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  1. Research article

    Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages

    Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infect...

    Ana Cristina Ferreira, Rogério Tenreiro, Maria Inácia Corrêa de Sá and Ricardo Dias

    BMC Genomics 2017 18:726

    Published on: 12 September 2017

  2. Research article

    Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease

    Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights i...

    Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya and Sanghamitra Bandyopadhyay

    BMC Genomics 2017 18:721

    Published on: 12 September 2017

  3. Research article

    Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation

    Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic me...

    Jia Zhou, Renee L. Sears, Xiaoyun Xing, Bo Zhang, Daofeng Li, Nicole B. Rockweiler, Hyo Sik Jang, Mayank N.K. Choudhary, Hyung Joo Lee, Rebecca F. Lowdon, Jason Arand, Brianne Tabers, C. Charles Gu, Theodore J. Cicero and Ting Wang

    BMC Genomics 2017 18:724

    Published on: 12 September 2017

  4. Research article

    Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup

    Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of...

    Robert Kammerer, Martin Mansfeld, Jana Hänske, Sophie Mißbach, Xiaocui He, Bernd Köllner, Susan Mouchantat and Wolfgang Zimmermann

    BMC Genomics 2017 18:717

    Published on: 11 September 2017

  5. Research article

    Integrated application of transcriptomics and metabolomics provides insights into glycogen content regulation in the Pacific oyster Crassostrea gigas

    The Pacific oyster Crassostrea gigas is an important marine fishery resource, which contains high levels of glycogen that contributes to the flavor and the quality of the oyster. However, little is known about th...

    Busu Li, Kai Song, Jie Meng, Li Li and Guofan Zhang

    BMC Genomics 2017 18:713

    Published on: 11 September 2017

  6. Research article

    Determining the optimal number of independent components for reproducible transcriptomic data analysis

    Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the nu...

    Ulykbek Kairov, Laura Cantini, Alessandro Greco, Askhat Molkenov, Urszula Czerwinska, Emmanuel Barillot and Andrei Zinovyev

    BMC Genomics 2017 18:712

    Published on: 11 September 2017

  7. Research article

    De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

    Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of cor...

    Monika Frazier, Martin Helmkampf, M. Renee Bellinger, Scott M. Geib and Misaki Takabayashi

    BMC Genomics 2017 18:710

    Published on: 11 September 2017

  8. Research article

    The dynamic landscape of gene regulation during Bombyx mori oogenesis

    Oogenesis in the domestic silkworm (Bombyx mori) is a complex process involving previtellogenesis, vitellogenesis and choriogenesis. During this process, follicles show drastic morphological and physiological cha...

    Qiang Zhang, Wei Sun, Bang-Yong Sun, Yang Xiao and Ze Zhang

    BMC Genomics 2017 18:714

    Published on: 11 September 2017

  9. Research article

    Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico

    Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and...

    Matthew A. Kost, Hugo R. Perales, Saranga Wijeratne, Asela J. Wijeratne, Eric Stockinger and Kristin L. Mercer

    BMC Genomics 2017 18:707

    Published on: 8 September 2017

  10. Research article

    Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma

    Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbati...

    Laurence Tessier, Olivier Côté, Mary Ellen Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders and Dorothee Bienzle

    BMC Genomics 2017 18:708

    Published on: 8 September 2017

  11. Research article

    Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

    Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. There...

    Khalil Eslamloo, Xi Xue, Jennifer R. Hall, Nicole C. Smith, Albert Caballero-Solares, Christopher C. Parrish, Richard G. Taylor and Matthew L. Rise

    BMC Genomics 2017 18:706

    Published on: 8 September 2017

  12. Research article

    Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense

    How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple a...

    Peng-tao Li, Mi Wang, Quan-wei Lu, Qun Ge, Md. Harun or Rashid, Ai-ying Liu, Ju-wu Gong, Hai-hong Shang, Wan-kui Gong, Jun-wen Li, Wei-wu Song, Li-xue Guo, Wei Su, Shao-qi Li, Xiao-ping Guo, Yu-zhen Shi…

    BMC Genomics 2017 18:705

    Published on: 8 September 2017

  13. Research article

    Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

    Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very lit...

    Chao Du, Lifang Zhang, Ting Lu, Jingnan Ma, Chenjuan Zeng, Bisong Yue and Xiuyue Zhang

    BMC Genomics 2017 18:698

    Published on: 6 September 2017

  14. Research article

    Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato

    Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important...

    Khadiza Khatun, Ujjal Kumar Nath, Arif Hasan Khan Robin, Jong-In Park, Do-Jin Lee, Min-Bae Kim, Chang Kil Kim, Ki-Byung Lim, Ill Sup Nou and Mi-Young Chung

    BMC Genomics 2017 18:695

    Published on: 6 September 2017

  15. Original Paper

    Genome-wide association study reveals putative role of gga-miR-15a in controlling feed conversion ratio in layer chickens

    Efficient use of feed resources for farm animals is a critical concern in animal husbandry. Numerous genetic and nutritional studies have been conducted to investigate feed efficiency during the regular laying...

    Jingwei Yuan, Sirui Chen, Fengying Shi, Guiqin Wu, Aiqiao Liu, Ning Yang and Congjiao Sun

    BMC Genomics 2017 18:699

    Published on: 6 September 2017

  16. Research article

    Lack of 14-3-3 proteins in Saccharomyces cerevisiae results in cell-to-cell heterogeneity in the expression of Pho4-regulated genes SPL2 and PHO84

    Ion homeostasis is an essential property of living organisms. The yeast Saccharomyces cerevisiae is an ideal model organism to investigate ion homeostasis at all levels. In this yeast genes involved in high-affin...

    Janneke H.M. Teunissen, Marjolein E. Crooijmans, Pepijn P.P. Teunisse and G. Paul H. van Heusden

    BMC Genomics 2017 18:701

    Published on: 6 September 2017

  17. Research

    Dual transcriptome of the immediate neutrophil and Candida albicans interplay

    Neutrophils are traditionally considered transcriptionally inactive. Compared to other immune cells, little is known about their transcriptional profile during interaction with pathogens.

    Maria J. Niemiec, Christian Grumaz, David Ermert, Christiane Desel, Madhu Shankar, José Pedro Lopes, Ian G. Mills, Philip Stevens, Kai Sohn and Constantin F. Urban

    BMC Genomics 2017 18:696

    Published on: 6 September 2017

  18. Research article

    Patterns of host gene expression associated with harboring a foregut microbial community

    Harboring foregut microbial communities is considered a key innovation that allows herbivorous mammals to colonize new ecological niches. However, the functions of these chambers have only been well studied at...

    Kevin D. Kohl, Kelly F. Oakeson, Diane Dunn, David K. Meyerholz, Colin Dale, Robert B. Weiss and M. Denise Dearing

    BMC Genomics 2017 18:697

    Published on: 6 September 2017

  19. Research article

    Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize

    Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tr...

    Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu and Yanli Lu

    BMC Genomics 2017 18:702

    Published on: 6 September 2017

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