On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network. - Wilfred Ndifon; Joshua B. Plotkin; Jonathan Dushoff (PLoS Comput. Biol., 2009)

Finding Attractors on a Folding Energy Landscape. - Wilfred Ndifon; Jonathan Dushoff (Handbook of Research on Computational and Systems Biology, 2011)

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. - Niclas Thomas; James M. Heather; Wilfred Ndifon; John Shawe-Taylor; Benjamin Chain (Bioinform., 2013)