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

    Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population

    Fasting glucose and fasting insulin are glycemic traits closely related to diabetes, and understanding the role of genetic factors in these traits can help reveal the etiology of type 2 diabetes. Although sing...

    Ren-Hua Chung, Yen-Feng Chiu, Yi-Jen Hung, Wen-Jane Lee, Kwan-Dun Wu, Hui-Ling Chen, Ming-Wei Lin, Yii-Der I. Chen, Thomas Quertermous and Chao A. Hsiung

    BMC Genomics 2017 18:591

    Published on: 8 August 2017

  2. Methodology Article

    GATE: an efficient procedure in study of pleiotropic genetic associations

    The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the...

    Wei Zhang, Liu Yang, Larry L. Tang, Aiyi Liu, James L. Mills, Yuanchang Sun and Qizhai Li

    BMC Genomics 2017 18:552

    Published on: 21 July 2017

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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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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