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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: Research Article

    Predicting disease-associated genes is helpful for understanding the molecular mechanisms during the disease progression. Since the pathological mechanisms of neurodegenerative diseases are very complex, tradi...

    Authors: Xue Jiang, Han Zhang, Feng Duan and Xiongwen Quan

    Citation: BMC Bioinformatics 2017 18:447

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  2. Content type: Software

    Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most ...

    Authors: Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass and John Quackenbush

    Citation: BMC Bioinformatics 2017 18:437

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  3. Content type: Software

    The evolution of next-generation sequencing (NGS) technologies has led to increased focus on RNA-Seq. Many bioinformatic tools have been developed for RNA-Seq analysis, each with unique performance characteris...

    Authors: Jérôme Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes and Nicolas Philippe

    Citation: BMC Bioinformatics 2017 18:428

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  4. Content type: Software

    RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previou...

    Authors: Matthias Zytnicki

    Citation: BMC Bioinformatics 2017 18:411

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  5. Content type: Software

    A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological p...

    Authors: Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos and Theodore Dalamagas

    Citation: BMC Bioinformatics 2017 18:399

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  6. Content type: Methodology Article

    As a newly emerged research area, RNA epigenetics has drawn increasing attention recently for the participation of RNA methylation and other modifications in a number of crucial biological processes. Thanks to...

    Authors: Lian Liu, Shao-Wu Zhang, Yufei Huang and Jia Meng

    Citation: BMC Bioinformatics 2017 18:387

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  7. Content type: Research Article

    Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent bu...

    Authors: Xin-Ping Xie, Yu-Feng Xie and Hong-Qiang Wang

    Citation: BMC Bioinformatics 2017 18:375

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  8. Content type: Research Article

    MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biologica...

    Authors: Daniel Amsel, Andreas Vilcinskas and André Billion

    Citation: BMC Bioinformatics 2017 18:359

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  9. 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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  10. Content type: Research Article

    Personalizing treatment regimes based on gene expression profiles of individual tumors will facilitate management of cancer. Although many methods have been developed to identify pathways perturbed in tumors, ...

    Authors: Michael I. Klein, David F. Stern and Hongyu Zhao

    Citation: BMC Bioinformatics 2017 18:317

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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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