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BMC Bioinformatics

Transcriptome analysis

Section edited by Adam Olshen

This section incorporates all aspects of transcriptomic analysis including but not limited to: methods and applications for the analysis of microarray and RNA-seq data.

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  1. Content type: Software

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to re...

    Authors: Giorgos Minas, Hiroshi Momiji, Dafyd J. Jenkins, Maria J. Costa, David A. Rand and Bärbel Finkenstädt

    Citation: BMC Bioinformatics 2017 18:316

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  2. Content type: Methodology Article

    Distance based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and relatively high correlation...

    Authors: Xiting Yan, Anqi Liang, Jose Gomez, Lauren Cohn, Hongyu Zhao and Geoffrey L. Chupp

    Citation: BMC Bioinformatics 2017 18:309

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  3. Content type: Methodology Article

    The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-s...

    Authors: Stephen J. Bush, Mary E. B. McCulloch, Kim M. Summers, David A. Hume and Emily L. Clark

    Citation: BMC Bioinformatics 2017 18:301

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  4. Content type: Research Article

    Despite advances in the gene-set enrichment analysis methods; inadequate definitions of gene-sets cause a major limitation in the discovery of novel biological processes from the transcriptomic datasets. Typic...

    Authors: Atif Khan, Dejan Katanic and Juilee Thakar

    Citation: BMC Bioinformatics 2017 18:295

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  5. Content type: Methodology Article

    Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes....

    Authors: Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrick W. H. Göhlmann and Ziv Shkedy

    Citation: BMC Bioinformatics 2017 18:273

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  6. Content type: Software

    Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantit...

    Authors: Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak and Kristina Gruden

    Citation: BMC Bioinformatics 2017 18:276

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  7. Content type: Research Article

    There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment...

    Authors: Joanna Zyla, Michal Marczyk, January Weiner and Joanna Polanska

    Citation: BMC Bioinformatics 2017 18:256

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  8. Content type: Methodology Article

    Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene...

    Authors: Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum and Hinrich Gronemeyer

    Citation: BMC Bioinformatics 2017 18:259

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  9. Content type: Software

    A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined fo...

    Authors: Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen and Carl J. Schmidt

    Citation: BMC Bioinformatics 2017 18:237

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  10. Content type: Methodology Article

    Sample size calculation and power estimation are essential components of experimental designs in biomedical research. It is very challenging to estimate power for RNA-Seq differential expression under complex ...

    Authors: Lianbo Yu, Soledad Fernandez and Guy Brock

    Citation: BMC Bioinformatics 2017 18:234

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  11. Content type: Methodology Article

    Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA...

    Authors: Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter and Pieter Mestdagh

    Citation: BMC Bioinformatics 2017 18:231

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  12. Content type: Research Article

    MicroRNAs always function cooperatively in their regulation of gene expression. Dysfunctions of these co-functional microRNAs can play significant roles in disease development. We are interested in those multi...

    Authors: Hui Peng, Chaowang Lan, Yi Zheng, Gyorgy Hutvagner, Dacheng Tao and Jinyan Li

    Citation: BMC Bioinformatics 2017 18:193

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  13. Content type: Research Article

    The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs fro...

    Authors: Giovanna M. M. Ventola, Teresa M. R. Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli and Luigi Cerulo

    Citation: BMC Bioinformatics 2017 18:187

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  14. Content type: Software

    Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate m...

    Authors: Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent and Baohong Zhang

    Citation: BMC Bioinformatics 2017 18:180

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  15. Content type: Research article

    Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is importan...

    Authors: Alain B. Tchagang, François Fauteux, Dan Tulpan and Youlian Pan

    Citation: BMC Bioinformatics 2017 18:174

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  16. Content type: Methodology article

    The purpose of gene set enrichment analysis (GSEA) is to find general trends in the huge lists of genes or proteins generated by many functional genomics techniques and bioinformatics analyses.

    Authors: Cedric Simillion, Robin Liechti, Heidi E.L. Lischer, Vassilios Ioannidis and Rémy Bruggmann

    Citation: BMC Bioinformatics 2017 18:151

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  17. Content type: Methodology Article

    A family of parsimonious Gaussian mixture models for the biclustering of gene expression data is introduced. Biclustering is accommodated by adopting a mixture of factor analyzers model with a binary, row-stoc...

    Authors: Monica H. T. Wong, David M. Mutch and Paul D. McNicholas

    Citation: BMC Bioinformatics 2017 18:150

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  18. Content type: Research article

    Recent studies illuminated a novel role of microRNA (miRNA) in the competing endogenous RNA (ceRNA) interaction: two genes (ceRNAs) can achieve coexpression by competing for a pool of common targeting miRNAs. ...

    Authors: Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu, Tzu-Hung Hsiao, Eric Y. Chuang and Yidong Chen

    Citation: BMC Bioinformatics 2017 18:132

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  19. Content type: Methodology Article

    Molecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to reproduce across studies. One solution is to combine independent studies into a single integr...

    Authors: Florian Rohart, Aida Eslami, Nicholas Matigian, Stéphanie Bougeard and Kim-Anh Lê Cao

    Citation: BMC Bioinformatics 2017 18:128

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