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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: 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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  2. 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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  3. 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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  4. Content type: Methodology article

    Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data fr...

    Authors: Wenbin Ye, Yuqi Long, Guoli Ji, Yaru Su, Pengchao Ye, Hongjuan Fu and Xiaohui Wu

    Citation: BMC Genomics 2019 20:75

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  5. Content type: Research article

    Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and acceler...

    Authors: Chen Huang, Dongliang Leng, Shixue Sun and Xiaohua Douglas Zhang

    Citation: BMC Genomics 2019 20:48

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  6. Content type: Research article

    Transcription factors (TFs) specifically bind to DNA sequences and control the expression of target genes. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamento...

    Authors: Hiroya Oka, Takaaki Kojima, Kunio Ihara, Tetsuo Kobayashi and Hideo Nakano

    Citation: BMC Genomics 2019 20:16

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  7. Content type: Research article

    3’ RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and...

    Authors: Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis and Matteo Pellegrini

    Citation: BMC Genomics 2019 20:9

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  8. Content type: Software

    Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by...

    Authors: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore and Manuel Garber

    Citation: BMC Genomics 2019 20:6

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  9. Content type: Research article

    MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in the regulation of gene expression. However, the role of miRNAs in bovine mammary gland responses to heat stress is not well u...

    Authors: Qiuling Li, Chunhong Yang, Juan Du, Baogui Zhang, Ying He, Qimeng Hu, Meiru Li, Yiming Zhang, Changfa Wang and Jifeng Zhong

    Citation: BMC Genomics 2018 19:975

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  10. Content type: Software

    New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina libr...

    Authors: Dario Romagnoli, Giulia Boccalini, Martina Bonechi, Chiara Biagioni, Paola Fassan, Roberto Bertorelli, Veronica De Sanctis, Angelo Di Leo, Ilenia Migliaccio, Luca Malorni and Matteo Benelli

    Citation: BMC Genomics 2018 19:960

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  11. Content type: Methodology article

    When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and resea...

    Authors: John R. Stevens, Jennifer S. Herrick, Roger K. Wolff and Martha L. Slattery

    Citation: BMC Genomics 2018 19:953

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  12. Content type: Research article

    Peanut is the world’s fourth largest oilseed crop that exhibits wide cultivar variations in cadmium (Cd) accumulation. To establish the mechanisms of Cd distribution and accumulation in peanut plants, eight cD...

    Authors: Rugang Yu, Yuanyuan Ma, Yue Li, Xin Li, Caifeng Liu, Xueling Du and Gangrong Shi

    Citation: BMC Genomics 2018 19:938

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  13. Content type: Research article

    The Pacific abalone, Haliotis discus hannai, is the most important cultivated abalone in China. Improving abalone muscle growth and increasing the rate of growth are important genetic improvement programs in this...

    Authors: Jianfang Huang, Xuan Luo, Miaoqin Huang, Guangmou Liu, Weiwei You and Caihuan Ke

    Citation: BMC Genomics 2018 19:915

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  14. Content type: Research article

    Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide app...

    Authors: Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecilia Maria Arraiano and Muriel Cocaign-Bousquet

    Citation: BMC Genomics 2018 19:848

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  15. Content type: Methodology article

    Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or tumor grade. Low-coverage sequencing for reporting ...

    Authors: Sangdi Lin, Chen Wang, Shabnam Zarei, Debra A. Bell, Sarah E. Kerr, George C. Runger and Jean-Pierre A. Kocher

    Citation: BMC Genomics 2018 19:841

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  16. Content type: Research article

    Antimicrobial peptides (AMPs) are multifunctional effector molecules that often combine direct antimicrobial activities with signaling or immunomodulatory functions. The skin secretions of anurans contain a va...

    Authors: Tomislav Rončević, Marco Gerdol, Francesca Spazzali, Fiorella Florian, Stjepan Mekinić, Alessandro Tossi and Alberto Pallavicini

    Citation: BMC Genomics 2018 19:827

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  17. Content type: Software

    Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, ...

    Authors: Amanda W. Ernlund, Robert J. Schneider and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:809

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  18. Content type: Research article

    Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of th...

    Authors: Luyun Ning, Zhiwei Lin, Jianwei Gu, Lu Gan, Yonghong Li, Hao Wang, Liyun Miao, Libin Zhang, Baoshan Wang and Maoteng Li

    Citation: BMC Genomics 2018 19:806

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  19. Content type: Methodology article

    Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count dat...

    Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli and Héctor Corrada Bravo

    Citation: BMC Genomics 2018 19:799

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  20. Content type: Methodology article

    Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover...

    Authors: Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang and Yudi Pawitan

    Citation: BMC Genomics 2018 19:786

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  21. Content type: Research article

    Transmissible gastroenteritis virus (TGEV) infection can activate NF-κB pathway in porcine intestinal epithelial cells and result in severe inflammation. Non-coding RNAs (ncRNAs) are not translated into protei...

    Authors: Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang and Dewen Tong

    Citation: BMC Genomics 2018 19:747

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  22. Content type: Research article

    Gray leaf spot (GLS), which is caused by the necrotrophic fungi Cercospora zeae-maydis and Cercospora zeina, is one of the most impactful diseases in maize worldwide. The aim of the present study is to identify t...

