Genomics

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads

Author(s): Serghei Mangul, Taegyun Harry Yang, Farhad Hormozdiari, Alexandra Marie Dainis, Elizabeth Tseng, Euan A. Ashley, Alex Zelikovsky, Eleazar Eskin
HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads 215 235 Transactions on NanoBioscience (TNB)

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…

read more

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…

read more

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,…

read more

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…

read more

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…

read more

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…

read more

A Generalized dSpliceType Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq

Author(s): Dongxiao Zhu, Nan Deng, Changxin Bai
A Generalized dSpliceType Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq 556 235 Transactions on NanoBioscience (TNB)

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…

read more