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

    Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

    Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire ...

    Farah R. Zahir, Jill C. Mwenifumbo, Hye-Jung E. Chun, Emilia L. Lim, Clara D. M. Van Karnebeek, Madeline Couse, Karen L. Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F. Boerkoel, Sylvie L. Langlois, Barbara M. McGillivray, Steven J. M. Jones, Jan M. Friedman and Marco A. Marra

    BMC Genomics 2017 18:403

    Published on: 24 May 2017

  2. Research article

    Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

    The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studie...

    Navin Rustagi, Anbo Zhou, W. Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A. Gibbs, Lynn B. Jorde, Fuli Yu and Jinchuan Xing

    BMC Genomics 2017 18:396

    Published on: 22 May 2017

  3. Research article

    Transversions have larger regulatory effects than transitions

    Transversions (Tv’s) are more likely to alter the amino acid sequence of proteins than transitions (Ts’s), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the...

    Cong Guo, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe and Timothy E. Reddy

    BMC Genomics 2017 18:394

    Published on: 19 May 2017

  4. Methodology article

    Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers

    Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the...

    Qi Liu, Russell Bonneville, Tianbao Li and Victor X. Jin

    BMC Genomics 2017 18:375

    Published on: 12 May 2017

  5. Research article

    The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model

    Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (poly...

    Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon-Mom, Perry D. Moerland and Pernette J. Verschure

    BMC Genomics 2017 18:373

    Published on: 12 May 2017

  6. Methodology article

    MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy

    Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can b...

    Julien Marquis, Gregory Lefebvre, Yiannis A. I. Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr and Patrick Descombes

    BMC Genomics 2017 18:326

    Published on: 26 April 2017

  7. 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

  8. 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

  9. 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

  10. 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

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