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Article
Chlorophyll fluorescence lifetime imaging provides new insight into the chlorosis induced by plant virus infection
Leaf chlorosis induced by plant virus infection has a short fluorescence lifetime, which reflects damaged photosynthetic complexes and degraded chloroplasts.
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Article
Open AccessThe first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe
The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species – D. longicornis was sequenced by next-generation sequencing ...
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Article
Open AccessSkewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter...
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Article
Improving cis-regulatory elements modeling by consensus scaffolded mixture models
A position weight matrix (PWM) is widely accepted as a probabilistic representation for modeling protein-DNA binding specificity. Previous studies showed that for factors which bind to divergent binding sites,...
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Chapter and Conference Paper
Searching Maximal Degenerate Motifs Guided by a Compact Suffix Tree
Compared to a mismatched consensus motif, a degenerate consensus motif is more suitable for modeling position-specific variations within motifs. In the literature, the state-of-art methods using degenerate con...
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Chapter and Conference Paper
Inferring Gene Regulatory Networks from Multiple Data Sources Via a Dynamic Bayesian Network with Structural EM
Using our dynamic Bayesian network with structural Expectation Maximization (SEM-DBN), we develop a new framework to model gene regulatory network from both gene expression data and transcriptional factor bind...
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Chapter and Conference Paper
Gene Regulatory Network Construction Using Dynamic Bayesian Network (DBN) with Structure Expectation Maximization (SEM)
Discovering gene relationship from gene expression data is a hot topic in the post-genomic era. In recent years, Bayesian network has become a popular method to reconstruct the gene regulatory network due to t...
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Chapter and Conference Paper
IA64 Oriented OpenMP Compiler: Design and Implementation of Fortran Front End
This paper presents an OpenMP compiler Fortran Front End. It introduces principles and algorithms to deal with the implicit data parallelism, which is directed by WORKSHARE directive in OpenMP Fortran API V2.0...
