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Maximum Test for a Sequence of Quadratic form Statistics about Score Test in Logistic Regression Model
This article proposes the maximum test for a sequence of quadratic form statistics about score test in logistic regression model which can be applied...
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Biomolecular Topology: Modelling and Analysis
With the great advancement of experimental tools, a tremendous amount of biomolecular data has been generated and accumulated in various databases....
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Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System
In modeling DNA chains, the number of alternations between Adenine–Thymine (AT) and Guanine–Cytosine (GC) base pairs can be considered as a measure...
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An Efficient Algorithm to Identify DNA Motifs
We consider the problem of identifying motifs that abstracts the task of finding short conserved sites in genomic DNA. The planted ( l , d )-motif...
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A study of biases of DNA copy number estimation based on PICR model
Affymetrix single-nucleotide polymorphism (SNP) arrays have been widely used for SNP genotype calling and copy number variation (CNV) studies, both...
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And I say to myself: “What a fractional world!”
This paper discusses several complex systems in the perspective of fractional dynamics. For prototype systems are considered the cases of...
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A fast algorithm for the partial digest problem
A fundamental problem in computational biology is the restriction site map**. When a particular restriction enzyme is added to a DNA, the DNA...
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Transition probabilities for general birth–death processes with applications in ecology, genetics, and evolution
A birth–death process is a continuous-time Markov chain that counts the number of particles in a system over time. In the general process with n ...
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Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure
The analysis of RNA structures is an important problem in computational biology. In this chapter we review various algorithms to predict and compare...
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Griffiths–Pakes branching process as a model for evolution of Alu elements
Alu elements occupy about eleven percent of the human genome and are still growing in copy numbers. Since Alu elements substantially impact the shape...
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Evolution of the ancestral recombination graph along the genome in case of selective sweep
We consider the genome of a sample of n individuals taken at the end of a selective sweep, which is the fixation of an advantageous allele in the...
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Phenotype spaces
The topological viewpoint on spaces of phenotypes presented in Stadler et al. (J Theor Biol 213:241–274, 2001) is revisited, and a quantified version...
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Construction of Constant GC-Content DNA Codes via a Variable Neighbourhood Search Algorithm
DNA codes are sets of words of fixed length n over the alphabet { A , C , G , T } which satisfy a number of combinatorial conditions. They have application...
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Counting labeled transitions in continuous-time Markov models of evolution
Counting processes that keep track of labeled changes to discrete evolutionary traits play critical roles in evolutionary hypothesis testing. If we...
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Multiple pattern matching: a Markov chain approach
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these...
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Reconstructing Words from Subwords in Linear Time
Almost 30 years ago, M. Schützenberger and L. Simon established that two n -words with letters drawn from a finite alphabet having identical sets of...
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Fibonacci-Cayley Numbers and Repetition Patterns in Genomic DNA
Let F(k) denote the k -th Fibonacci number in the Fibonacci sequence F(0) := 0, F(1) := 1,..., F( k +1) := F( k -1)+F( k ). Motivated by proposals...
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Symbolic analysis of finite words: the complexity function
We present several properties of the complexity function of finite words, the function counting the number of different factors in a word, for each...
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Minimal entropy probability paths between genome families
We develop a metric for probability distributions with applications to biological sequence analysis. Our distance metric is obtained by minimizing a...
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Permanence in Nonautonomous Predator-prey Lotka-Voterra Systems
In this paper some easily verifiable sufficient conditions on the permanence of solutions for general nonautonomous two-species predator-prey model...