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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. Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcri...

    Authors: Reema Singh, Hajara M. Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J. Barton, Pauline Schaap and Christian Cole

    Citation: BMC Genomics 2017 18:120

    Content type: Research article

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  2. Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play importan...

    Authors: Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang and Cunshuan Xu

    Citation: BMC Genomics 2017 18:80

    Content type: Research Article

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  3. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute le...

    Authors: Stephenie D. Prokopec, Kathleen E. Houlahan, Ren X. Sun, John D. Watson, Cindy Q. Yao, Jamie Lee, Christine P’ng, Renee Pang, Alexander H. Wu, Lauren C. Chong, Ashley B. Smith, Nicholas J. Harding, Ivy D. Moffat, Jere Lindén, Sanna Lensu, Allan B. Okey…

    Citation: BMC Genomics 2017 18:78

    Content type: Software

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  4. Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mamma...

    Authors: Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Chun-Chi Liu and Jeremy J.W. Chen

    Citation: BMC Genomics 2017 18:61

    Content type: Methodology article

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  5. Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties...

    Authors: Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee and Laiq ur Rahman

    Citation: BMC Genomics 2017 18:54

    Content type: Research

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  6. Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome’s limitations in describing higher functional phenotypes and protein events. Perhaps the mos...

    Authors: Quin F. Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes…

    Citation: BMC Genomics 2017 18:53

    Content type: Methodology article

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  7. The GII.4 Sydney 2012 strain of human norovirus (HuNoV) is a pandemic strain that is responsible for the majority of norovirus outbreaks in healthcare settings. The function of the non-structural (NS)1-2 prote...

    Authors: Zabeen Lateef, Gregory Gimenez, Estelle S. Baker and Vernon K. Ward

    Citation: BMC Genomics 2017 18:39

    Content type: Research Article

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  8. The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging insect pest of corn in Asia. However, the lack of genome or transcriptome information heavily hinders our further understandi...

    Authors: Li Cui, Changhui Rui, Daibin Yang, Zhenying Wang and Huizhu Yuan

    Citation: BMC Genomics 2017 18:20

    Content type: Research Article

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  9. Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or ...

    Authors: Bernardo Rodríguez-Martín, Emilio Palumbo, Santiago Marco-Sola, Thasso Griebel, Paolo Ribeca, Graciela Alonso, Alberto Rastrojo, Begoña Aguado, Roderic Guigó and Sarah Djebali

    Citation: BMC Genomics 2017 18:7

    Content type: Methodology Article

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  10. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed process.

    Authors: Qianglong Zhu, Peng Gao, Shi Liu, Zicheng Zhu, Sikandar Amanullah, Angela R. Davis and Feishi Luan

    Citation: BMC Genomics 2017 18:3

    Content type: Research Article

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  11. Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of sin...

    Authors: Hannah R. Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian-Bing Fan, Stephen A. Fisher, Jennifer S. Herstein, Tae Kyung Kim, Jae Mun (Hugo) Kim, Ming-Yi Lin, Rui Liu, William J. Mack, Sean McGroty, Joseph D. Nguyen…

    Citation: BMC Genomics 2016 17:966

    Content type: Research article

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  12. The fight against grapevine diseases due to biotrophic pathogens usually requires the massive use of chemical fungicides with harmful environmental effects. An alternative strategy could be the use of compound...

    Authors: Marie-Cécile Dufour, Noël Magnin, Bernard Dumas, Sophie Vergnes and Marie-France Corio-Costet

    Citation: BMC Genomics 2016 17:957

    Content type: Research article

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  13. Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal fo...

    Authors: A. L. De Oliveira, T. Wollesen, A. Kristof, M. Scherholz, E. Redl, C. Todt, C. Bleidorn and A. Wanninger

    Citation: BMC Genomics 2016 17:905

    Content type: Research article

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  14. Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and...

    Authors: Daisuke Komura, Takayuki Isagawa, Kazuki Kishi, Ryohei Suzuki, Reiko Sato, Mariko Tanaka, Hiroto Katoh, Shogo Yamamoto, Kenji Tatsuno, Masashi Fukayama, Hiroyuki Aburatani and Shumpei Ishikawa

    Citation: BMC Genomics 2016 17:899

    Content type: Methodology article

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  15. Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps...

    Authors: Julien Prados, Patrick Linder and Peter Redder

    Citation: BMC Genomics 2016 17:849

    Content type: Methodology article

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  16. RNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can caus...

