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Chapter and Conference Paper
Probe Selection with Fault Tolerance
Microarray techniques play an important role for testing some reactions of diseases which are caused by viruses. Probes in microarray are one kind of the most important materials. Usually, scientists use a uni...
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Article
Open AccessTranscriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome
Human eosinophil-derived neurotoxin (edn) and eosinophil cationic protein (ecp) are members of a subfamily of primate ribonuclease (rnase) genes. Although they are generated by gene duplication event, distinct ed...
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Chapter and Conference Paper
BioPortal: A Portal for Deployment of Bioinformatics Applications on Cluster and Grid Environments
Over last few years, interest on biotechnology has increased dramatically. With the completion of sequencing of the human genome, such interest is likely to expand even more rapidly. The size of genetic inform...
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Chapter and Conference Paper
3-Points Relationship Based Parallel Algorithm for Minimum Ultrametric Tree Construction
To construct an evolutionary tree is an important topic in computational biology. An evolutionary tree can symbolize the relationship and histories for a set of species. There are many models had been proposed...
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Chapter and Conference Paper
Approximation Algorithms for 2-Source Minimum Routing Cost k-Tree Problems
In this paper, we investigate some k-tree problems of graphs with given two sources. Let G = (V,E,w) be an undirected graph with nonnegative edge lengths and two sources s 1, s 2 ∈...
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Chapter and Conference Paper
On the Diversity-Performance Relationship for Majority Voting in Classifier Ensembles
Combining multiple classifier systems (MCS’) has been shown to outperform single classifier system. It has been demonstrated that improvement for ensemble performance depends on either the diversity among or t...
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Article
Open AccessA reinforced merging methodology for map** unique peptide motifs in members of protein families
Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with hig...
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Chapter and Conference Paper
An Efficient Parallel Algorithm for Ultrametric Tree Construction Based on 3PR
In the computational biology and taxonomy, to construct phylogenetic tree is an important problem. A phylogenetic tree can represent the relationship and histories for a set of species and helpful for biologis...
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Chapter and Conference Paper
Efficient Algorithms for Regular Expression Constrained Sequence Alignment
Imposing constraints is an effective means to incorporate biological knowledge into alignment procedures. As in the PROSITE database, functional sites of proteins can be effectively described as regular expres...
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Chapter and Conference Paper
The Bottleneck Tree Alignment Problems
Given a set W of k sequences (strings) and a tree structure T with k leaves, each of which is labeled with a unique sequence in W, a tree alignment is to label a sequence to each internal node of T. The weight of...
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Chapter and Conference Paper
Comparative Gene Prediction Based on Gene Structure Conservation
Identifying protein coding genes is one of most important task in newly sequenced genomes. With increasing numbers of gene annotations verified by experiments, it is feasible to identify genes in newly sequenc...
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Chapter and Conference Paper
Modeling Signal Transduction of Neural System by Hybrid Petri Net Representation
Biological neural system can be considered as a series of biochemical reactions and signal transmission. It is important to provide an intuitive representation of the neural system to biologists while kee** ...
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Chapter and Conference Paper
A Fast Technique for Constructing Evolutionary Tree with the Application of Compact Sets
Constructing an evolutionary tree has many techniques, and usually biologists use distance matrix on this activity. The evolutionary tree can assist in taxonomy for biologists to analyze the phylogeny. In this...
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Chapter and Conference Paper
Disjoint Segments with Maximum Density
Given a sequence A of numbers and two positive integers ℓ and k, we study the problem to find k disjoint segments of A, each has length at least ℓ, such that their sum of densities is maximized. We give the first...
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Chapter and Conference Paper
Approximation Algorithms for k-Source Bottleneck Routing Cost Spanning Tree Problems
In this paper, we investigate two spanning tree problems of graphs with k given sources. Let G=(V,E,w) be an undirected graph with nonnegative edge lengths and S ⊂ V a set of k specified sources. The first proble...
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Chapter and Conference Paper
On the Full and Bottleneck Full Steiner Tree Problems
Given a graph G = (V, E) with a length function on edges and a subset R of V, the full Steiner tree is defined to be a Steiner tree in G with all the vertices of R as its leaves. Then the full Steiner tree proble...
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Chapter and Conference Paper
The Full Steiner Tree Problem in Phylogeny
Motivated by the reconstruction of phylogenetic tree in biology, we study the full Steiner tree problem in this paper. Given a complete graph G = (V, E) with a length function on E and a proper subset R ⊂ V, the ...
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Chapter and Conference Paper
A New Measure of Edit Distance between Labeled Trees
One of the most important problem in computational biology is the tree editing problem which is to determine the edit distance between two rooted labeled trees. It has been shown to have significant applicatio...
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Chapter and Conference Paper
Efficient Minus and Signed Domination in Graphs
We show that the efficient minus (resp., signed) domination problem is NP-complete for chordal graphs, chordal bipartite graphs, planar bipartite graphs and planar graphs of maximum degree 4 (resp., for chorda...
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Article
Approximation and Exact Algorithms for Constructing Minimum Ultrametric Trees from Distance Matrices
An edge-weighted tree is called ultrametric if the distances from the root to all the leaves in the tree are equal. For an n by n distance matrix M, the minimum ultrametric tree for M is an ultrametric tree T ...
