78 citations · 231 across the 10 of their papers we have counts for
6 papers · 1 filter
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
Anthony Szedlak, Spencer Sims, Nicholas Smith +2
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmace…
Evolutionary and topological properties of gene modules and driver mutations in a leukemia gene regulatory network
Anthony Szedlak, Nicholas Smith, Li Liu +2
The diverse, specialized genes in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is co…
A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia
Edison Ong, Anthony Szedlak, Yunyi Kang +9
A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particula…
Control of asymmetric Hopfield networks and application to cancer attractors
Anthony Szedlak, Giovanni Paternostro, Carlo Piermarocchi
The asymmetric Hopfield model is used to simulate signaling dynamics in gene/transcription factor networks. The model allows for a direct mapping of a gene expression pattern into…
Biological control networks suggest the use of biomimetic sets for combinatorial therapies
Jacob D. Feala, Jorge Cortes, Phillip M. Duxbury +3
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly unde…
Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue
Laurence Coquin, Jacob D. Feala, Andrew D. McCulloch +1
The fruit fly D. melanogaster is increasingly used as a model organism for studying acute hypoxia tolerance and for studying aging, but the interactions between these two factors a…