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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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

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  13. 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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  14. 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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  15. 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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  16. 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

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  17. 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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  18. 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

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  19. 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

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  20. 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

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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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

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  27. 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:

  28. 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

    Published on:

  29. 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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  30. 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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  31. 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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  32. 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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  33. RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapt...

    Authors: Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger and Joo Heon Shin

    Citation: BMC Genomics 2019 20:513

    Content type: Methodology article

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  34. Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a nov...

    Authors: Kevin Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, Daniel W. Lambert, Stephen Brown and James R. Bradford

    Citation: BMC Genomics 2019 20:454

    Content type: Research article

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  35. Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expressio...

    Authors: Ryan K.Y. Wong, Meabh MacMahon, Jayne V. Woodside and David A. Simpson

    Citation: BMC Genomics 2019 20:446

    Content type: Research article

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  36. Alternative splicing (AS) is a regulatory mechanism used to create many forms of mature messengers RNAs (mRNAs) from the same gene. Sequencing of RNA (RNA-Seq) is an advanced technology, which has been utilized b...

    Authors: Vishwas Sharma, Amrita Nandan, Harpreet Singh, Suyash Agarwal, Richa Tripathi, Dhirendra Narain Sinha and Ravi Mehrotra

    Citation: BMC Genomics 2019 20:442

    Content type: Research article

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  37. In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global tra...

    Authors: Johanna Brodhagen, Rosemarie Weikard, Ulrike Thom, Annika Heimes, Juliane Günther, Frieder Hadlich, Holm Zerbe, Wolfgang Petzl, Marie M. Meyerholz, Martina Hoedemaker, Hans-Joachim Schuberth, Susanne Engelmann and Christa Kühn

    Citation: BMC Genomics 2019 20:400

    Content type: Research article

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  38. Phenotypic plasticity is a common and highly adaptive phenomenon where the same genotype produces different phenotypes in response to environmental cues. Sogatella furcifera, a migratory pest of rice exhibits win...

    Authors: Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang and Qingfa Wu

    Citation: BMC Genomics 2019 20:396

    Content type: Research article

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  39. Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequ...

    Authors: Qiuyun Wu, Junwei Wang, Shuxiang Mao, Haoran Xu, Qi Wu, Mantian Liang, Yiming Yuan, Mingyue Liu and Ke Huang

    Citation: BMC Genomics 2019 20:377

    Content type: Research article

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  40. Data normalization and identification of significant differential expression represent crucial steps in RNA-Seq analysis. Many available tools rely on assumptions that are often not met by real data, including...

    Authors: Wentao Yang, Philip Rosenstiel and Hinrich Schulenburg

    Citation: BMC Genomics 2019 20:364

    Content type: Software

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  41. Gene-set analysis (GSA) has been commonly used to identify significantly altered pathways or functions from omics data. However, GSA often yields a long list of gene-sets, necessitating efficient post-processi...

    Authors: Sora Yoon, Jinhwan Kim, Seon-Kyu Kim, Bukyung Baik, Sang-Mun Chi, Seon-Young Kim and Dougu Nam

    Citation: BMC Genomics 2019 20:352

    Content type: Methodology article

    Published on:

  42. Single-cell RNA-sequencing (scRNA-seq) is fast becoming a powerful tool for profiling genome-scale transcriptomes of individual cells and capturing transcriptome-wide cell-to-cell variability. However, scRNA-s...

    Authors: Wenbin Ye, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yaru Su and Xiaohui Wu

    Citation: BMC Genomics 2019 20:347

    Content type: Methodology article

    Published on:

  43. Triploid coho salmon are excellent models for studying gene dosage and the effects of increased cell volume on gene expression. Triploids have an additional haploid genome in each cell and have fewer but large...

    Authors: Kris A. Christensen, Dionne Sakhrani, Eric B. Rondeau, Jeffery Richards, Ben F. Koop and Robert H. Devlin

    Citation: BMC Genomics 2019 20:336

    Content type: Research article

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  44. Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more tra...

    Authors: Mark Lammers, Ken Kraaijeveld, Janine Mariën and Jacintha Ellers

    Citation: BMC Genomics 2019 20:309

    Content type: Research article

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  45. Protein kinases are enzymes controlling different cellular functions. Genetic alterations often result in kinase dysregulation, making kinases a very attractive class of druggable targets in several human dise...

    Authors: Giovanni Carapezza, Carlo Cusi, Ettore Rizzo, Laura Raddrizzani, Sebastiano Di Bella, Alessio Somaschini, Antonella Leone, Rosita Lupi, Margherita Mutarelli, Vincenzo Nigro, Diego di Bernardo, Paolo Magni, Antonella Isacchi and Roberta Bosotti

    Citation: BMC Genomics 2019 20:307

    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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