Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer.

For breast cancer, clinically important subtypes are well characterized at the molecular level in terms of gene expression profiles. In addition, signaling pathways in breast cancer have been extensively studied as therapeutic targets due to their roles in tumor growth and metastasis. However, it is challenging to put signaling pathways and gene expression profiles together to characterize biological mechanisms of breast cancer subtypes since many signaling events result from post-translational modifications, rather than gene expression differences.

Soft Set Theory for Decision Making in Computational Biology under Incomplete Information.

The study of biological systems is complex and of great importance. There exist numerous approaches to signal transduction processes, including symbolic modeling of cellular adaptation. The use of formal methods for computational systems biology eases the analysis of cellular models and the establishment of the causes and consequences of certain cellular situations associated to diseases.

Analysis of survival for lung cancer resections cases with fuzzy and soft set theory in surgical decision making.

Objective: Lung cancer is the most common type of cancer around the world, and it represents the main cause of death in the USA. Surgical treatment is the optimal therapeutic strategy for resectable non-small cell lung cancer. The principal factor for long-term survival after complete resection is the anatomic extension of the neoplasm.

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search.

In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation.