Transactions on NanoBioscience

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HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads
Sequencing of RNA provides the possibility to study an individual’s transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts, allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental... Read more
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OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads
Detection of somatic mutations from tumor and matched normal sequencing data has become a standard approach in cancer research. Although a number of mutation callers have been developed, it is still difficult to detect mutations with low-allele frequency even in... Read more
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Block-Constraint Robust Principal Component Analysis and its Application to Integrated Analysis of TCGA Data
The Cancer Genome Atlas (TCGA) dataset provides us more opportunities to systematically and comprehensively learn some biological mechanism of cancers formation, growth and metastasis. Since TCGA dataset includes heterogeneous data, it is one of the bioinformatics bottlenecks to mine some... Read more
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Integrating Omics Data With a Multiplex Network-Based Approach for the Identification of Cancer Subtypes
Comprehensive characterization and identification of cancer subtypes have a number of applications and implications in life science and cancer research. Technologies centered on the integration of omics data hold great promise in this endeavor. This paper proposed a multiplex network-based... Read more
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Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more
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Identification Exon Skipping Events From High-Throughput RNA Sequencing Data
The emergence of next-generation high-throughput RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate identification of alternative splicing events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS)... Read more
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A Generalized dSpliceType Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Transcriptomes are routinely compared in term of a list of differentially expressed genes followed by functional enrichment analysis. Due to the technology limitations of microarray, the molecular mechanisms of differential expression is poorly... Read more