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Systems Biology

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Conceptual Challenges in the Theoretical Foundations of Systems Biology.

Methods in molecular biology (Clifton, N.J.)
In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, w...

Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model.

IEEE/ACM transactions on computational biology and bioinformatics
This study considers the problem of describing and predicting cleft formation during the early stages of branching morphogenesis in mouse submandibular salivary glands (SMG) under the influence of varied concentrations of epidermal growth factors (EG...

Classifying pairs with trees for supervised biological network inference.

Molecular bioSystems
Networks are ubiquitous in biology, and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measureme...

Optimizing artificial neural network models for metabolomics and systems biology: an example using HPLC retention index data.

Bioanalysis
BACKGROUND: Artificial Neural Networks (ANN) are extensively used to model 'omics' data. Different modeling methodologies and combinations of adjustable parameters influence model performance and complicate model optimization.