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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. Genes are regulated by various types of regulators and most of them are still unknown or unobserved. Current gene regulatory networks (GRNs) reverse engineering methods often neglect the unknown regulators and...

    Authors: Ming Shi, Sheng Tan, Xin-Ping Xie, Ao Li, Wulin Yang, Tao Zhu and Hong-Qiang Wang

    Citation: BMC Genomics 2020 21:711

    Content type: Methodology article

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  2. Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, l...

    Authors: S. Lam, J. Zeidan, F. Miglior, A. Suárez-Vega, I. Gómez-Redondo, P. A. S. Fonseca, L. L. Guan, S. Waters and A. Cánovas

    Citation: BMC Genomics 2020 21:703

    Content type: Research article

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  3. Head and neck squamous cell carcinoma (HNSCC) is a fatal malignancy owing to the lack of effective tools to predict overall survival (OS). MicroRNAs (miRNAs) play an important role in HNSCC occurrence, develop...

    Authors: Yusheng Huang, Zhiguo Liu, Limei Zhong, Yi Wen, Qixiang Ye, Donglin Cao, Peiwu Li and Yufeng Liu

    Citation: BMC Genomics 2020 21:691

    Content type: Research article

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  4. The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with...

    Authors: Huamei Li, Amit Sharma, Wenglong Ming, Xiao Sun and Hongde Liu

    Citation: BMC Genomics 2020 21:652

    Content type: Research article

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  5. The small number of samples and the curse of dimensionality hamper the better application of deep learning techniques for disease classification. Additionally, the performance of clustering-based feature selec...

    Authors: Da Xu, Jialin Zhang, Hanxiao Xu, Yusen Zhang, Wei Chen, Rui Gao and Matthias Dehmer

    Citation: BMC Genomics 2020 21:650

    Content type: Research article

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  6. In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick viru...

    Authors: Xiaofeng Xu, Jinlong Bei, Yibo Xuan, Jiayuan Chen, Defu Chen, Stephen C. Barker, Samuel Kelava, Xiaoai Zhang, Shan Gao and Ze Chen

    Citation: BMC Genomics 2020 21:641

    Content type: Research article

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  7. Functional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of...

    Authors: Natalia Rubanova, Guillaume Pinna, Jeremie Kropp, Anna Campalans, Juan Pablo Radicella, Anna Polesskaya, Annick Harel-Bellan and Nadya Morozova

    Citation: BMC Genomics 2020 21:632

    Content type: Methodology article

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  8. Alternative splicing (AS) offers a main mechanism to form protein polymorphism. A growing body of evidence indicates the correlation between splicing disorders and carcinoma. Nevertheless, an overall analysis ...

    Authors: Yuanyuan Zhang, Shengling Ma, Qian Niu, Yun Han, Xingyu Liu, Jie Jiang, Simiao Chen and Haolong Lin

    Citation: BMC Genomics 2020 21:580

    Content type: Research article

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  9. The increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data qualit...

    Authors: Austin N. Southard-Smith, Alan J. Simmons, Bob Chen, Angela L. Jones, Marisol A. Ramirez Solano, Paige N. Vega, Cherie’ R. Scurrah, Yue Zhao, Michael J. Brenan, Jiekun Xuan, Martha J. Shrubsole, Ely B. Porter, Xi Chen, Colin J. H. Brenan, Qi Liu, Lauren N. M. Quigley…

    Citation: BMC Genomics 2020 21:456

    Content type: Methodology article

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  10. Japanese encephalitis virus (JEV) is one of the common causes of acute encephalitis in humans. Japanese encephalitis is characterized by the uncontrolled release of inflammatory cytokines, which ultimately res...

    Authors: Yunchuan Li, Usama Ashraf, Zheng Chen, Dengyuan Zhou, Muhammad Imran, Jing Ye, Huanchun Chen and Shengbo Cao

    Citation: BMC Genomics 2020 21:409

    Content type: Research article

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  11. The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of dat...

    Authors: Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber and Alper Kucukural

    Citation: BMC Genomics 2020 21:310

    Content type: Software

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  12. Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to a...

    Authors: Wei Zhang, Raphael Petegrosso, Jae-Woong Chang, Jiao Sun, Jeongsik Yong, Jeremy Chien and Rui Kuang

    Citation: BMC Genomics 2020 21:272

    Content type: Research Article

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  13. Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individua...

    Authors: Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda and Itoshi Nikaido

    Citation: BMC Genomics 2020 21:177

    Content type: Software

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  14. In silico functional genomics have become a driving force in the way we interpret and use gene expression data, enabling researchers to understand which biological pathways are likely to be affected by the tre...

    Authors: Jeffrey A. Thompson and Devin C. Koestler

    Citation: BMC Genomics 2020 21:180

    Content type: Methodology article

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  15. Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of c...

    Authors: Ying Chen, Meng Zhang, Xiaofei Jin, Haoran Tao, Yamin Wang, Bo Peng, Chunhua Fu and Longjiang Yu

    Citation: BMC Genomics 2020 21:168

    Content type: Research article

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  16. Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcr...

