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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. Meat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the hi...

    Authors: Larissa Fernanda Simielli Fonseca, Daniele Fernanda Jovino Gimenez, Danielly Beraldo dos Santos Silva, Roger Barthelson, Fernando Baldi, Jesus Aparecido Ferro and Lucia Galvão Albuquerque

    Citation: BMC Genomics 2017 18:945

    Content type: Research article

    Published on:

  2. It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals.

    Authors: Huaping Liu, Yawei Li, Jun He, Qingzhou Guan, Rou Chen, Haidan Yan, Weicheng Zheng, Kai Song, Hao Cai, You Guo, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2017 18:913

    Content type: Research article

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  3. 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

    Content type: Software

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  4. 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

    Content type: Methodology article

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Methodology article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Software

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Methodology Article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research Article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Methodology article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. 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...

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

    Citation: BMC Genomics 2017 18:574

    Content type: Research article

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  21. Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the ...

    Authors: Maureen A. Carey, Jason A. Papin and Jennifer L. Guler

    Citation: BMC Genomics 2017 18:543

    Content type: Research article

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  22. 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...

    Authors: 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…

    Citation: BMC Genomics 2017 18:519

    Content type: Methodology article

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  23. 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...

    Authors: 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…

    Citation: BMC Genomics 2017 18:515

    Content type: Methodology article

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  24. The Cancer Genome Atlas (TCGA) has generated comprehensive molecular profiles. We aim to identify a set of genes whose expression patterns can distinguish diverse tumor types. Those features may serve as bioma...

    Authors: Yuanyuan Li, Kai Kang, Juno M. Krahn, Nicole Croutwater, Kevin Lee, David M. Umbach and Leping Li

    Citation: BMC Genomics 2017 18:508

    Content type: Research article

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  25. A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to ...

    Authors: Paulina Jackowiak, Anna Hojka-Osinska, Anna Philips, Agnieszka Zmienko, Lucyna Budzko, Patrick Maillard, Agata Budkowska and Marek Figlerowicz

    Citation: BMC Genomics 2017 18:502

    Content type: Research article

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  26. In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progr...

    Authors: Alexey V. Beletsky, Alexander N. Malyavko, Maria V. Sukhanova, Eugenia S. Mardanova, Maria I. Zvereva, Olga A. Petrova, Yulia Yu. Parfenova, Maria P. Rubtsova, Andrey V. Mardanov, Olga I. Lavrik, Olga A. Dontsova and Nikolai V. Ravin

    Citation: BMC Genomics 2017 18:492

    Content type: Research article

    Published on:

  27. High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation o...

    Authors: Haibo Liu, Timothy P.L. Smith, Dan J. Nonneman, Jack C.M. Dekkers and Christopher K. Tuggle

    Citation: BMC Genomics 2017 18:479

    Content type: Research article

    Published on:

  28. Alternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification...

    Authors: Peter Zhang, Emmanuel Dimont, Thomas Ha, Douglas J. Swanson, Winston Hide and Dan Goldowitz

    Citation: BMC Genomics 2017 18:461

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:39

  29. Grass carp is an important farmed fish in China that is affected by serious disease, especially hemorrhagic disease caused by grass carp reovirus (GCRV). The mechanism underlying the hemorrhagic symptoms in in...

    Authors: Libo He, Aidi Zhang, Yongyan Pei, Pengfei Chu, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu and Yaping Wang

    Citation: BMC Genomics 2017 18:452

    Content type: Research article

    Published on:

  30. RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Il...

    Authors: Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Maximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar and Laurent Vallar

    Citation: BMC Genomics 2017 18:443

    Content type: Research article

    Published on:

  31. RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive,...

    Authors: Sven Schuierer, Walter Carbone, Judith Knehr, Virginie Petitjean, Anita Fernandez, Marc Sultan and Guglielmo Roma

    Citation: BMC Genomics 2017 18:442

    Content type: Methodology article

    Published on:

  32. Influenza A virus (IAV) is a major public health concern, being responsible for the death of approximately half a million people each year. Zoonotic transmissions of the virus from swine and avian origin hav...

    Authors: Biruhalem Taye, Hui Chen, Myint Zu Myaing, Boon Huan Tan, Sebastian Maurer-Stroh and Richard J. Sugrue

    Citation: BMC Genomics 2017 18:420

    Content type: Research article

    Published on:

  33. RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kit...

    Authors: Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam and Marc R. Wilkins

    Citation: BMC Genomics 2017 18:399

    Content type: Research article

    Published on:

  34. Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treati...

    Authors: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural, Manuel Garber and Scot A. Wolfe

    Citation: BMC Genomics 2017 18:379

    Content type: Software

    Published on:

  35. Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time poi...

    Authors: Han Rauwerda, Johanna F. B. Pagano, Wim C. de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P. Spaink and Timo M. Breit

    Citation: BMC Genomics 2017 18:287

    Content type: Research Article

    Published on:

  36. Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretati...

    Authors: Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Ines Pomposiello and Laura Badi

    Citation: BMC Genomics 2017 18:277

    Content type: Software

    Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:558

  37. MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions...

    Authors: Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu and Diyan Li

    Citation: BMC Genomics 2017 18:255

    Content type: Research article

    Published on:

  38. We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched con...

    Authors: Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A. Kyrtopoulos, Ingvar A. Bergdahl, Ann-Sofie Johansson, Dennie D.G.A.J. Hebels, Theo M.C.M. de Kok, Paolo Vineis and Roel C.H. Vermeulen

    Citation: BMC Genomics 2017 18:239

    Content type: Research article

    Published on:

  39. Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible ...

    Authors: Vincent Doublet, Yvonne Poeschl, Andreas Gogol-Döring, Cédric Alaux, Desiderato Annoscia, Christian Aurori, Seth M. Barribeau, Oscar C. Bedoya-Reina, Mark J. F. Brown, James C. Bull, Michelle L. Flenniken, David A. Galbraith, Elke Genersch, Sebastian Gisder, Ivo Grosse, Holly L. Holt…

    Citation: BMC Genomics 2017 18:207

    Content type: Research article

    Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:256

  40. While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribos...

    Authors: Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim and Siegfried Scherer

    Citation: BMC Genomics 2017 18:216

    Content type: Research article

    Published on:

  41. Drought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance r...

    Authors: Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, Ram Sewak Singh Tomar, Ashish Kumar Chaturvedi, Kishor Gaikwad and Madan Pal

    Citation: BMC Genomics 2017 18:206

    Content type: Research article

    Published on:

  42. The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic...

    Authors: Libo He, Aidi Zhang, Pengfei Chu, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu and Yaping Wang

    Citation: BMC Genomics 2017 18:195

    Content type: Research article

    Published on:

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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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