bioinformatics

OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads

Author(s): Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads 215 235 Transactions on NanoBioscience (TNB)

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…

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TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine

Author(s): Guang-Qing Li, Zi Liu, Hong-Bin Shen, Dong-Jun Yu
TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine 215 220 Transactions on NanoBioscience (TNB)

As one of the most ubiquitous post-transcriptional modifications of RNA, N6-methyladenosine ( m 6 A  ) plays an essential role in many vital biological processes. The identification of m 6 A  sites in RNAs…

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Block-Constraint Robust Principal Component Analysis and its Application to Integrated Analysis of TCGA Data

Author(s): Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng, Yong Xu, Jiguo Yu
Block-Constraint Robust Principal Component Analysis and its Application to Integrated Analysis of TCGA Data 215 259 Transactions on NanoBioscience (TNB)

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,…

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Integrating Omics Data With a Multiplex Network-Based Approach for the Identification of Cancer Subtypes

Author(s): Haiying Wang, Huiru Zheng, Jianxin Wang, Chaoyang Wang, Fang-Xiang Wu
Integrating Omics Data With a Multiplex Network-Based Approach for the Identification of Cancer Subtypes 556 235 Transactions on NanoBioscience (TNB)

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…

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Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana

Author(s): Qiwen Hu, Catharina Merchante, Anna N. Stepanova, Jose M. Alonso, Steffen Heber
Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana 556 235 Transactions on NanoBioscience (TNB)

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…

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Identification Exon Skipping Events From High-Throughput RNA Sequencing Data

Author(s): Yang Bai, Shufan Ji, Qinghua Jiang, Yadong Wang
Identification Exon Skipping Events From High-Throughput RNA Sequencing Data 266 114 Transactions on NanoBioscience (TNB)

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…

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