Skip to main content

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.

Page 1 of 12

  1. The behavior of cells in vivo is complex and highly dynamic, as it results from an interplay between intercellular matrix proteins with surface receptors and other microenvironmental cues. Although the effects...

    Authors: Souvik Ghosh, Anastasiya Börsch, Shreemoyee Ghosh and Mihaela Zavolan

    Citation: BMC Genomics 2021 22:238

    Content type: Research article

    Published on:

  2. Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set o...

    Authors: Peter D. Karp, Peter E. Midford, Ron Caspi and Arkady Khodursky

    Citation: BMC Genomics 2021 22:191

    Content type: Research article

    Published on:

  3. Despite the increasing use of RNAseq for transcriptome analysis, microarrays remain a widely-used methodology for genomic studies. The latest generation of Affymetrix/Thermo-Fisher microarrays, the ClariomD/XT...

    Authors: Guy M. Harris, Shahroze Abbas and Michael F. Miles

    Citation: BMC Genomics 2021 22:96

    Content type: Software

    Published on:

  4. Co-localized combinations of histone modifications (“chromatin states”) have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points (“chromatin state...

    Authors: Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander and Uwe Ohler

    Citation: BMC Genomics 2021 22:84

    Content type: Methodology article

    Published on:

  5. Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to f...

    Authors: Benjamin P. Kellman, Hratch M. Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne and Nathan E. Lewis

    Citation: BMC Genomics 2021 22:69

    Content type: Research article

    Published on:

  6. Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. ...

    Authors: Tracy M. Yamawaki, Daniel R. Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang and Chi-Ming Li

    Citation: BMC Genomics 2021 22:66

    Content type: Research article

    Published on:

  7. Biological functions of biomolecules rely on the cellular compartments where they are located in cells. Importantly, RNAs are assigned in specific locations of a cell, enabling the cell to implement diverse bi...

    Authors: Hao Wang, Yijie Ding, Jijun Tang, Quan Zou and Fei Guo

    Citation: BMC Genomics 2021 22:56

    Content type: Methodology article

    Published on:

  8. The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act a...

    Authors: Nonno Hasegawa, Maeva Techer and Alexander S. Mikheyev

    Citation: BMC Genomics 2021 22:54

    Content type: Methodology article

    Published on:

  9. Single-cell RNA-Sequencing (scRNA-Seq) has provided single-cell level insights into complex biological processes. However, the high frequency of gene expression detection failures in scRNA-Seq data make it cha...

    Authors: Tao Cui and Tingting Wang

    Citation: BMC Genomics 2021 22:47

    Content type: Methodology article

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:223

  10. The major pathogenesis associated with Fasciola hepatica infection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and deve...

    Authors: Krystyna Cwiklinski, Mark W. Robinson, Sheila Donnelly and John P. Dalton

    Citation: BMC Genomics 2021 22:46

    Content type: Research article

    Published on:

  11. Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we ...

    Authors: Hongyu Liu, N. M. Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova and Anelia Horvath

    Citation: BMC Genomics 2021 22:40

    Content type: Methodology article

    Published on:

  12. Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progress...

    Authors: Yao Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu and Haiyun Wang

    Citation: BMC Genomics 2021 22:27

    Content type: Research article

    Published on:

  13. Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complex...

    Authors: Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac Neuhaus, Alice M. Walsh and Zachary W. Pitluk

    Citation: BMC Genomics 2021 22:5

    Content type: Database

    Published on:

  14. There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 8...

    Authors: Jin Sung Jang, Brianna Berg, Eileen Holicky, Bruce Eckloff, Mark Mutawe, Minerva M. Carrasquillo, Nilüfer Ertekin-Taner and Julie M. Cuninngham

    Citation: BMC Genomics 2020 21:890

    Content type: Methodology article

    Published on:

  15. Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current hig...

    Authors: Chentao Yang, Yuxuan Zheng, Shangjin Tan, Guanliang Meng, Wei Rao, Caiqing Yang, David G. Bourne, Paul A. O’Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-bing Zhang and Shanlin Liu

    Citation: BMC Genomics 2020 21:862

    Content type: Methodology article

    Published on:

  16. As a heavy metal, manganese (Mn) can be toxic to plants. Stylo (Stylosanthes) is an important tropical legume that exhibits tolerance to high levels of Mn. However, little is known about the adaptive responses of...

    Authors: Yidan Jia, Xinyong Li, Qin Liu, Xuan Hu, Jifu Li, Rongshu Dong, Pandao Liu, Guodao Liu, Lijuan Luo and Zhijian Chen

    Citation: BMC Genomics 2020 21:861

    Content type: Research article

    Published on:

  17. Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impac...

    Authors: Xiaofei Yang, Shenghan Gao, Tingjie Wang, Boyu Yang, Ningxin Dang and Kai Ye

    Citation: BMC Genomics 2020 21:823

    Content type: Methodology article

    Published on:

  18. Cytoplasmic male sterility (CMS) is very important in hybrid breeding. The restorer-of-fertility (Rf) nuclear genes rescue the sterile phenotype. Most of the Rf genes encode pentatricopeptide repeat (PPR) protein...

    Authors: Luyun Ning, Hao Wang, Dianrong Li, Yonghong Li, Kang Chen, Hongbo Chao, Huaixin Li, Jianjie He and Maoteng Li

    Citation: BMC Genomics 2020 21:765

    Content type: Research article

    Published on:

  19. The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein codi...

    Authors: Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald and David W. Burt

    Citation: BMC Genomics 2020 21:751

    Content type: Research article

    Published on:

  20. Early diagnosis is crucial for effective medical management of cancer patients. Tissue biopsy has been widely used for cancer diagnosis, but its invasive nature limits its application, especially when repeated...

    Authors: Chitrita Goswami, Smriti Chawla, Deepshi Thakral, Himanshu Pant, Pramod Verma, Prabhat Singh Malik, Jayadeva, Ritu Gupta, Gaurav Ahuja and Debarka Sengupta

    Citation: BMC Genomics 2020 21:744

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:877

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

Annual Journal Metrics

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.

\