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  1. Research article

    Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

    Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty n...

    K. O. Skaftnesmo, R. B. Edvardsen, T. Furmanek, D. Crespo, E. Andersson, L. Kleppe, G. L. Taranger, J. Bogerd, R. W. Schulz and A. Wargelius

    BMC Genomics 2017 18:801

    Published on: 18 October 2017

  2. Methodology article

    A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts

    In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An importan...

    Hugo W. Schneider, Taina Raiol, Marcelo M. Brigido, Maria Emilia M. T. Walter and Peter F. Stadler

    BMC Genomics 2017 18:804

    Published on: 18 October 2017

  3. Research article

    Candidate lethal haplotypes and causal mutations in Angus cattle

    If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating ...

    Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel and Jeremy F. Taylor

    BMC Genomics 2017 18:799

    Published on: 18 October 2017

  4. Research article

    The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

    The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using ...

    Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K. Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger and Melanie Waldenberger

    BMC Genomics 2017 18:805

    Published on: 18 October 2017

  5. Research article

    Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

    Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its ...

    Xianfeng Guo, Shenghui Li, Jiachun Zhang, Feifan Wu, Xiangchun Li, Dan Wu, Min Zhang, Zihao Ou, Zhuye Jie, Qiulong Yan, Peng Li, Jiangfeng Yi and Yongzheng Peng

    BMC Genomics 2017 18:800

    Published on: 18 October 2017

  6. Research article

    Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

    The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome fr...

    Chen Wu, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens and Thomas R. Buckley

    BMC Genomics 2017 18:795

    Published on: 17 October 2017

  7. Database

    Institute collection and analysis of Nanobodies (iCAN): a comprehensive database and analysis platform for nanobodies

    Nanobodies are single-domain antibodies that contain the unique structural and functional properties of naturally-occurring heavy chain in camelidae. As a novel class of antibody, they show many advantages com...

    Jing Zuo, Jian Li, Rongxin Zhang, Longsheng Xu, Hanhan Chen, Xiaohuan Jia, Zhipeng Su, Linhong Zhao, Xing Huang and Wei Xie

    BMC Genomics 2017 18:797

    Published on: 17 October 2017

  8. Methodology article

    Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure

    Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome...

    Jinyoung Byun, Younghun Han, Ivan P. Gorlov, Jonathan A. Busam, Michael F. Seldin and Christopher I. Amos

    BMC Genomics 2017 18:789

    Published on: 16 October 2017

  9. Software

    TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

    High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach...

    Daniela Beisser, Nadine Graupner, Lars Grossmann, Henning Timm, Jens Boenigk and Sven Rahmann

    BMC Genomics 2017 18:787

    Published on: 16 October 2017

  10. Research article

    Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

    Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and applicat...

    Jin Xiao, Keli Dai, Lian Fu, Jan Vrána, Marie Kubaláková, Wentao Wan, Haojie Sun, Jing Zhao, Chunyan Yu, Yufeng Wu, Michael Abrouk, Haiyan Wang, Jaroslav Doležel and Xiue Wang

    BMC Genomics 2017 18:791

    Published on: 16 October 2017

  11. Research article

    De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

    Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despi...

    Paulina Deptula, Pia K. Laine, Richard J. Roberts, Olli-Pekka Smolander, Helena Vihinen, Vieno Piironen, Lars Paulin, Eija Jokitalo, Kirsi Savijoki, Petri Auvinen and Pekka Varmanen

    BMC Genomics 2017 18:790

    Published on: 16 October 2017

  12. Research article

    Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda

    Our main purpose was to evaluate the expression of plastic and evolved genes involved in ecological speciation in the noctuid moth Spodoptera frugiperda, the fall armyworm (FAW); and to demonstrate how host plant...

    Karina Lucas Silva-Brandão, Renato Jun Horikoshi, Daniel Bernardi, Celso Omoto, Antonio Figueira and Marcelo Mendes Brandão

    BMC Genomics 2017 18:792

    Published on: 16 October 2017

  13. Methodology article

    Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

    Trypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant dis...

    Rafael Luis Kessler, Daniela Parada Pavoni, Marco Aurelio Krieger and Christian Macagnan Probst

    BMC Genomics 2017 18:793

    Published on: 16 October 2017

  14. Research article

    miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

    Sterile and fertile flowers are important evolutionary developmental phenotypes in angiosperm flowers. The development of floral organs, critical in angiosperm reproduction, is regulated by microRNAs (miRNAs)....

    Weixing Li, Zhichong He, Li Zhang, Zhaogeng Lu, Jing Xu, Jiawen Cui, Li Wang and Biao Jin

    BMC Genomics 2017 18:783

    Published on: 13 October 2017

  15. Research article

    Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration

    Asparagine is a very important nitrogen transport and storage compound in plants due to its high nitrogen/carbon ratio and stability. Asparagine intracellular concentration depends on a balance between asparag...

    Margarita García-Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti and Antonio J. Márquez

    BMC Genomics 2017 18:781

    Published on: 12 October 2017

  16. Research article

    Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry

    Trichoderma harzianum is used in biotechnology applications due to its ability to produce powerful enzymes for the conversion of lignocellulosic substrates into soluble sugars. Active ...

    Jaire Alves Ferreira Filho, Maria Augusta Crivelente Horta, Lilian Luzia Beloti, Clelton Aparecido dos Santos and Anete Pereira de Souza

    BMC Genomics 2017 18:779

    Published on: 12 October 2017

  17. Research article

    Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus

    Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from div...

    Nadia Raboanatahiry, Hongbo Chao, Liangxing Guo, Jianping Gan, Jun Xiang, Mingli Yan, Libin Zhang, Longjiang Yu and Maoteng Li

    BMC Genomics 2017 18:776

    Published on: 12 October 2017

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