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  1. Research article

    Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses

    Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association s...

    Long Yan, Nicolle Hofmann, Shuxian Li, Marcio Elias Ferreira, Baohua Song, Guoliang Jiang, Shuxin Ren, Charles Quigley, Edward Fickus, Perry Cregan and Qijian Song

    BMC Genomics 2017 18:529

    Published on: 12 July 2017

  2. Methodology Article

    Scaffolding of long read assemblies using long range contact information

    Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually do...

    Jay Ghurye, Mihai Pop, Sergey Koren, Derek Bickhart and Chen-Shan Chin

    BMC Genomics 2017 18:527

    Published on: 12 July 2017

  3. Research article

    Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study

    An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks ...

    Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M. Earl and Carlos Caldas

    BMC Genomics 2017 18:526

    Published on: 11 July 2017

  4. Research article

    Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

    The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted ...

    Bárbara S. F. Müller, Leandro G. Neves, Janeo E. de Almeida Filho, Márcio F. R. Resende Jr, Patricio R. Muñoz, Paulo E. T. dos Santos, Estefano Paludzyszyn Filho, Matias Kirst and Dario Grattapaglia

    BMC Genomics 2017 18:524

    Published on: 11 July 2017

  5. Research article

    Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

    A restricted set of aerobic bacteria dominated by the Acinetobacter genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they prot...

    Azadeh Saffarian, Marie Touchon, Céline Mulet, Régis Tournebize, Virginie Passet, Sylvain Brisse, Eduardo P. C. Rocha, Philippe J. Sansonetti and Thierry Pédron

    BMC Genomics 2017 18:525

    Published on: 11 July 2017

  6. Research article

    Assembling metagenomes, one community at a time

    Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes,...

    Andries Johannes van der Walt, Marc Warwick van Goethem, Jean-Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva and Don Arthur Cowan

    BMC Genomics 2017 18:521

    Published on: 10 July 2017

  7. Methodology article

    Massively parallel nanowell-based single-cell gene expression profiling

    Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expre...

    Leonard D. Goldstein, Ying-Jiun Jasmine Chen, Jude Dunne, Alain Mir, Hermann Hubschle, Joseph Guillory, Wenlin Yuan, Jingli Zhang, Jeremy Stinson, Bijay Jaiswal, Kanika Bajaj Pahuja, Ishminder Mann, Thomas Schaal, Leo Chan, Sangeetha Anandakrishnan, Chun-wah Lin…

    BMC Genomics 2017 18:519

    Published on: 7 July 2017

  8. Research article

    Interpreting whole genome and exome sequencing data of individual gastric cancer samples

    Gastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one m...

    Daniela Esser, Niklas Holze, Jochen Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel and Christoph Röcken

    BMC Genomics 2017 18:517

    Published on: 6 July 2017

  9. Methodology article

    Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing

    RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutation...

    Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A. Moore, Andrew J. Mungall, Jacquie Schein, Robin J. Coope…

    BMC Genomics 2017 18:515

    Published on: 5 July 2017

  10. Research article

    Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

    Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolu...

    Umberto Palatini, Pascal Miesen, Rebeca Carballar-Lejarazu, Lino Ometto, Ettore Rizzo, Zhijian Tu, Ronald P. van Rij and Mariangela Bonizzoni

    BMC Genomics 2017 18:512

    Published on: 5 July 2017

  11. Research article

    Identification of long non-coding RNA in the horse transcriptome

    Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet ...

    E. Y. Scott, T. Mansour, R. R. Bellone, C. T. Brown, M. J. Mienaltowski, M. C. Penedo, P. J. Ross, S. J. Valberg, J. D. Murray and C. J. Finno

    BMC Genomics 2017 18:511

    Published on: 4 July 2017

  12. Research article

    Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice

    Nuclear Factor Erythroid-derived 2-like 2 (Nrf2) senses oxidative environments and/or stress and initiates a cytoprotective response through transcriptional activation of antioxidant and detoxification genes. ...

    Justin M. Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John R. Hoidal and Namakkal S. Rajasekaran

    BMC Genomics 2017 18:509

    Published on: 3 July 2017

  13. Research article

    Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface

    Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic sq...

    Henk Bolhuis, Ana Belén Martín-Cuadrado, Riccardo Rosselli, Lejla Pašić and Francisco Rodriguez-Valera

    BMC Genomics 2017 18:510

    Published on: 3 July 2017

  14. Research article

    Comparative muscle transcriptome associated with carcass traits of Nellore cattle

    Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measur...

    Bárbara Silva-Vignato, Luiz L. Coutinho, Aline S. M. Cesar, Mirele D. Poleti, Luciana C. A. Regitano and Júlio C. C. Balieiro

    BMC Genomics 2017 18:506

    Published on: 3 July 2017

  15. Research article

    Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)

    Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inherit...

    Xiaobo Luo, Liang Xu, Dongyi Liang, Yan Wang, Wei Zhang, Xianwen Zhu, Yuelin Zhu, Haiyan Jiang, Mingjia Tang and Liwang Liu

    BMC Genomics 2017 18:505

    Published on: 3 July 2017

  16. Research article

    The PIN gene family in cotton (Gossypium hirsutum): genome-wide identification and gene expression analyses during root development and abiotic stress responses

    Cell elongation and expansion are significant contributors to plant growth and morphogenesis, and are often regulated by environmental cues and endogenous hormones. Auxin is one of the most important phytohorm...

    Peng He, Peng Zhao, Limin Wang, Yuzhou Zhang, Xiaosi Wang, Hui Xiao, Jianing Yu and Guanghui Xiao

    BMC Genomics 2017 18:507

    Published on: 3 July 2017

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