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Theoretical biology encompasses a broad range of biological disciplines ranging from mathematical biology and biomathematics to philosophy of biology. Adopting a broad definition of "biology", Theoretical Biology and Medical Modelling, an open access journal, considers original research studies that focus on theoretical ideas and models associated with(More)
Next-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing. We describe a massively parallel interactome-mapping pipeline, Stitch-seq, that combines PCR stitching with next-generation sequencing and(More)
— We describe several techniques for using bulk matter for special purpose computation. In each case it is necessary to use an evolutionary algorithm to program the substrate on which the computation is to take place. In addition, the computation comes about as a result of nearest neighbour interactions at the nano-micro-and meso-scale. In our first example(More)
Experimental results from adaptive learning using an optically controlled neural network are presented. The authors have used example problems in nonlinear system identification and signal prediction, two areas of potential neural network application, to study the capabilities of analog neural hardware. These experiments investigated the effects of a(More)
B iological systems are increasingly viewed and analyzed as highly complex networks of interlinked macromolecules and metabolites. Network analysis has been applied to in-teractome maps of protein–protein, protein–DNA, and protein–RNA interactions as well as transcriptional, metabolic, and genetic data. Such network views of biological systems should(More)
We are proposing an innovative approach to neural computation with applications to adaptive robots. This approach will enable robots to have complex responses to unfamiliar situations without the need for either a computationally intensive central processor or preprogrammed prior anticipation of all possible situations. Conventional robots achieve adaptive(More)
We u s e e v olutionary search to nd automatically electronic circuits that toggle an output line at, or close to, a given target frequency. Reconngurable hardware in the form of eld-programmable gate arrays|as opposed to circuit simulation|computes the tness of a circuit which guides the evolutionary search. We nd empirically that oscillating circuits can(More)
We describe experimental results to demonstrate the wide-ranging computational ability of quasiperiodic oscillators built from rings of differentiating Schmitt triggers. We describe a theoretical model based on necklace functions to compute the number of states supportable by a ring circuit of a given size. Experimental results are presented to demonstrate(More)
Tumor dormancy is a highly prevalent stage in cancer progression. We have previously generated and characterized in vivo experimental models of human tumor dormancy in which micro-tumors remain occult until they spontaneously shift into rapid tumor growth. We showed that the dormant micro-tumors undergo a stable microRNA (miRNA) switch during their(More)