Nice SBGN Maps

Process Description map of a simple gene network

Simple two-gene system that can display different behaviours, such as monostability and bistability or oscillations, depending on the parameter values. See "Le Novère N. Quantitative and logic modelling of gene and molecular networks. Nature Reviews Genetics (2015) 16: 146–158" doi:10.1038/nrg3885
 

Process Description map of amyloid-beta, amyloid protein and alpha-synuclein aggregation

Mechanistic description of aggregation and APP breakdown in ND: Potential future direction. The formation of protein aggregation is represented in three stages, native proteins→misfolded proteins→aggregated proteins for Alzheimer's Disease, Neurodegenerative Diseases in general, and Parkinson's Disease. See "Lloret i Villas A., Varusai T. M., Juty N., Laibe C., Le Novère N., Hermjakob H., Chelliah, V. The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions CPT: Pharmacometrics & Systems Pharmacology (2016), 6:73–86"  doi:10.1002/psp4.12155

Activity Flow map of Amyloid Protein Precursor's processing

The transmembrane protein APP can be processed through four different routes: 1) it may remain at the cell surface; 2) be internalized and recycled or degraded; 3) cleaved via the nonamyloidogenic α-pathway; 4) or cleaved via the amyloidogenic β-pathway. Modeled events are colored in green. The components that are colored red illustrate the gap between the experimental knowledge and the mechanistic understanding. See "Lloret i Villas A., Varusai T. M., Juty N., Laibe C., Le Novère N., Hermjakob H., Chelliah, V. The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions. CPT: Pharmacometrics & Systems Pharmacology (2016), 6:73–86"  doi:10.1002/psp4.12155

Regulation of Calcium/Calmodulin Kinase II by Calmodulin

For clarity, only one monomeric subunit is shown. In the actual model, six such subunits form a ring, and autophosphorylation at Thr286 of one subunit is dependent on the neighbouring subunit being open. See "Stefan M.I., Marshall D.P., Le Novère N. Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PLoS ONE (2012), 7(1): e29406" doi:10.1371/journal.pone.0029406

Interactions between EGFR, AR, ER, Ki67, INFa, Il-1, Il-6, VEGF, MMP9, alcohol consumption and smoking in tumour microenvironment of OSCC.

See "Boras V., Fusic A., Virag M., Gabric D., Blivajs I., Tomasovic-Longaric C., Rakusic Z., Bisof V., Le Novère N., Vrdoljak D.V. Significance of stroma in biology of oral squamous cell carcinoma. Tumori (2017) Adv publ" doi:10.5301/tj.5000673