    Authors: Vimla Kany G. Ami, Rami Balasubramanian and Shubhada R. Hegde

    Citation: BMC Genomics 2020 21:167

    Content type: Research article

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  17. Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is respo...

    Authors: Nicholas L. Panchy, John P. Lloyd and Shin-Han Shiu

    Citation: BMC Genomics 2020 21:159

    Content type: Research article

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  18. With the rapid development of high-throughput sequencing technologies, many datasets on the same biological subject are generated. A meta-analysis is an approach that combines results from different studies on...

    Authors: Nan Wang, Jun Zhang, Li Xu, Jing Qi, Beibei Liu, Yiyang Tang, Yinan Jiang, Liang Cheng, Qinghua Jiang, Xunbo Yin and Shuilin Jin

    Citation: BMC Genomics 2020 21:149

    Content type: Research Article

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  19. Intron retention (IR) has been traditionally overlooked as ‘noise’ and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating...

    Authors: Hong-Dong Li, Cory C. Funk and Nathan D. Price

    Citation: BMC Genomics 2020 21:128

    Content type: Software

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  20. High-throughput RNA sequencing (RNA-seq) has evolved as an important analytical tool in molecular biology. Although the utility and importance of this technique have grown, uncertainties regarding the proper a...

    Authors: Xiaohong Li, Nigel G. F. Cooper, Timothy E. O’Toole and Eric C. Rouchka

    Citation: BMC Genomics 2020 21:75

    Content type: Research article

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  21. The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the high costs of full-length mRNA sequencing have posed a limit on the accessibility and sca...

    Authors: Gabriel Sholder, Thomas A. Lanz, Robert Moccia, Jie Quan, Estel Aparicio-Prat, Robert Stanton and Hualin S. Xi

    Citation: BMC Genomics 2020 21:64

    Content type: Methodology article

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  22. RNA sequencing allows the measuring of gene expression at a resolution unmet by expression arrays or RT-qPCR. It is however necessary to normalize sequencing data by library size, transcript size and compositi...

    Authors: Karen Cristine Gonçalves dos Santos, Isabel Desgagné-Penix and Hugo Germain

    Citation: BMC Genomics 2020 21:35

    Content type: Methodology article

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  23. Tumor purity is the percent of cancer cells present in a sample of tumor tissue. The non-cancerous cells (immune cells, fibroblasts, etc.) have an important role in tumor biology. The ability to determine tumo...

    Authors: Yuanyuan Li, David M. Umbach, Adrienna Bingham, Qi-Jing Li, Yuan Zhuang and Leping Li

    Citation: BMC Genomics 2019 20:1021

    Content type: Research article

    Published on:

  24. The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as...

    Authors: Paulo Rapazote-Flores, Micha Bayer, Linda Milne, Claus-Dieter Mayer, John Fuller, Wenbin Guo, Pete E. Hedley, Jenny Morris, Claire Halpin, Jason Kam, Sarah M. McKim, Monika Zwirek, M. Cristina Casao, Abdellah Barakate, Miriam Schreiber, Gordon Stephen…

    Citation: BMC Genomics 2019 20:968

    Content type: Research article

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  25. The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence...

    Authors: Iana V. Kim, Eric J. Ross, Sascha Dietrich, Kristina Döring, Alejandro Sánchez Alvarado and Claus-D. Kuhn

    Citation: BMC Genomics 2019 20:909

    Content type: Methodology article

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  26. Targeted therapy for non-small cell lung cancer is histology dependent. However, histological classification by routine pathological assessment with hematoxylin-eosin staining and immunostaining for poorly dif...

    Authors: Xin Li, Gengen Shi, Qingsong Chu, Wenbin Jiang, Yixin Liu, Sainan Zhang, Zheyang Zhang, Zixin Wei, Fei He, Zheng Guo and Lishuang Qi

    Citation: BMC Genomics 2019 20:881

    Content type: Research article

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  27. Recent studies have shown that long non-coding RNAs (lncRNAs) play a crucial role in the induction of cancer through epigenetic regulation, transcriptional regulation, post-transcriptional regulation and other...

    Authors: Tao Chen, Cangui Zhang, Yingqiao Liu, Yuyun Zhao, Dingyi Lin, Yanfeng Hu, Jiang Yu and Guoxin Li

    Citation: BMC Genomics 2019 20:846

    Content type: Research article

    Published on:

  28. Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative p...

    Authors: Zsolt Balázs, Dóra Tombácz, Zsolt Csabai, Norbert Moldován, Michael Snyder and Zsolt Boldogkői

    Citation: BMC Genomics 2019 20:824

    Content type: Research article

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  29. Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatelli...

    Authors: Yelin Fu, Lishuang Qi, Wenbing Guo, Liangliang Jin, Kai Song, Tianyi You, Shuobo Zhang, Yunyan Gu, Wenyuan Zhao and Zheng Guo

    Citation: BMC Genomics 2019 20:769

    Content type: Research article

    Published on:

  30. The development of next generation sequencing (NGS) methods led to a rapid rise in the generation of large genomic datasets, but the development of user-friendly tools to analyze and visualize these datasets h...