    Authors: Jaime I. Davila, Numrah M. Fadra, Xiaoke Wang, Amber M. McDonald, Asha A. Nair, Barbara, R. Crusan, Xianglin Wu, Joseph H. Blommel, Jin Jen, Kandelaria M. Rumilla, Robert B. Jenkins, Umut Aypar, Eric W. Klee, Benjamin R. Kipp and Kevin C. Halling

    Citation: BMC Genomics 2016 17:814

    Content type: Research article

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  17. MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known...

    Authors: Christian Wake, Adam Labadorf, Alexandra Dumitriu, Andrew G. Hoss, Joli Bregu, Kenneth H. Albrecht, Anita L. DeStefano and Richard H. Myers

    Citation: BMC Genomics 2016 17:776

    Content type: Research article

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  18. Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data ana...

    Authors: Weizhong Li, R. Alexander Richter, Yunsup Jung, Qiyun Zhu and Robert W. Li

    Citation: BMC Genomics 2016 17:761

    Content type: Software

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  19. The motif ACTAYRNNNCCCR (Y being C or T, R being A or G, and N any nucleotide), called M4, was discovered as a putative cis-regulatory element, present 520 times in human promoter regions. Of these, 317 (61 %)...

    Authors: Ngo Tat Trung, Elisabeth Kremmer and Gerhard Mittler

    Citation: BMC Genomics 2016 17:693

    Content type: Research article

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  20. Long non-coding RNAs (lncRNAs) have been studied extensively over the past few years. Large numbers of lncRNAs have been identified in mouse, rat, and human, and some of them have been shown to play important ...

    Authors: Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li and Hongping Zhang

    Citation: BMC Genomics 2016 17:666

    Content type: Research article

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  21. A combined supplement of vitamins B9 and B12 was reported to increase milk and milk component yields of dairy cows without effect on feed intake. The present study was undertaken to verify whether this supplem...

    Authors: Bazoumana Ouattara, Nathalie Bissonnette, Melissa Duplessis and Christiane L. Girard

    Citation: BMC Genomics 2016 17:640

    Content type: Research article

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  22. The selection of suitable internal control genes is crucial for proper interpretation of real-time PCR data. Here we outline a strategy to identify housekeeping genes that could serve as suitable internal cont...

    Authors: Tatiana M. Tilli, Cláudio da Silva Castro, Jack A. Tuszynski and Nicolas Carels

    Citation: BMC Genomics 2016 17:639

    Content type: Research article

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  23. ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution...

    Authors: Gergely Nagy, Erik Czipa, László Steiner, Tibor Nagy, Sándor Pongor, László Nagy and Endre Barta

    Citation: BMC Genomics 2016 17:637

    Content type: Research article

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  24. Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors ...

    Authors: Chia-Chun Yang, Erik H. Andrews, Min-Hsuan Chen, Wan-Yu Wang, Jeremy J. W. Chen, Mark Gerstein, Chun-Chi Liu and Chao Cheng

    Citation: BMC Genomics 2016 17:632

    Content type: Database

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  25. Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete cha...

    Authors: Tsviya Olender, Ifat Keydar, Jayant M. Pinto, Pavlo Tatarskyy, Anna Alkelai, Ming-Shan Chien, Simon Fishilevich, Diego Restrepo, Hiroaki Matsunami, Yoav Gilad and Doron Lancet

    Citation: BMC Genomics 2016 17:619

    Content type: Research article

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  26. Fusarium fujikuroi is the causal agent of bakanae, the most significant seed-borne disease of rice. Molecular mechanisms regulating defence responses of rice towards this fungus are no...

    Authors: Slavica Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orru’, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valé, Maria Lodovica Gullino and Davide Spadaro

    Citation: BMC Genomics 2016 17:608

    Content type: Research article

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  27. Peanut zygotes typically divide a few times to form a pre-embryo before further embryonic development halts under normal day/night photoperiods. Ovary elongation, however, continuesforming a downward growing p...

    Authors: Ye Zhang, Pengfei Wang, Han Xia, Chuanzhi Zhao, Lei Hou, Changsheng Li, Chao Gao, Shuzhen Zhao and Xingjun Wang

    Citation: BMC Genomics 2016 17:606

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2016 17:836

  28. The RNA-seq technique is applied for the investigation of transcriptional behaviour. The reduction in sequencing costs has led to an unprecedented trove of gene expression data from diverse biological systems....

    Authors: Deepak Karthik, Gil Stelzer, Sivan Gershanov, Danny Baranes and Mali Salmon-Divon

    Citation: BMC Genomics 2016 17:595

    Content type: Research article

    Published on:

  29. The giant freshwater prawn, Macrobrachium rosenbergii, is a decapod crustacean that is commercially important as a food source. Farming of commercial crustaceans requires an efficient management strategy because ...

