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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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

  14. 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

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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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

    Published on:

  24. 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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  25. 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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  26. 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:

  27. Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previ...

    Authors: Ping Gong, Xiaofei Nan, Natalie D. Barker, Robert E. Boyd, Yixin Chen, Dawn E. Wilkins, David R. Johnson, Burton C. Suedel and Edward J. Perkins

    Citation: BMC Genomics 2016 17:205

    Content type: Methodology article

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  28. The initiating nucleotide found at the 5’ end of primary transcripts has a distinctive triphosphorylated end that distinguishes these transcripts from all other RNA species. Recognizing this distinction is key...

    Authors: Laurence Ettwiller, John Buswell, Erbay Yigit and Ira Schildkraut

    Citation: BMC Genomics 2016 17:199

    Content type: Methodology article

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  29. Rhizobium tropici strain CIAT 899 establishes effective symbioses with several legume species, including Phaseolus vulgaris and Leucaena leucocephala. This bacterium synthesizes a larg...

    Authors: Francisco Pérez-Montaño, Pablo del Cerro, Irene Jiménez-Guerrero, Francisco Javier López-Baena, Maria Teresa Cubo, Mariangela Hungria, Manuel Megías and Francisco Javier Ollero

    Citation: BMC Genomics 2016 17:198

    Content type: Research article

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  30. Low fertility remains a leading cause of poor productivity in dairy cattle. In this context, there is significant interest in developing novel tools for accurate early diagnosis of pregnancy. MicroRNAs (miRNAs...

    Authors: Jason Ioannidis and F. Xavier Donadeu

    Citation: BMC Genomics 2016 17:184

    Content type: Research article

    Published on:

  31. The formation of the pre-initiation complex in eukaryotic genes is a key step in transcription initiation. The TATA-binding protein (TBP) is a universal component of all pre-initiation complexes for all kinds ...

    Authors: Natalia Gómez-Navarro, Antonio Jordán-Pla, Francisco Estruch and José E. Pérez-Ortín

    Citation: BMC Genomics 2016 17:183

    Content type: Research article

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  32. Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach...

    Authors: Seth Raithel, Loretta Johnson, Matthew Galliart, Sue Brown, Jennifer Shelton, Nicolae Herndon and Nora M. Bello

    Citation: BMC Genomics 2016 17:140

    Content type: Research article

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  33. Alternative σ factors are important transcriptional regulators in bacteria. While σB has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria mo...

    Authors: Yichang Liu, Renato Hohl Orsi, Kathryn Jean Boor, Martin Wiedmann and Veronica Guariglia-Oropeza

    Citation: BMC Genomics 2016 17:115

    Content type: Research article

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  34. Dynamic transcriptional regulation is critical for an organism’s response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factor...

    Authors: Joan Doidy, Ying Li, Benjamin Neymotin, Molly B. Edwards, Kranthi Varala, David Gresham and Gloria M. Coruzzi

    Citation: BMC Genomics 2016 17:92

    Content type: Research article

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  35. A very large and rapidly growing collection of transcriptomic profiles in public repositories is potentially of great value to developing data-driven bioinformatics applications for toxicology/ecotoxicology. M...

    Authors: Rong-Lin Wang, Adam D. Biales, Natalia Garcia-Reyero, Edward J. Perkins, Daniel L. Villeneuve, Gerald T. Ankley and David C. Bencic

    Citation: BMC Genomics 2016 17:84

    Content type: Research article

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  36. Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by...

    Authors: Aaron R. Shifman, Radia M. Johnson and Brian T. Wilhelm

    Citation: BMC Genomics 2016 17:75

    Content type: Software

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  37. Identification of synthetic lethal interactions in cancer cells could offer promising new therapeutic targets. Large-scale functional genomic screening presents an opportunity to test large numbers of cancer s...

    Authors: Mark Wappett, Austin Dulak, Zheng Rong Yang, Abdullatif Al-Watban, James R. Bradford and Jonathan R. Dry

    Citation: BMC Genomics 2016 17:65

    Content type: Research article

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  38. Advances in second-generation sequencing of RNA made a near-complete characterization of transcriptomes affordable. However, the reconstruction of full-length mRNAs via de novo RNA-seq assembly is still diffic...

    Authors: Martin Bens, Arne Sahm, Marco Groth, Niels Jahn, Michaela Morhart, Susanne Holtze, Thomas B. Hildebrandt, Matthias Platzer and Karol Szafranski

    Citation: BMC Genomics 2016 17:54

    Content type: Software

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  39. Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer termina...

    Authors: Dmitry Velmeshev, Patrick Lally, Marco Magistri and Mohammad Ali Faghihi

    Citation: BMC Genomics 2016 17:49

    Content type: Software

    Published on:

  40. RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the ...

    Authors: Shanrong Zhao, Li Xi, Jie Quan, Hualin Xi, Ying Zhang, David von Schack, Michael Vincent and Baohong Zhang

    Citation: BMC Genomics 2016 17:39

    Content type: Software

    Published on:

  41. The most common ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reprodu...

    Authors: Xiaoyang Qi, Lisheng Zhang, Yanhua Han, Xiaoyun Ren, Jian Huang and Hongyin Chen

    Citation: BMC Genomics 2015 16:1086

    Content type: Research article

    Published on:

  42. Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amou...

    Authors: Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett and Ulrich Broeckel

    Citation: BMC Genomics 2015 16:1069

    Content type: Research article

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