periodic Phenomena by Circular PCA
Experimental time courses often reveal a nonlinear behaviour. Analysing these nonlinearities is even more challenging when the observed phenomenon is cyclic or oscillatory. This me...
Matthias Scholz
BMCBI
2007
130views more  BMCBI 2007»
13 years 8 months ago
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression da
Background: Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, th...
Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra,...
BMCBI
2010
172views more  BMCBI 2010»
13 years 2 months ago
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Background: The correlation between the expression levels of transcription factors and their target genes can be used to infer interactions within animal regulatory networks, but ...
Anil Aswani, Soile V. E. Keränen, James Brown...