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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. Content type: Methodology article

    MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conv...

    Authors: Chung Wah Wu, Jared M. Evans, Shengbing Huang, Douglas W. Mahoney, Brian A. Dukek, William R. Taylor, Tracy C. Yab, Thomas C. Smyrk, Jin Jen, John B. Kisiel and David A. Ahlquist

    Citation: BMC Genomics 2018 19:401

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  2. Content type: Research article

    The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicti...

    Authors: Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée and Didier Mazel

    Citation: BMC Genomics 2018 19:373

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  3. Content type: Research article

    Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analy...

    Authors: Felix Seifert, Alexander Thiemann, Tobias A. Schrag, Dominika Rybka, Albrecht E. Melchinger, Matthias Frisch and Stefan Scholten

    Citation: BMC Genomics 2018 19:371

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  4. Content type: Research article

    Caponization results in reduced androgen levels, which leads to abdominal fat accumulation in capons. In this study, we sought to understand the molecular mechanisms behind this fat accumulation.

    Authors: Xiaoyan Cui, Huanxian Cui, Lu Liu, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2018 19:344

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  5. Content type: Research article

    337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory f...

    Authors: Longqing Sun, Genlou Sun, Chenxia Shi and Dongfa Sun

    Citation: BMC Genomics 2018 19:333

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  6. Content type: Methodology article

    Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA seque...

    Authors: Ashish Yeri, Amanda Courtright, Kirsty Danielson, Elizabeth Hutchins, Eric Alsop, Elizabeth Carlson, Michael Hsieh, Olivia Ziegler, Avash Das, Ravi V. Shah, Joel Rozowsky, Saumya Das and Kendall Van Keuren-Jensen

    Citation: BMC Genomics 2018 19:331

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  7. Content type: Methodology article

    Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable ...

    Authors: Wells W. Wu, Je-Nie Phue, Chun-Ting Lee, Changyi Lin, Lai Xu, Rong Wang, Yaqin Zhang and Rong-Fong Shen

    Citation: BMC Genomics 2018 19:326

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  8. Content type: Research article

    Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during panc...

    Authors: Zhihua Li and Rodney Rouse

    Citation: BMC Genomics 2018 19:297

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  9. Content type: Research article

    Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas ae...

    Authors: Erin E. Gill, Luisa S. Chan, Geoffrey L. Winsor, Neil Dobson, Raymond Lo, Shannan J. Ho Sui, Bhavjinder K. Dhillon, Patrick K. Taylor, Raunak Shrestha, Cory Spencer, Robert E. W. Hancock, Peter J. Unrau and Fiona S. L. Brinkman

    Citation: BMC Genomics 2018 19:223

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  10. Content type: Research article

    The anthocyanins are highly enriched in eggplants (Solanum melongena L.) with purple peel. However, our previous study showed that anthocyanins biosynthesis in eggplant cultivar ‘Lanshan Hexian’ was completely re...

    Authors: Jing Li, Yong-Jun He, Lu Zhou, Yang Liu, Mingmin Jiang, Li Ren and Huoying Chen

    Citation: BMC Genomics 2018 19:201

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    The Correction to this article has been published in BMC Genomics 2018 19:324

  11. Content type: Methodology article

    Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires ei...

    Authors: Zachary T. Herbert, Jamie P. Kershner, Vincent L. Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc…

    Citation: BMC Genomics 2018 19:199

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  12. Content type: Methodology article

    Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functio...

    Authors: Sebastian J. Teran Hidalgo and Shuangge Ma

    Citation: BMC Genomics 2018 19:198

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  13. Content type: Methodology article

    The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measuremen...

    Authors: P. Scott Pine, Steven P. Lund, Jerod R. Parsons, Lindsay K. Vang, Ashish A. Mahabal, Luca Cinquini, Sean C. Kelly, Heather Kincaid, Daniel J. Crichton, Avrum Spira, Gang Liu, Adam C. Gower, Harvey I. Pass, Chandra Goparaju, Steven M. Dubinett, Kostyantyn Krysan…

    Citation: BMC Genomics 2018 19:180

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  14. Content type: Methodology article

    Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene region...

    Authors: Bai-Han Zhu, Jun Xiao, Wei Xue, Gui-Cai Xu, Ming-Yuan Sun and Jiong-Tang Li

    Citation: BMC Genomics 2018 19:175

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  15. Content type: Research article

    RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs...

    Authors: Yaron Orenstein, Uwe Ohler and Bonnie Berger

    Citation: BMC Genomics 2018 19:154

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  16. Content type: Research article

    Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The down...

    Authors: Tian Gao, Jiang Shu and Juan Cui

    Citation: BMC Genomics 2018 19:146

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  17. Content type: Software

    Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of...

    Authors: Jackson A. Killian, Taha M. Topiwala, Alex R. Pelletier, David E. Frankhouser, Pearlly S. Yan and Ralf Bundschuh

    Citation: BMC Genomics 2018 19:139

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  18. Content type: Methodology article

    High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method would greatly expand the scope of feasible multi-site collaborations and max...

    Authors: Wanxin Wang, Lolita Penland, Ozgun Gokce, Derek Croote and Stephen R. Quake

    Citation: BMC Genomics 2018 19:140

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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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