    Authors: Alberto Luiz P. Reyes, Tiago C. Silva, Simon G. Coetzee, Jasmine T. Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther and Michelle R. Jones

    Citation: BMC Genomics 2019 20:745

    Content type: Software

    Published on:

  31. Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expert...

    Authors: Di Feng, Charles E. Whitehurst, Dechao Shan, Jon D. Hill and Yong G. Yue

    Citation: BMC Genomics 2019 20:676

    Content type: Software

    Published on:

  32. Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes...

    Authors: Igor Marín de Mas, Laura Torrents, Carmen Bedia, Lars K. Nielsen, Marta Cascante and Romà Tauler

    Citation: BMC Genomics 2019 20:652

    Content type: Research article

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  33. The males of many Bactrocera species (Diptera: Tephritidae) respond strongly to plant-derived chemicals (male lures) and can be divided into cue lure/raspberry ketone (CL/RK) responders, methyl eugenol (ME) respo...

    Authors: Zhongzhen Wu, Cong Kang, Mengqiu Qu, Junlong Chen, Mingshun Chen, Shuying Bin and Jintian Lin

    Citation: BMC Genomics 2019 20:646

    Content type: Research article

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  34. Genetic polymorphisms are known to influence milk production and composition. However, the genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. Micro...

    Authors: P. A. Billa, Y. Faulconnier, T. Ye, M. Chervet, F. Le Provost, J. A. A. Pires and C. Leroux

    Citation: BMC Genomics 2019 20:621

    Content type: Research article

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  35. Reporter methods to quantitatively measure the efficiency and specificity of genome editing tools are important for the development of novel editing techniques and successful applications of available ones. Ho...

    Authors: Akhilesh Kumar, Michael D. Birnbaum, Balaji T. Moorthy, Jayanti Singh, Anna Palovcak, Devang M. Patel and Fangliang Zhang

    Citation: BMC Genomics 2019 20:609

    Content type: Methodology article

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  36. RNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much shoul...

    Authors: Jordan Patterson, Eric J. Carpenter, Zhenzhen Zhu, Dan An, Xinming Liang, Chunyu Geng, Radoje Drmanac and Gane Ka-Shu Wong

    Citation: BMC Genomics 2019 20:604

    Content type: Research article

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  37. The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential...

    Authors: Nai-Tong Yu, Hui-Min Xie, Yu-Liang Zhang, Jian-Hua Wang, Zhongguo Xiong and Zhi-Xin Liu

    Citation: BMC Genomics 2019 20:573

    Content type: Research article

    Published on:

  38. Tree peony (Paeonia suffruticosa Andrews) is a globally famous ornamental flower, with large and colorful flowers and abundant flower types. However, a relatively short and uniform flowering period hinders the ap...

    Authors: Shunli Wang, Jie Gao, Jingqi Xue, Yuqian Xue, Dandan Li, Yanren Guan and Xiuxin Zhang

    Citation: BMC Genomics 2019 20:572

    Content type: Research article

    Published on:

  39. RNA-Seq is currently the most widely used tool to analyze whole-transcriptome profiles. There are numerous commercial kits available to facilitate preparing RNA-Seq libraries; however, it is still not clear ho...

    Authors: Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason S. Kirk, Melissa S. Simper, Carol D. Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu and Jianjun Shen

    Citation: BMC Genomics 2019 20:571

    Content type: Methodology article

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  40. Transcriptomic profiles can improve our understanding of the phenotypic molecular basis of biological research, and many statistical methods have been proposed to identify differentially expressed genes (DEGs)...

    Authors: Kyungtaek Park, Jaehoon An, Jungsoo Gim, Minseok Seo, Woojoo Lee, Taesung Park and Sungho Won

    Citation: BMC Genomics 2019 20:540

    Content type: Methodology article

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  41. Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miR...

    Authors: Rui Wang, Zhongyi Yang, Yuhan Fei, Jiejie Feng, Hui Zhu, Fang Huang, Hongsheng Zhang and Ji Huang

    Citation: BMC Genomics 2019 20:534

    Content type: Methodology article

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  42. Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related dise...

    Authors: Fernando Carazo, Marian Gimeno, Juan A. Ferrer-Bonsoms and Angel Rubio

    Citation: BMC Genomics 2019 20:521

    Content type: Research article

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  43. The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed...

    Authors: Danielly Beraldo dos Santos Silva, Larissa Fernanda Simielli Fonseca, Daniel Guariz Pinheiro, Maria Malane Magalhães Muniz, Ana Fabrícia Braga Magalhães, Fernando Baldi, Jesus Aparecido Ferro, Luis Artur Loyola Chardulo and Lucia Galvão de Albuquerque

    Citation: BMC Genomics 2019 20:520

    Content type: Research article

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