Human and rodent genomics

Section edited by Leonid Bystrykh, Leonard Schalkwyck and Stefan Wiemann

This section covers the genome structure and function in humans, primates and rodents.

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  1. Research article

    Reduced changes in protein compared to mRNA levels across non-proliferating tissues

    The quantitative relations between RNA and protein are fundamental to biology and are still not fully understood. Across taxa, it was demonstrated that the protein-to-mRNA ratio in steady state varies in a dir...

    Kobi Perl, Kathy Ushakov, Yair Pozniak, Ofer Yizhar-Barnea, Yoni Bhonker, Shaked Shivatzki, Tamar Geiger, Karen B. Avraham and Ron Shamir

    BMC Genomics 2017 18:305

    Published on: 18 April 2017

  2. Research article

    Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer

    Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA ...

    Verena Zuber, Francesco Bettella, Aree Witoelar, Ole A. Andreassen, Ian G. Mills and Alfonso Urbanucci

    BMC Genomics 2017 18:270

    Published on: 31 March 2017

  3. Research article

    Population diversity of the genetically determined TTR expression in human tissues and its implications in TTR amyloidosis

    Transthyretin (TTR) amyloidosis is a hereditary disease with a complex genotype-phenotype correlation. We conducted a literature survey to define the clinical landscape of TTR amyloidosis across populations wo...

    Andrea Iorio, Flavio De Angelis, Marco Di Girolamo, Marco Luigetti, Luca G. Pradotto, Anna Mazzeo, Sabrina Frusconi, Filomena My, Dario Manfellotto, Maria Fuciarelli and Renato Polimanti

    BMC Genomics 2017 18:254

    Published on: 23 March 2017

  4. Research article

    Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo

    DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not be...

    Jesper L. V. Maag, Dominik C. Kaczorowski, Debabrata Panja, Timothy J. Peters, Clive R. Bramham, Karin Wibrand and Marcel E. Dinger

    BMC Genomics 2017 18:250

    Published on: 23 March 2017

  5. Research Article

    Bicodon bias can determine the role of synonymous SNPs in human diseases

    For a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered dis...

    Christina McCarthy, Alejandra Carrea and Luis Diambra

    BMC Genomics 2017 18:227

    Published on: 13 March 2017

  6. Research article

    Gene expression regional differences in human subcutaneous adipose tissue

    Accumulation of visceral adipose tissue (VAT) is clearly associated with an increased risk of obesity-related diseases and all-cause mortality, whereas gluteal subcutaneous fat accumulation (g-SAT) is associat...

    Angelina Passaro, Maria Agata Miselli, Juana Maria Sanz, Edoardo Dalla Nora, Mario Luca Morieri, Rossella Colonna, Rado Pišot and Giovanni Zuliani

    BMC Genomics 2017 18:202

    Published on: 23 February 2017

  7. Research article

    Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

    Malignant breast cancer with complex molecular mechanisms of progression and metastasis remains a leading cause of death in women. To improve diagnosis and drug development, it is critical to identify panels o...

    Ying Cai, Ruben Nogales-Cadenas, Quanwei Zhang, Jhih-Rong Lin, Wen Zhang, Kelly O’Brien, Cristina Montagna and Zhengdong D. Zhang

    BMC Genomics 2017 18:185

    Published on: 17 February 2017

  8. Research article

    Genome-wide identification of direct HBx genomic targets

    The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modula...

    Francesca Guerrieri, Laura Belloni, Daniel D’Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, Cecilia Scisciani, Oceane Floriot, Fabien Zoulim, Anna Tramontano and Massimo Levrero

    BMC Genomics 2017 18:184

    Published on: 17 February 2017

  9. Research article

    An integrative metabolomics and transcriptomics study to identify metabolic alterations in aged skin of humans in vivo

    Aging human skin undergoes significant morphological and functional changes such as wrinkle formation, reduced wound healing capacity, and altered epidermal barrier function. Besides known age-related alterati...

    Andreas Kuehne, Janosch Hildebrand, Joern Soehle, Horst Wenck, Lara Terstegen, Stefan Gallinat, Anja Knott, Marc Winnefeld and Nicola Zamboni

    BMC Genomics 2017 18:169

    Published on: 15 February 2017

  10. Research article

    Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing

    Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord...

    Ling-Ling Shi, Nan Zhang, Xiu-Mei Xie, Yue-Juan Chen, Rui Wang, Lin Shen, Jian-Sheng Zhou, Jian-Guo Hu and He-Zuo Lü

    BMC Genomics 2017 18:173

    Published on: 15 February 2017

  11. Software

    PreMeta: a tool to facilitate meta-analysis of rare-variant associations

    Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perf...

    Zheng-Zheng Tang, Paul Bunn, Ran Tao, Zhouwen Liu and Dan-Yu Lin

    BMC Genomics 2017 18:160

    Published on: 14 February 2017

  12. Research article

    2.7 million samples genotyped for HLA by next generation sequencing: lessons learned

    At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences...

    Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A. Hofmann, Julia Pingel, Alexander H. Schmidt and Vinzenz Lange

    BMC Genomics 2017 18:161

    Published on: 14 February 2017

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