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BMC Genomics

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. Content type: Software

    Molecular signatures are collections of genes characteristic of a particular cell type, tissue, disease, or perturbation. Signatures can also be used to interpret expression profiles generated from heterogeneo...

    Authors: David Lopez, Dennis Montoya, Michael Ambrose, Larry Lam, Leah Briscoe, Claire Adams, Robert L. Modlin and Matteo Pellegrini

    Citation: BMC Genomics 2017 18:824

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  2. Content type: Methodology article

    In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An importan...

    Authors: Hugo W. Schneider, Taina Raiol, Marcelo M. Brigido, Maria Emilia M. T. Walter and Peter F. Stadler

    Citation: BMC Genomics 2017 18:804

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  3. Content type: Research article

    Our main purpose was to evaluate the expression of plastic and evolved genes involved in ecological speciation in the noctuid moth Spodoptera frugiperda, the fall armyworm (FAW); and to demonstrate how host plant...

    Authors: Karina Lucas Silva-Brandão, Renato Jun Horikoshi, Daniel Bernardi, Celso Omoto, Antonio Figueira and Marcelo Mendes Brandão

    Citation: BMC Genomics 2017 18:792

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  4. Content type: Methodology article

    RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression...

    Authors: Billy T. Lau and Hanlee P. Ji

    Citation: BMC Genomics 2017 18:745

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  5. Content type: Research article

    Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the nu...

    Authors: Ulykbek Kairov, Laura Cantini, Alessandro Greco, Askhat Molkenov, Urszula Czerwinska, Emmanuel Barillot and Andrei Zinovyev

    Citation: BMC Genomics 2017 18:712

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  6. Content type: Research article

    Cotton fibre is a single cell and it is one of the best platforms for unraveling the genes express during various stages of fibre development. There are reports devoted to comparative transcriptome study on fi...

    Authors: Atul S. Hande, Ishwarappa S. Katageri, Mangesh P. Jadhav, Sateesh Adiger, Savita Gamanagatti, Kethireddy Venkata Padmalatha, Gurusamy Dhandapani, Mogilicherla Kanakachari, Polumetla Ananda Kumar and Vanga Siva Reddy

    Citation: BMC Genomics 2017 18:675

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  7. Content type: Software

    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...

    Authors: Daniel Gebert, Charlotte Hewel and David Rosenkranz

    Citation: BMC Genomics 2017 18:644

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  8. Content type: Research article

    The natural history of type 1 diabetes (T1D) is challenging to investigate, especially as pre-diabetic individuals are difficult to identify. Numerous T1D consortia have been established to collect whole blood...

    Authors: Linda Yip, Rebecca Fuhlbrigge, Mark A. Atkinson and C. Garrison Fathman

    Citation: BMC Genomics 2017 18:636

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  9. Content type: Research article

    RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the met...

    Authors: Ashwini Kumar, Matti Kankainen, Alun Parsons, Olli Kallioniemi, Pirkko Mattila and Caroline A. Heckman

    Citation: BMC Genomics 2017 18:629

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  10. Content type: Methodology Article

    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...

    Authors: Sebastian J. Teran Hidalgo, Mengyun Wu and Shuangge Ma

    Citation: BMC Genomics 2017 18:623

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  11. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:622

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  12. Content type: Research Article

    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...

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

    Citation: BMC Genomics 2017 18:611

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  13. Content type: Methodology article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:601

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  14. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:602

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  15. Content type: Research article

    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 ...

    Authors: 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

    Citation: BMC Genomics 2017 18:595

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  16. Content type: Research article

    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 ...

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

    Citation: BMC Genomics 2017 18:587

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  17. Content type: Research article

    Predatory syrphid larvae are an important natural enemy of aphids in cotton agro-ecosystems in China. Their behaviors in prey foraging, localization and oviposition greatly rely on the perception of chemical c...

    Authors: Bing Wang, Yang Liu and Gui-Rong Wang

    Citation: BMC Genomics 2017 18:586

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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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