    Authors: Saowaros Suwansa-ard, Wilairat Kankuan, Tipsuda Thongbuakaew, Jirawat Saetan, Napamanee Kornthong, Thanapong Kruangkum, Kanjana Khornchatri, Scott F. Cummins, Ciro Isidoro and Prasert Sobhon

    Citation: BMC Genomics 2016 17:587

    Content type: Research article

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  30. Alternative splicing (AS) is a major source of variability in the transcriptome of eukaryotes. There is an increasing interest in its role in different pathologies. Before sequencing technology appeared, AS wa...

    Authors: Juan P. Romero, Ander Muniategui, Fernando J. De Miguel, Ander Aramburu, Luis Montuenga, Ruben Pio and Angel Rubio

    Citation: BMC Genomics 2016 17:467

    Content type: Methodology article

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  31. Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although impr...

    Authors: Zhilong Jia, Ying Liu, Naiyang Guan, Xiaochen Bo, Zhigang Luo and Michael R. Barnes

    Citation: BMC Genomics 2016 17:414

    Content type: Software

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  32. RNA-seq based on short reads generated by next generation sequencing technologies has become the main approach to study differential gene expression. Until now, the main applications of this technique have bee...

    Authors: Montserrat Torres-Oliva, Isabel Almudi, Alistair P. McGregor and Nico Posnien

    Citation: BMC Genomics 2016 17:392

    Content type: Methodology article

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  33. Mammalian genomes encode for thousands of microRNAs, which can potentially regulate the majority of protein-coding genes. They have been implicated in development and disease, leading to great interest in unde...

    Authors: Cesaré Ovando-Vázquez, Daniel Lepe-Soltero and Cei Abreu-Goodger

    Citation: BMC Genomics 2016 17:364

    Content type: Methodology article

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  34. Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis. Single-cell analysis tools such as FACS, FISH-F...

    Authors: Maurizio Pellegrino, Adam Sciambi, Jamie L. Yates, Joshua D. Mast, Charles Silver and Dennis J. Eastburn

    Citation: BMC Genomics 2016 17:361

    Content type: Methodology article

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  35. Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots ...

    Authors: Yun Ji Park, Xiaohua Li, Seung Jae Noh, Jae Kwang Kim, Soon Sung Lim, Nam Il Park, Soonok Kim, Yeon Bok Kim, Young Ock Kim, Sang Won Lee, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park

    Citation: BMC Genomics 2016 17:303

    Content type: Research article

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  36. It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive mod...

    Authors: Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert C. Wilson, Chadrick E. Denlinger, Dennis K. Watson and Paul E. Anderson

    Citation: BMC Genomics 2016 17:263

    Content type: Research Article

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  37. We have previously found substantial animal-to-animal and age-dependent variation in the response of Holstein fibroblast cultures challenged with LPS. To expand on this finding, fibroblast cultures were establ...

    Authors: Aimee L. Benjamin, Benjamin B. Green, Brian A. Crooker, Stephanie D. McKay and David E. Kerr

    Citation: BMC Genomics 2016 17:258

    Content type: Research article

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  38. Inference of gene regulation from expression data may help to unravel regulatory mechanisms involved in complex diseases or in the action of specific drugs. A challenging task for many researchers working in t...

    Authors: Angela Grassi, Barbara Di Camillo, Francesco Ciccarese, Valentina Agnusdei, Paola Zanovello, Alberto Amadori, Lorenzo Finesso, Stefano Indraccolo and Gianna Maria Toffolo

    Citation: BMC Genomics 2016 17:228

    Content type: Research article

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  39. Chlamydomonas reinhardtii is the model organism that serves as a reference for studies in algal genomics and physiology. It is of special interest in the study of the evolution of regu...

    Authors: Francisco J. Romero-Campero, Ignacio Perez-Hurtado, Eva Lucas-Reina, Jose M. Romero and Federico Valverde

    Citation: BMC Genomics 2016 17:227

    Content type: Research article

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  40. Recent advances in sequencing technology have opened a new era in RNA studies. Novel types of RNAs such as long non-coding RNAs (lncRNAs) have been discovered by transcriptomic sequencing and some lncRNAs have...

    Authors: Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-An Tung, Kwei-Yan Liu, Hsueh-Tzu Shih, Yi-Jyun Chen, Yan-Liang Lin, Li-Ting Ma, Jian-Long Huang, Po-Chun Wu, Ming-Yi Hong, Fang-Hua Chu, June-Tai Wu…

    Citation: BMC Genomics 2016 17:220

    Content type: Research 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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