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The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent…
Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One…
The potential benefit of migrating software design from Structured to Object Oriented Paradigm is manifolded including modularity, manageability and extendability. This design migration should be automated as it will reduce the time…
Introducing genetic algorithms as a reliable and efficient tool to find ordered equilibrium structures, we predict minimum energy configurations of the square shoulder system for different values of corona width $\lambda$. Varying…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
Many research works have been carried out recently to find the optimal path in network routing. Among them the evolutionary algorithms is an area where work is carried out extensively. We in this paper, have used PSO for finding the optimal…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Self organizing maps (SOMs) are widely-used for unsupervised classification. For this application, they must be combined with some partitioning scheme that can identify boundaries between distinct regions in the maps they produce. We…
Surface registration is a technique that is used in various areas such as object recognition and 3D model reconstruction. Problem of surface registration can be analyzed as an optimization problem of seeking a rigid motion between two…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of…
Nowadays, optimization problem have more application in all major but they have problem in computation. Computation global point in continuous functions have high calculation and this became clearer in large space .In this paper, we…
Challenges in natural sciences can often be phrased as optimization problems. Machine learning techniques have recently been applied to solve such problems. One example in chemistry is the design of tailor-made organic materials and…
One of the problems in applying Genetic Algorithm is that there is some situation where the evolutionary process converges too fast to a solution which causes it to be trapped in local optima. To overcome this problem, a proper diversity in…