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Article
Effects of Triclosan on the Development of Antimicrobial Resistance in the Environment: A Review
Triclosan (TCS), a widely used broad-spectrum antimicrobial agent, enters to wastewater treatment plants (WWTPs) and the environment ultimately after its usage. Notably, the use of TCS has surged during the ou...
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Article
Sorting a Permutation by Best Short Swaps
A permutation is happy, if it can be transformed into the identity permutation using as many short swaps as one third times the number of inversions in the permutation. The complexity of the decision version of s...
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Article
Open AccessDTA-SiST: de novo transcriptome assembly by using simplified suffix trees
Alternative splicing allows the pre-mRNAs of a gene to be spliced into various mRNAs, which greatly increases the diversity of proteins. High-throughput sequencing of mRNAs has revolutionized our ability for t...
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Chapter and Conference Paper
An Approximation Algorithm for Sorting by Bounded Singleton Moves
Sorting permutations by block moves is a fundamental combinatorial problem in genome rearrangements. The classic block move operation is called transposition, which switches two consecutive blocks, or equivale...
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Chapter and Conference Paper
DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees
In this article, we develop a novel radical framework for de novo transcriptome assembly based on suffix trees, called DTAST. DTAST extends contigs by reads that have the longest overlaps with the contigs’ termin...
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Chapter and Conference Paper
PASA: Identifying More Credible Structural Variants of Hedou12
In this paper, we devote to find structural variants including deletions, insertions, and inversions which occur in Hedou12 genome in constrast to Williams82 genome. To find as many as possible potential stru...
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Chapter and Conference Paper
IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads
High-throughput sequencing of mRNA has made the deep and efficient probing of transcriptomes more affordable. However, the vast amounts of short RNA-seq reads make de novo transcriptome assembly an algorithmic...
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Chapter and Conference Paper
Improved Approximation Algorithm for the Maximum Base Pair Stackings Problem in RNA Secondary Structures Prediction
We investigate the maximum base pair stackings problem from RNA Secondary Structures prediction in this paper. Previously, Ieong et al. defined a basic version of this maximum base pair stackings problem as: give...
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Chapter and Conference Paper
A Polynomial Time Algorithm for Finding a Spanning Tree with Maximum Number of Internal Vertices on Interval Graphs
This paper studies the Maximum Internal Spanning Tree problem which is to find a spanning tree with the maximum number of internal vertices on a graph. We prove that the problem can be solved in polynomial tim...
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Chapter and Conference Paper
An 5/4-Approximation Algorithm for Sorting Permutations by Short Block Moves
Sorting permutations by short block moves is an interesting combinatorial problem derived from genome rearrangements. A short block move is an operation on a permutation that moves an element at most two posit...
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Chapter and Conference Paper
Prediction of Protein Subcellular Locations by Combining K-Local Hyperplane Distance Nearest Neighbor
A huge number of protein sequences have been generated and collected. However, the functions of most of them are still unknown. Protein subcellular localization is important to elucidate protein function. It w...
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Article
A PTAS for Semiconductor Burn-in Scheduling
In this paper a polynomial time approximation scheme, PTAS for short, is presented for the problem of scheduling jobs in a batch processing system. Each job has a pre-defined release date, which indicates when...
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Chapter and Conference Paper
Unsupervised Segmentation of Chinese Corpus Using Accessor Variety
The lack of word delimiters such as spaces in Chinese texts makes word segmentation a special issue in Chinese text processing. As the volume of Chinese texts grows rapidly on the Internet, the number of unkno...
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Article
Minimizing Mean Completion Time in a Batch Processing System
We consider batch processing jobs to minimize the mean completion time. A batch processing machine can handle up to $B$ jobs simultaneously. Each job is represented by an arrival time and a processing time. J...
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Chapter and Conference Paper
Text Distinguishers Used in an Interactive Meta Search Engine
With the explosion of the Internet, search engines are more and more popular. Up to now, most of the search engines will provide the same results to the different users on the same query. However, users may ha...
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Chapter and Conference Paper
A PTAS for Minimizing Total Completion Time of Bounded Batch Scheduling
We consider a batch processing system {p i: i = 1, 2,..., n} where p i is the processing time of job i, and up to B jobs can be processed together such that the handling time of a batc...
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Chapter and Conference Paper
(g, f)-Factorizations Orthogonal to k Subgraphs
We establish two results for (g, f)-factorizations:
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every (mg + m − 1, mf − m + 1 )—graph with 9k/4 ≤ g ≤ f has a (g, f)—factorization...
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Chapter and Conference Paper
A Polynomial Time Approximation Scheme for Minimizing Total Completion Time of Unbounded Batch Scheduling
We study the unbounded batch machine scheduling of n jobs to minimize the total completion time.A batch machine can handle up to B ≥ n jobs simultaneously.Eac h job is characterized by a release(arrival) time and...
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Chapter and Conference Paper
Some Results on Orthogonal Factorizations
Consider a graph G = (V,E) with an [a, b]-factorization F = F 1, F 2,..., F m.It is proved in this paper that:
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