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DNA-binding proteins are vital for the study of cellular processes. In recent genome engineering studies, the identification of proteins with certain functions has become increasingly important and needs to be performed rapidly and efficiently. In previous years, several approaches have been developed to improve the identification of DNA-binding proteins.(More)
In this paper we continue previous studies on the computational efficiency of spiking neural P systems, under the assumption that some pre-computed resources of exponential size are given in advance. Specifically, we give a deterministic solution for each of two well known PSPACE-complete problems: QSAT and Q3SAT. In the case of QSAT, the answer to any(More)
Spiking neural P systems are a class of distributed parallel computing models inspired from the way the neurons communicate with each other by means of electrical impulses (called " spikes "). In this paper, we consider a restricted variant of spiking neural P systems, called homogeneous spiking neural P systems, where each neuron has the same set of rules.(More)
Spiking neural P systems are a class of distributed parallel computing models inspired from the way neurons communicate with each other by means of electrical impulses, where there is a synapse between each pair of connected neurons. However, in a biological system, there can be several synapses for each pair of connected neurons. In this study, inspired by(More)
In this paper, we consider the two-dimensional variable-sized bin packing problem (2DVSBPP) with guillotine constraint. 2DVSBPP is a well-known NP-hard optimization problem which has several real applications. A mixed bin packing algorithm (MixPacking) which combines a heuristic packing algorithm with the Best Fit algorithm is proposed to solve the single(More)
Looking for small universal computing devices is a natural and well investigated topic in computer science. Recently, this topic was also investigated in the framework of spiking neural P systems. One of small universality results is that a small weakly universal extended spiking neural P system with 12 neurons was constructed. In this paper, a new way is(More)
MicroRNAs (miRNA) play critical roles in regulating gene expressions at the posttranscriptional levels. The prediction of disease-related miRNA is vital to the further investigation of miRNA's involvement in the pathogenesis of disease. In previous years, biological experimentation is the main method used to identify whether miRNA was associated with a(More)
Various microRNAs have been demonstrated to play roles in a number of human diseases. Several microRNA-disease network reconstruction methods have been used to describe the association from a systems biology perspective. The key problem for the network is the similarity computation model. In this article, we reviewed the main similarity computation methods(More)
Different biological processes take different times to be completed, which can also be influenced by many environmental factors. In this work, a realistic definition of nonsynchronized spiking neural P systems (SN P systems, for short) is considered: during the work of an SN P system, the execution times of spiking rules cannot be known exactly (i.e., they(More)
Spiking neural P systems are a class of distributed parallel computing devices inspired from the way neurons communicate by means of spikes. In this paper, the problem of looking for small universal computing devices is investigated in the framework of spiking neural P systems. A new approach is introduced to simulate register machines by spiking neural P(More)