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Modeling Evolution of Crosstalk in Noisy Signal Transduction Networks
Ammar Tareen, Ned S. Wingreen, Ranjan Mukhopadhyay
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To be…
Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome
Jean-Charles Walter, Nils-Ole Walliser, Gabriel David +6
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in vario…
Hidden long evolutionary memory in a model biochemical network
Md. Zulfikar Ali, Ned S. Wingreen, Ranjan Mukhopadhyay
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in…