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  1. Research article

    Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern

    N 6 -methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes a...

    Xuelian Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Yan Chen, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen…

    BMC Genomics 2017 18:336

    Published on: 28 April 2017

  2. Research article

    A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

    Examination of complex biological systems has long been achieved through methodical investigation of the system’s individual components. While informative, this strategy often leads to inappropriate conclusion...

    Sarah L. Grady, Stephanie A. Malfatti, Thusitha S. Gunasekera, Brian K. Dalley, Matt G. Lyman, Richard C. Striebich, Michael B. Mayhew, Carol L. Zhou, Oscar N. Ruiz and Larry C. Dugan

    BMC Genomics 2017 18:334

    Published on: 28 April 2017

  3. Research article

    Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana)

    Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, wh...

    Patrick R.N. Lenz, Jean Beaulieu, Shawn D. Mansfield, Sébastien Clément, Mireille Desponts and Jean Bousquet

    BMC Genomics 2017 18:335

    Published on: 28 April 2017

  4. Research Article

    Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack

    Parasitoid resistance in Drosophila varies considerably, among and within species. An immune response, lamellocyte-mediated encapsulation, evolved in a subclade of Drosophila and was subsequently lost in at least...

    Laura Salazar-Jaramillo, Kirsten M. Jalvingh, Ammerins de Haan, Ken Kraaijeveld, Henk Buermans and Bregje Wertheim

    BMC Genomics 2017 18:331

    Published on: 27 April 2017

  5. Software

    CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

    The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuit...

    Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar and W. Florian Fricke

    BMC Genomics 2017 18:332

    Published on: 27 April 2017

  6. Research article

    Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae

    The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evide...

    Jenny M. Greenwood, Barbara Milutinović, Robert Peuß, Sarah Behrens, Daniela Esser, Philip Rosenstiel, Hinrich Schulenburg and Joachim Kurtz

    BMC Genomics 2017 18:329

    Published on: 26 April 2017

  7. Methodology article

    MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy

    Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can b...

    Julien Marquis, Gregory Lefebvre, Yiannis A. I. Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr and Patrick Descombes

    BMC Genomics 2017 18:326

    Published on: 26 April 2017

  8. Research article

    Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci

    ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, ...

    Lixia Tian, Tianxue Song, Rongjun He, Yang Zeng, Wen Xie, Qingjun Wu, Shaoli Wang, Xuguo Zhou and Youjun Zhang

    BMC Genomics 2017 18:330

    Published on: 26 April 2017

  9. Research article

    Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements

    DNA elimination is developmentally programmed in a wide variety of eukaryotes, including unicellular ciliates, and leads to the generation of distinct germline and somatic genomes. The ciliate Paramecium tetraure...

    Frédéric Guérin, Olivier Arnaiz, Nicole Boggetto, Cyril Denby Wilkes, Eric Meyer, Linda Sperling and Sandra Duharcourt

    BMC Genomics 2017 18:327

    Published on: 26 April 2017

  10. Research article

    Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

    Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The p...

    Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo and Youxiong Que

    BMC Genomics 2017 18:325

    Published on: 24 April 2017

  11. Research article

    Genome adaptive evolution of Lactobacillus casei under long-term antibiotic selection pressures

    The extensive use of antibiotics in medicine has raised serious concerns about biosafety. However, the effect of antibiotic application on the adaptive evolution of microorganisms, especially to probiotic bact...

    Jicheng Wang, Xiao Dong, Yuyu Shao, Huiling Guo, Lin Pan, Wenyan Hui, Lai-Yu Kwok, Heping Zhang and Wenyi Zhang

    BMC Genomics 2017 18:320

    Published on: 24 April 2017

  12. Methodology article

    A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

    Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material.

    Tran Thi Ngoc Dung, Pham Thanh Duy, October M. Sessions, Uma K. Sangumathi, Voong Vinh Phat, Pham Thi Thanh Tam, Nguyen Thi Nguyen To, Tran My Phuc, Tran Thi Hong Chau, Nguyen Ngoc Minh Chau, Ngoc Nguyen Minh, Guy E. Thwaites, Maia A. Rabaa and Stephen Baker

    BMC Genomics 2017 18:324

    Published on: 24 April 2017

  13. Research article

    Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells

    The function of the prion protein, involved in the so-called prion diseases, remains a subject of intense debate and the possibility that it works as a pleiotropic protein through the interaction with multiple...

    J. A. Macedo, D. Schrama, I. Duarte, E. Tavares, J. Renaut, M. E. Futschik, P. M. Rodrigues and E. P. Melo

    BMC Genomics 2017 18:319

    Published on: 22 April 2017

  14. Research article

    A reference floral transcriptome of sexual and apomictic Paspalum notatum

    Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associa...

    Juan Pablo A. Ortiz, Santiago Revale, Lorena A. Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc and Silvina C. Pessino

    BMC Genomics 2017 18:318

    Published on: 21 April 2017

  15. Research article

    Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3

    The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a highly destructive pest of pine forests in western North America. During flight to a new host tree and initiation of feeding, mountain pine bee...

    J. A. Nadeau, J. Petereit, R. L. Tillett, K. Jung, M. Fotoohi, M. MacLean, S. Young, K. Schlauch, G. J. Blomquist and C. Tittiger

    BMC Genomics 2017 18:311

    Published on: 20 April 2017

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