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  1. Research article

    A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

    Small auxin-up RNA (SAUR) gene family is the largest family of early auxin response genes in higher plants, which have been implicated in the regulation of multiple biological processes. However, no comprehensive...

    Xihua Li, Guoyuan Liu, Yanhui Geng, Man Wu, Wenfeng Pei, Honghong Zhai, Xinshan Zang, Xingli Li, Jinfa Zhang, Shuxun Yu and Jiwen Yu

    BMC Genomics 2017 18:815

    Published on: 23 October 2017

  2. Research article

    Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling

    Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is ...

    Jana Maršíková, Derek Wilkinson, Otakar Hlaváček, Gregor D. Gilfillan, Alexandru Mizeranschi, Timothy Hughes, Markéta Begany, Stanislava Rešetárová, Libuše Váchová and Zdena Palková

    BMC Genomics 2017 18:814

    Published on: 23 October 2017

  3. Research article

    Uncovering the embryonic development-related proteome and metabolome signatures in breast muscle and intramuscular fat of fast-and slow-growing chickens

    Skeletal muscle development is closely linked to meat production and its quality. This study is the first to quantify the proteomes and metabolomes of breast muscle in two distinct chicken breeds at embryonic ...

    Ranran Liu, Hongyang Wang, Jie Liu, Jie Wang, Maiqing Zheng, Xiaodong Tan, Siyuan Xing, Huanxian Cui, Qinghe Li, Guiping Zhao and Jie Wen

    BMC Genomics 2017 18:816

    Published on: 23 October 2017

  4. Research article

    An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes

    Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid specie...

    Nora Hohmann and Marcus A. Koch

    BMC Genomics 2017 18:810

    Published on: 23 October 2017

  5. Research article

    Proteomic analysis of trochophore and veliger larvae development in the small abalone Haliotis diversicolor

    Haliotis diversicolor is commercially important species. The trochophore and veliger are distinct larval stages in gastropod development. Their development involves complex morphologic...

    Guilan Di, Xianghui Kong, Xiulian Miao, Yifang Zhang, Miaoqin Huang, Yuting Gu, Weiwei You, Jianxin Zhang and Caihuan Ke

    BMC Genomics 2017 18:809

    Published on: 23 October 2017

  6. Research article

    Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

    Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mec...

    Lei Wang, Hong-Ling Wang, Lan Yin and Chang-Yan Tian

    BMC Genomics 2017 18:806

    Published on: 19 October 2017

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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