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Interdisciplinary problem solving in computational biology requires a fundamental understanding of complex biological adaptive systems, from cellular to molecular level in order to tackle challenging problems such as neurodegenerative diseases. In this work we present a description and an initial evaluation of a Spiking Neural Network-Genetic Algorithm (SNN-GA) system we are developing for the computational...
Extracting motifs in the sea of DNA sequences is an intricate task but have great significance. We propose an alternative solution integrating bacterial foraging optimization (BFO) algorithm and Tabu search (TS) algorithm namely TS-BFO. We modify the original BFO via established a self-control multi-length chemotactic step mechanism, and introduce Rao metric. The experiments on real data set extracted...
A fuzzy logic approach, called FuzzyTRN, to infer transcriptional regulatory networks (TRN) in Saccharomycescerevisiae is proposed. FuzzyTRN predicts potential regulators and their target genes using sequences analysis on transcription factor binding sites (TFBS) of transcriptional factors (TF) and promoter region of target genes. Those potential regulators and target genes are used to form vertices...
For the motif discovery problem of DNA sequences, a greedy two-stage Gibbs sampling algorithm is presented, and the related software package is called Greedy MotifSAM. Based on position weight matrix (PWM) motif model, a greedy strategy for choosing the initial parameters of PWM is employed. Two sampling methods, site sampler and motif sampler, are used. Site sampler is used to find one occurrence...
This paper presents a novel motif discovery algorithm based on multi-objective genetic algorithms to extract non-dominated motifs in DNA sequences. The main advantage of our approach is that a large number of tradeoff (non-dominated) motifs can be obtained by a single run with respect to conflicting objectives: similarity, motif length and support maximization. In this paper, the method extracts non-dominated...
The serpinB9 protein, known as proteinase inhibitor 9 (PI-9) in human, can potently inhibit the proteinase, granzyme B, which is the major granzyme immune system cells use to kill intracellular pathogen infected or neoplastic cells. Over-expression of PI-9 in tumor cells is considered as a mechanism for tumor evasion against immunosurveillance carried out by cytotoxic T lymphocytes (CTL) and natural...
This paper describes a novel approach to constructing position-specific weight matrices (PWM) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database, and the comparison of the thus generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were...
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