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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. Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to iden...

    Authors: C. Peraldo-Neia, P. Ostano, G. Cavalloni, Y. Pignochino, D. Sangiolo, L. De Cecco, E. Marchesi, D. Ribero, A. Scarpa, A. M. De Rose, A. Giuliani, F. Calise, C. Raggi, P. Invernizzi, M. Aglietta, G. Chiorino…

    Citation: BMC Genomics 2018 19:440

    Content type: Research article

    Published on:

  2. CCHCR1 (Coiled-Coil α-Helical Rod protein 1) is a putative psoriasis candidate gene with the risk alleles CCHCR1*WWCC and *Iso3, the latter inhibiting the translation of isoform 1. CCHCR1 was recently shown to be...

    Authors: Mari H. Tervaniemi, Shintaro Katayama, Tiina Skoog, H. Annika Siitonen, Jyrki Vuola, Kristo Nuutila, Kristiina Tammimies, Sari Suomela, Esko Kankuri, Juha Kere and Outi Elomaa

    Citation: BMC Genomics 2018 19:432

    Content type: Research article

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  3. Scylla paramamosain (Crustacea: Decapoda: Portunidae: Syclla De Hann) is a commercially important mud crab distributed along the coast of southern China and other Indo-Pacific countries (Lin Z, Hao M, Zhu D, et a...

    Authors: Huan Wang, Lei Tang, Hongling Wei, Junkai Lu, Changkao Mu and Chunlin Wang

    Citation: BMC Genomics 2018 19:421

    Content type: Research article

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  4. Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been ...

    Authors: Kuan Feng, Justin Costa and Jeremy S. Edwards

    Citation: BMC Genomics 2018 19:416

    Content type: Methodology article

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  5. Small RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next...

    Authors: Mohamed El-Mogy, Bernard Lam, Taha A. Haj-Ahmad, Shannon McGowan, Darrick Yu, Lucas Nosal, Nezar Rghei, Pam Roberts and Yousef Haj-Ahmad

    Citation: BMC Genomics 2018 19:408

    Content type: Research article

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  6. Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular ch...

    Authors: Wenjie Sun, Ting Duan, Panmeng Ye, Kelie Chen, Guanling Zhang, Maode Lai and Honghe Zhang

    Citation: BMC Genomics 2018 19:405

    Content type: Software

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  7. 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

    Content type: Methodology article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Methodology article

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  13. 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

    Content type: Methodology article

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  14. 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

    Content type: Research article

    Published on:

  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

    Published on:

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

  17. 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

    Content type: Methodology article

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  18. 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

    Content type: Methodology article

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  19. 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

    Content type: Methodology article

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  20. 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

    Content type: Methodology article

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    The Correction to this article has been published in BMC Genomics 2019 20:524

  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Methodology article

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  24. 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

    Content type: Software

    Published on:

  25. 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

    Content type: Methodology article

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  26. 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

    Content type: Methodology article

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  27. 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

    Content type: Methodology

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  28. 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

    Content type: Research article

    Published on:

  29. 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

    Content type: Methodology article

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  30. 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

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  31. 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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  32. 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

    Published on:

  33. 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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  34. 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

    Published on:

  35. 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

    Published on:

  36. 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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  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

  42. 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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  43. 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

    Published on:

  44. 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

    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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