    Authors: Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Haichun Shi, Yongpei Ke and Qun Sun

    Citation: BMC Genomics 2018 19:742

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  23. Content type: Research article

    Transcription factors are essential regulators of gene expression and play critical roles in development, differentiation, and in many cancers. To carry out their regulatory programs, they must cooperate in ne...

    Authors: Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo and Kevin R. Coombes

    Citation: BMC Genomics 2018 19:738

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  24. Content type: Research article

    Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and ...

    Authors: Yuan Li, Rong-Hong Li, Ming-Xia Ran, Yan Zhang, Kai Liang, Ying-Nan Ren, Wen-Cheng He, Ming Zhang, Guang-Bin Zhou, Izhar Hyder Qazi and Chang-Jun Zeng

    Citation: BMC Genomics 2018 19:736

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  25. Content type: Research article

    RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to spl...

    Authors: Juan P. Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pío, Matthew W. B. Trotter and Angel Rubio

    Citation: BMC Genomics 2018 19:703

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  26. Content type: Research article

    Cell type-specific ribosome-pulldown has become an increasingly popular method for analysis of gene expression. It allows for expression analysis from intact tissues and monitoring of protein synthesis in vivo...

    Authors: Yang Song, Beatrice Milon, Sandra Ott, Xuechu Zhao, Lisa Sadzewicz, Amol Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar and Ronna Hertzano

    Citation: BMC Genomics 2018 19:696

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  27. Content type: Research article

    The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during co...

    Authors: Maria Ballester, Marcel Amills, Olga González-Rodríguez, Tainã F. Cardoso, Mariam Pascual, Rayner González-Prendes, Núria Panella-Riera, Isabel Díaz, Joan Tibau and Raquel Quintanilla

    Citation: BMC Genomics 2018 19:682

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  28. Content type: Software

    The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity g...

    Authors: Seokhyun Yoon, Daeseung Kim, Keunsoo Kang and Woong June Park

    Citation: BMC Genomics 2018 19:653

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  29. Content type: Research article

    Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a widely cultivated medicinal and edible crop with excellent economic and nutritional value. The development of tartary buckwheat seeds is a very complex process...

    Authors: Moyang Liu, Zhaotang Ma, Tianrun Zheng, Wenjun Sun, Yanjun Zhang, Weiqiong Jin, Junyi Zhan, Yuntao Cai, Yujia Tang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2018 19:648

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  30. Content type: Database

    The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology w...

    Authors: Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman and Stephan Q. Schneider

    Citation: BMC Genomics 2018 19:618

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  31. Content type: Research article

    Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to n...

    Authors: Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang and Ming Chen

    Citation: BMC Genomics 2018 19:607

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  32. Content type: Methodology article

    The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression ...

    Authors: Stephen J. Bush, Lucy Freem, Amanda J. MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers and David A. Hume

    Citation: BMC Genomics 2018 19:594

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  33. Content type: Research article

    Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating an...

    Authors: C. Llorens, S. C. Arcos, L. Robertson, R. Ramos, R. Futami, B. Soriano, S. Ciordia, M. Careche, M. González-Muñoz, Y. Jiménez-Ruiz, N. Carballeda-Sangiao, I. Moneo, J. P. Albar, M. Blaxter and A. Navas

    Citation: BMC Genomics 2018 19:592

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  34. Content type: Research article

    The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflo...

    Authors: Jiang Chen, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yiyun Wu, Qinghua Wu and Jin Pei

    Citation: BMC Genomics 2018 19:548

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  35. Content type: Research article

    Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and im...

    Authors: Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds and Inanc Birol

    Citation: BMC Genomics 2018 19:536

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  36. Content type: Methodology article

    RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting materi...

    Authors: Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore and Zhiping Weng

    Citation: BMC Genomics 2018 19:531

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  37. Content type: Research article

    Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based...

    Authors: Robin Kosch, Julien Delarocque, Peter Claus, Stefanie C. Becker and Klaus Jung

    Citation: BMC Genomics 2018 19:530

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  38. Content type: Research article

    The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, a...

    Authors: Lixiao Du, Xincheng Zhao, Xiangzhi Liang, Xiwu Gao, Yang Liu and Guirong Wang

    Citation: BMC Genomics 2018 19:518

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  39. Content type: Research article

    Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify small RNAs as a...

    Authors: Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz and Claus O. Wilke

    Citation: BMC Genomics 2018 19:510

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  40. Content type: Methodology article

    Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipoten...

    Authors: Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom and Sandrine Dudoit

    Citation: BMC Genomics 2018 19:477

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  41. Content type: Research article

    Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynogloss...

    Authors: Yufeng Si, Haishen Wen, Yun Li, Feng He, Jifang Li, Siping Li and Huiwen He

    Citation: BMC Genomics 2018 19:464

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  42. Content type: Software

    Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methyla...

    Authors: Julien Richard Albert, Tasuku Koike, Hamid Younesy, Richard Thompson, Aaron B. Bogutz, Mohammad M. Karimi and Matthew C. Lorincz

    Citation: BMC Genomics 2018 19:463

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  43. Content type: Research article

    Iron (Fe) is an essential micronutrient for plants. Utilization of Fe deficiency-tolerant rootstock is an effective strategy to prevent Fe deficiency problems in fruit trees production. Malus halliana is an apple...

    Authors: Yan-xiu Wang, Ya Hu, Yan-fang Zhu, Abdul Wahid Baloch, Xu-mei Jia and Ai-xia Guo

    Citation: BMC Genomics 2018 19:461

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