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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. Content type: Software

    Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is re...

    Authors: Matthias Barann, Ralf Zimmer and Fabian Birzele

    Citation: BMC Bioinformatics 2017 18:120

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  9. Content type: Software

    Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate ort...

    Authors: Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof and Oliver Niehuis

    Citation: BMC Bioinformatics 2017 18:111

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  10. Content type: Research article

    Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help ...

    Authors: Yanhui Hu, Aram Comjean, Norbert Perrimon and Stephanie E. Mohr

    Citation: BMC Bioinformatics 2017 18:98

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  11. Content type: Methodology article

    Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) r...

    Authors: Seung Hoan Choi, Adam T. Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis and Anita L. DeStefano

    Citation: BMC Bioinformatics 2017 18:91

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  12. Content type: Software

    Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlat...

    Authors: Rui Henriques, Francisco L. Ferreira and Sara C. Madeira

    Citation: BMC Bioinformatics 2017 18:82

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    The Erratum to this article has been published in BMC Bioinformatics 2017 18:162

  13. Content type: Methodology article

    The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is ty...

    Authors: Rob Eisinga, Tom Heskes, Ben Pelzer and Manfred Te Grotenhuis

    Citation: BMC Bioinformatics 2017 18:68

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  14. Content type: Research article

    RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of to...

    Authors: Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish and Charles C. Kim

    Citation: BMC Bioinformatics 2017 18:38

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  15. Content type: Methodology Article

    The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quic...

    Authors: Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn and Franziska Matthäus

    Citation: BMC Bioinformatics 2017 18:33

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  16. Content type: Methodology article

    Performing statistical tests is an important step in analyzing genome-wide datasets for detecting genomic features differentially expressed between conditions. Each type of statistical test has its own advanta...

    Authors: Yuanzhe Bei and Pengyu Hong

    Citation: BMC Bioinformatics 2016 17:541

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  17. Content type: Research Article

    Competitive gene set analysis is a standard exploratory tool for gene expression data. Permutation-based competitive gene set analysis methods are preferable to parametric ones because the latter make strong s...

    Authors: Pashupati P. Mishra, Alan Medlar, Liisa Holm and Petri Törönen

    Citation: BMC Bioinformatics 2016 17:526

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  18. Content type: Methodology article

    Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonco...

    Authors: Nicolas Cerveau and Daniel J. Jackson

    Citation: BMC Bioinformatics 2016 17:525

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  19. Content type: Database

    Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers...

    Authors: Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted and Lior Pachter

    Citation: BMC Bioinformatics 2016 17:490

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  20. Content type: Software

    Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Prevailing analytical approaches applied to this technology make use of sequence fragment length profilin...

    Authors: Sang Y. Chun, Caitlin M. Rodriguez, Peter K. Todd and Ryan E. Mills

    Citation: BMC Bioinformatics 2016 17:482

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  21. Content type: Software

    Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expres...

    Authors: Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger and Avi Ma’ayan

    Citation: BMC Bioinformatics 2016 17:461

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  22. Content type: Research Article

    Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and con...

    Authors: Narayan Jayaram, Daniel Usvyat and Andrew C. R. Martin

    Citation: BMC Bioinformatics 2016 :1298

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  23. Content type: Software

    Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3’UTRs have been found to...

    Authors: Elena Grassi, Elisa Mariella, Antonio Lembo, Ivan Molineris and Paolo Provero

    Citation: BMC Bioinformatics 2016 17:423

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  24. Content type: Methodology article

    Although metatranscriptomics—the study of diverse microbial population activity based on RNA-seq data—is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Cu...

    Authors: Samuel T. Westreich, Ian Korf, David A. Mills and Danielle G. Lemay

    Citation: BMC Bioinformatics 2016 17:399

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  25. Content type: Software

    Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality redu...

    Authors: David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani and Koji Tsuda

    Citation: BMC Bioinformatics 2016 17:363

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  26. Content type: Methodology Article

    Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these dataset...

    Authors: David Angeles-Albores, Raymond Y. N. Lee, Juancarlos Chan and Paul W. Sternberg

    Citation: BMC Bioinformatics 2016 17:366

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  27. Content type: Methodology article

    Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used t...

    Authors: Alan Hodgkinson, Jean-Christophe Grenier, Elias Gbeha and Philip Awadalla

    Citation: BMC Bioinformatics 2016 17:364

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  28. Content type: Methodology article

    Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most benign, they reduce the power of statistical tes...

    Authors: Yalchin Oytam, Fariborz Sobhanmanesh, Konsta Duesing, Joshua C. Bowden, Megan Osmond-McLeod and Jason Ross

    Citation: BMC Bioinformatics 2016 17:332

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  29. Content type: Methodology Article

    Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available method...

    Authors: Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong and Ping Ma

    Citation: BMC Bioinformatics 2016 17:324

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  30. Content type: Software

    The interplay among genetic, environment and epigenetic variation is not fully understood. Advances in high-throughput genotyping methods, high-density DNA methylation detection and well-characterized sample c...

    Authors: Hong Pan, Joanna D. Holbrook, Neerja Karnani and Chee Keong Kwoh

    Citation: BMC Bioinformatics 2016 17:299

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  31. Content type: Research Article

    Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) Class I molecules bind to peptide fragments of proteins degraded inside the cell and display them on the cell surface. We are interested ...

    Authors: Ankur Dhanik, Jessica R. Kirshner, Douglas MacDonald, Gavin Thurston, Hsin C. Lin, Andrew J. Murphy and Wen Zhang

    Citation: BMC Bioinformatics 2016 17:286

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  32. Content type: Methodology article

    It is now clearly evident that cancer outcome and response to therapy is guided by diverse immune-cell activity in tumors. Presently, a key challenge is to comprehensively identify networks of distinct immune-...

    Authors: Trevor Clancy and Eivind Hovig

    Citation: BMC Bioinformatics 2016 17:263

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  33. Content type: Methodology article

    Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types.

    Authors: E. Andres Houseman, Molly L. Kile, David C. Christiani, Tan A. Ince, Karl T. Kelsey and Carmen J. Marsit

    Citation: BMC Bioinformatics 2016 17:259

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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