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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. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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

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  12. 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

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  13. 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

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

  14. 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:

  15. 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:

  16. 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

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  17. 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

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  18. 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

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  19. 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

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  20. 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

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  21. 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

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

  22. 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:

  23. 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

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  24. 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

  25. 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:

  26. 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:

  27. 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:

  28. Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcri...

    Authors: Reema Singh, Hajara M. Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J. Barton, Pauline Schaap and Christian Cole

    Citation: BMC Genomics 2017 18:120

    Content type: Research article

    Published on:

  29. Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play importan...

    Authors: Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang and Cunshuan Xu

    Citation: BMC Genomics 2017 18:80

    Content type: Research Article

    Published on:

  30. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute le...

    Authors: Stephenie D. Prokopec, Kathleen E. Houlahan, Ren X. Sun, John D. Watson, Cindy Q. Yao, Jamie Lee, Christine P’ng, Renee Pang, Alexander H. Wu, Lauren C. Chong, Ashley B. Smith, Nicholas J. Harding, Ivy D. Moffat, Jere Lindén, Sanna Lensu, Allan B. Okey…

    Citation: BMC Genomics 2017 18:78

    Content type: Software

    Published on:

  31. Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mamma...

    Authors: Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Chun-Chi Liu and Jeremy J.W. Chen

    Citation: BMC Genomics 2017 18:61

    Content type: Methodology article

    Published on:

  32. Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties...

    Authors: Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee and Laiq ur Rahman

    Citation: BMC Genomics 2017 18:54

    Content type: Research

    Published on:

  33. Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome’s limitations in describing higher functional phenotypes and protein events. Perhaps the mos...

    Authors: Quin F. Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes…

    Citation: BMC Genomics 2017 18:53

    Content type: Methodology article

    Published on:

  34. The GII.4 Sydney 2012 strain of human norovirus (HuNoV) is a pandemic strain that is responsible for the majority of norovirus outbreaks in healthcare settings. The function of the non-structural (NS)1-2 prote...

    Authors: Zabeen Lateef, Gregory Gimenez, Estelle S. Baker and Vernon K. Ward

    Citation: BMC Genomics 2017 18:39

    Content type: Research Article

    Published on:

  35. The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging insect pest of corn in Asia. However, the lack of genome or transcriptome information heavily hinders our further understandi...

    Authors: Li Cui, Changhui Rui, Daibin Yang, Zhenying Wang and Huizhu Yuan

    Citation: BMC Genomics 2017 18:20

    Content type: Research Article

    Published on:

  36. Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or ...

    Authors: Bernardo Rodríguez-Martín, Emilio Palumbo, Santiago Marco-Sola, Thasso Griebel, Paolo Ribeca, Graciela Alonso, Alberto Rastrojo, Begoña Aguado, Roderic Guigó and Sarah Djebali

    Citation: BMC Genomics 2017 18:7

    Content type: Methodology Article

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  37. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed process.

    Authors: Qianglong Zhu, Peng Gao, Shi Liu, Zicheng Zhu, Sikandar Amanullah, Angela R. Davis and Feishi Luan

    Citation: BMC Genomics 2017 18:3

    Content type: Research Article

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  38. Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of sin...

    Authors: Hannah R. Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian-Bing Fan, Stephen A. Fisher, Jennifer S. Herstein, Tae Kyung Kim, Jae Mun (Hugo) Kim, Ming-Yi Lin, Rui Liu, William J. Mack, Sean McGroty, Joseph D. Nguyen…

    Citation: BMC Genomics 2016 17:966

    Content type: Research article

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  39. The fight against grapevine diseases due to biotrophic pathogens usually requires the massive use of chemical fungicides with harmful environmental effects. An alternative strategy could be the use of compound...

    Authors: Marie-Cécile Dufour, Noël Magnin, Bernard Dumas, Sophie Vergnes and Marie-France Corio-Costet

    Citation: BMC Genomics 2016 17:957

    Content type: Research article

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  40. Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal fo...

    Authors: A. L. De Oliveira, T. Wollesen, A. Kristof, M. Scherholz, E. Redl, C. Todt, C. Bleidorn and A. Wanninger

    Citation: BMC Genomics 2016 17:905

    Content type: Research article

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  41. Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and...

    Authors: Daisuke Komura, Takayuki Isagawa, Kazuki Kishi, Ryohei Suzuki, Reiko Sato, Mariko Tanaka, Hiroto Katoh, Shogo Yamamoto, Kenji Tatsuno, Masashi Fukayama, Hiroyuki Aburatani and Shumpei Ishikawa

    Citation: BMC Genomics 2016 17:899

    Content type: Methodology 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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