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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: 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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  2. 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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  3. 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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  4. 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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  5. Content type: Methodology article

    Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during ada...

    Authors: Cloelia Dard-Dascot, Delphine Naquin, Yves d’Aubenton-Carafa, Karine Alix, Claude Thermes and Erwin van Dijk

    Citation: BMC Genomics 2018 19:118

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  6. Content type: Methodology article

    Exosomes and other extracellular vesicles (EVs) have emerged as an important mechanism of cell-to-cell communication. However, previous studies either did not fully resolve what genetic materials were shuttled...

    Authors: Jialiang Yang, Jacob Hagen, Kalyani V. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stephane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev…

    Citation: BMC Genomics 2017 18:987

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  7. Content type: Methodology

    Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well estab...

    Authors: Jian Zhong, Zhenqing Ye, Samuel W. Lenz, Chad R. Clark, Adil Bharucha, Gianrico Farrugia, Keith D. Robertson, Zhiguo Zhang, Tamas Ordog and Jeong-Heon Lee

    Citation: BMC Genomics 2017 18:985

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  8. Content type: Research article

    Transcriptome and proteome analyses on fruit pulp from the blood orange ‘Zaohong’ and the navel orange ‘twenty-first century’ were performed to study Citrus sinensis quality-related molecular changes during conse...

    Authors: Jian-hui Wang, Jian-jun Liu, Ke-ling Chen, Hong-wen Li, Jian He, Bin Guan and Li He

    Citation: BMC Genomics 2017 18:984

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  9. Content type: Methodology article

    In order to better understand the multifactorial nature of osteoporosis, animal models are utilized and compared to healthy controls. Female sheep are well established as a model for osteoporosis induced by ov...

    Authors: Felix Schulze, Deeksha Malhan, Thaqif El Khassawna, Christian Heiss, Anja Seckinger, Dirk Hose and Angela Rösen-Wolff

    Citation: BMC Genomics 2017 18:975

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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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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