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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. Content type: Software

    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

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  2. Content type: Software

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Methodology article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Methodology article

    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

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  11. Content type: Methodology article

    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

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  12. Content type: Methodology article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Methodology article

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Software

    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

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  23. Content type: Methodology article

    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

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  24. Content type: Methodology article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Methodology article

    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

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  28. Content type: Methodology article

    RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The ...

    Authors: Alberto Berral-Gonzalez, Angela L. Riffo-Campos and Guillermo Ayala

    Citation: BMC Genomics 2019 20:259

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  29. Content type: Research article

    Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, whic...

    Authors: Shuonan Duan, Binhui Liu, Yuanyuan Zhang, Guoliang Li and Xiulin Guo

    Citation: BMC Genomics 2019 20:257

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  30. Content type: Software

    The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two fi...

    Authors: Mathieu Bahin, Benoit F. Noël, Valentine Murigneux, Charles Bernard, Leila Bastianelli, Hervé Le Hir, Alice Lebreton and Auguste Genovesio

    Citation: BMC Genomics 2019 20:250

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  31. Content type: Methodology article

    Epigenetic dysregulation is involved in the etiology and progression of various human diseases. Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and ...

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

    Citation: BMC Genomics 2019 20:249

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  32. Content type: Research article

    Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on t...

    Authors: Annageldi Tayyrov, Claire E. Stanley, Sophie Azevedo and Markus Künzler

    Citation: BMC Genomics 2019 20:243

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  33. Content type: Methodology article

    Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield...

    Authors: Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Frank Speleman and Kaat Durinck

    Citation: BMC Genomics 2019 20:228

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  34. Content type: Research article

    Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability ...

    Authors: Shan-Shan Zhou, Zhen Xing, Hui Liu, Xian-Ge Hu, Qiong Gao, Jie Xu, Si-Qian Jiao, Kai-Hua Jia, Yu Qing Jin, Wei Zhao, Ilga Porth, Yousry A. El-Kassaby and Jian-Feng Mao

    Citation: BMC Genomics 2019 20:213

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  35. Content type: Research article

    Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell pop...

    Authors: H. L. Smith, A. Stevens, B. Minogue, S. Sneddon, L. Shaw, L. Wood, T. Adeniyi, H. Xiao, P. Lio, S. J. Kimber and D. R. Brison

    Citation: BMC Genomics 2019 20:171

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  36. Content type: Research article

    Microglia are multifunctional cells that are key players in brain development and homeostasis. Recent years have seen tremendous growth in our understanding of the role microglia play in neurodegeneration, CNS...

    Authors: Christine E. Cho, Sagar S. Damle, Edward V. Wancewicz, Swagatam Mukhopadhyay, Christopher E. Hart, Curt Mazur, Eric E. Swayze and Fredrik Kamme

    Citation: BMC Genomics 2019 20:164

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  37. Content type: Methodology article

    Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expressi...

    Authors: Xue Qing David Wang, Christopher J. F. Cameron, Denis Paquette, Dana Segal, Reid Warsaba, Mathieu Blanchette and Josée Dostie

    Citation: BMC Genomics 2019 20:162

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  38. Content type: Methodology article

    Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means o...

    Authors: Yun Zhao, Ke Wang, Wen-li Wang, Ting-ting Yin, Wei-qi Dong and Chang-jie Xu

    Citation: BMC Genomics 2019 20:160

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  39. Content type: Research article

    Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity...

    Authors: Xiaoling Zhang, Yanli Wang, Yuanyuan Yan, Hua Peng, Yun Long, Yinchao Zhang, Zhou Jiang, Peng Liu, Chaoying Zou, Huanwei Peng, Guangtang Pan and Yaou Shen

    Citation: BMC Genomics 2019 20:159

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  40. Content type: Research article

    Identifying mRNA targets of miRNAs is critical for studying gene expression regulation at the whole-genome level. Multiple computational tools have been developed to predict miRNA:mRNA interactions. Nonetheles...

    Authors: Bi Zhao and Bin Xue

    Citation: BMC Genomics 2019 20:158

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  41. Content type: Research article

    Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and co...

    Authors: Adrian C. Paskey, Kenneth G. Frey, Gary Schroth, Stephen Gross, Theron Hamilton and Kimberly A. Bishop-Lilly

    Citation: BMC Genomics 2019 20:155

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  42. Content type: Research article

    Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on...

    Authors: Bharat Bhusan Patnaik, Jong Min Chung, Hee Ju Hwang, Min Kyu Sang, Jie Eun Park, Hye Rin Min, Hang Chul Cho, Neha Dewangan, Snigdha Baliarsingh, Se Won Kang, So Young Park, Yong Hun Jo, Hong Seog Park, Wan Jong Kim, Yeon Soo Han, Jun Sang Lee…

    Citation: BMC Genomics 2019 20:154

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  43. Content type: Methodology article

    Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA’s functional versatility includes epigenetic modification, nuclear domain organization, transcriptional c...

    Authors: Sarah C. Pyfrom, Hong Luo and Jacqueline E. Payton

    Citation: BMC Genomics 2019 20:137

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  44. Content type: Research article

    Methanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newl...

    Authors: Anh Duc Nguyen, Donghyuk Kim and Eun Yeol Lee

    Citation: BMC Genomics 2019 20:130

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  45. Content type: Research article

    Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation,...

    Authors: Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny and Krzysztof Fujarewicz

    Citation: BMC Genomics 2019 20:114

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