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

    Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls

    Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibl...

    Alexandra R. Buckley, Kristopher A. Standish, Kunal Bhutani, Trey Ideker, Roger S. Lasken, Hannah Carter, Olivier Harismendy and Nicholas J. Schork

    BMC Genomics 2017 18:458

    Published on: 12 June 2017

  2. Methodology article

    Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries

    Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleoti...

    Dmitriy A. Shagin, Maria A. Turchaninova, Irina A. Shagina, Mikhail Shugay, Andrew R. Zaretsky, Olga I. Zueva, Dmitriy A. Bolotin, Sergey Lukyanov and Dmitriy M. Chudakov

    BMC Genomics 2017 18:440

    Published on: 5 June 2017

  3. Research Article

    Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues

    Nicotinic acetylcholine receptors (nAChRs) play an important role in cellular physiology and human nicotine dependence, and are closely associated with many human diseases including cancer. For example, previo...

    Bo Zhang, Pamela Madden, Junchen Gu, Xiaoyun Xing, Savita Sankar, Jennifer Flynn, Kristen Kroll and Ting Wang

    BMC Genomics 2017 18:439

    Published on: 5 June 2017

  4. Software

    lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets

    Long non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successfu...

    Yixiao Gong, Hsuan-Ting Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis and Aristotelis Tsirigos

    BMC Genomics 2017 18:434

    Published on: 5 June 2017

  5. Research article

    High-throughput validation of ceRNA regulatory networks

    MicroRNAs (miRNAs) play multiple roles in tumor biology. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration. Specifically, co...

    Hua-Sheng Chiu, María Rodríguez Martínez, Mukesh Bansal, Aravind Subramanian, Todd R. Golub, Xuerui Yang, Pavel Sumazin and Andrea Califano

    BMC Genomics 2017 18:418

    Published on: 30 May 2017

  6. Research article

    Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort

    The cerebrospinal fluid (CSF) levels of total tau (t-tau) and Aβ1–42 are potential early diagnostic markers for probable Alzheimer’s disease (AD). The influence of genetic variation on these CSF biomarkers has be...

    Wang Cong, Xianglian Meng, Jin Li, Qiushi Zhang, Feng Chen, Wenjie Liu, Ying Wang, Sipu Cheng, Xiaohui Yao, Jingwen Yan, Sungeun Kim, Andrew J. Saykin, Hong Liang and Li Shen

    BMC Genomics 2017 18:421

    Published on: 30 May 2017

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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