Transcriptomic methods

This section covers novel experimental and analytical approaches for transcriptomic, epigenetic, and related high-throughput genomic studies. Studies which use transcriptomic and high-throughput genomic methods, but which do not present a novel methodological approach, should be submitted to the section in the journal relating to the organism studied.

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  1. Software

    unitas: the universal tool for annotation of small RNAs

    Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotat...

    Daniel Gebert, Charlotte Hewel and David Rosenkranz

    BMC Genomics 2017 18:644

    Published on: 22 August 2017

  2. Methodology Article

    Assisted clustering of gene expression data using ANCut

    In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful...

    Sebastian J. Teran Hidalgo, Mengyun Wu and Shuangge Ma

    BMC Genomics 2017 18:623

    Published on: 16 August 2017

  3. Research article

    Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus

    The Norway lobster, Nephrops norvegicus, is economically important in European fisheries and is a key organism in local marine ecosystems. Despite multi-faceted scientific interest in this species, our current kn...

    Guiomar Rotllant, Tuan Viet Nguyen, Valerio Sbragaglia, Lifat Rahi, Kevin J. Dudley, David Hurwood, Tomer Ventura, Joan B. Company, Vincent Chand, Jacopo Aguzzi and Peter B. Mather

    BMC Genomics 2017 18:622

    Published on: 16 August 2017

  4. Research Article

    Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ

    The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of...

    Maria Stavrianakou, Ricardo Perez, Cheng Wu, Matthew S. Sachs, Rodolfo Aramayo and Mark Harlow

    BMC Genomics 2017 18:611

    Published on: 14 August 2017

  5. Methodology article

    Fungal biomarker discovery by integration of classifiers

    The human immune system is responsible for protecting the host from infection. However, in immunocompromised individuals the risk of infection increases substantially with possible drastic consequences. In ext...

    João Pedro Saraiva, Marcus Oswald, Antje Biering, Daniela Röll, Cora Assmann, Tilman Klassert, Markus Blaess, Kristin Czakai, Ralf Claus, Jürgen Löffler, Hortense Slevogt and Rainer König

    BMC Genomics 2017 18:601

    Published on: 10 August 2017

  6. Research article

    A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

    Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analy...

    Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Eun Ji Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug and Gregory R. Grant

    BMC Genomics 2017 18:602

    Published on: 10 August 2017

  7. Research article

    Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components

    A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective ...

    Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, Charlotte L. McGivney, Katie F. Gough, David E. MacHugh, Lisa M. Katz and Emmeline W. Hill

    BMC Genomics 2017 18:595

    Published on: 9 August 2017

  8. Research article

    Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars

    Cadmium translocation from roots to shoots is a complex biological process that is controlled by gene regulatory networks. Pak choi exhibits wide cultivar variations in Cd accumulation. However, the molecular ...

    Rugang Yu, Dan Li, Xueling Du, Shenglan Xia, Caifeng Liu and Gangrong Shi

    BMC Genomics 2017 18:587

    Published on: 8 August 2017

  9. Research article

    Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

    Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at le...

    Wessam Galia, Francoise Leriche, Stéphane Cruveiller, Cindy Garnier, Vincent Navratil, Audrey Dubost, Stéphanie Blanquet-Diot and Delphine Thevenot-Sergentet

    BMC Genomics 2017 18:574

    Published on: 3 August 2017

  10. Methodology article

    A permutation-based non-parametric analysis of CRISPR screen data

    Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or a...

    Gaoxiang Jia, Xinlei Wang and Guanghua Xiao

    BMC Genomics 2017 18:545

    Published on: 19 July 2017

  11. Methodology article

    Massively parallel nanowell-based single-cell gene expression profiling

    Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expre...

    Leonard D. Goldstein, Ying-Jiun Jasmine Chen, Jude Dunne, Alain Mir, Hermann Hubschle, Joseph Guillory, Wenlin Yuan, Jingli Zhang, Jeremy Stinson, Bijay Jaiswal, Kanika Bajaj Pahuja, Ishminder Mann, Thomas Schaal, Leo Chan, Sangeetha Anandakrishnan, Chun-wah Lin…

    BMC Genomics 2017 18:519

    Published on: 7 July 2017

  12. Methodology article

    Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing

    RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutation...

    Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A. Moore, Andrew J. Mungall, Jacquie Schein, Robin J. Coope…

    BMC Genomics 2017 18:515

    Published on: 5 July 2017

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Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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