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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.

Page 6 of 22

  1. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:458

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  2. Content type: Methodology article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:440

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  3. Content type: Research Article

    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...

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

    Citation: BMC Genomics 2017 18:439

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  4. Content type: Software

    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...

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

    Citation: BMC Genomics 2017 18:434

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  5. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:421

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  6. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:418

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  7. Content type: Methodology article

    One problem that plagues epigenome-wide association studies is the potential confounding due to cell mixtures when purified target cells are not available. Reference-free adjustment of cell mixtures has become...

    Authors: Jun Chen, Ehsan Behnam, Jinyan Huang, Miriam F. Moffatt, Daniel J. Schaid, Liming Liang and Xihong Lin

    Citation: BMC Genomics 2017 18:413

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  8. Content type: Research Article

    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 ...

    Authors: 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

    Citation: BMC Genomics 2017 18:403

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  9. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:396

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  10. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:394

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  11. Content type: Research article

    Development of primary open-angle glaucoma (POAG) is associated with the malfunctioning trabecular meshwork (TM). Cell therapy offers great potential for the treatment of POAG, but requires the generation of f...

    Authors: Padmapriya Sathiyanathan, Cheryl Y. Tay and Lawrence W. Stanton

    Citation: BMC Genomics 2017 18:383

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  12. Content type: Methodology article

    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...

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

    Citation: BMC Genomics 2017 18:375

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  13. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:373

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  14. Content type: Methodology article

    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...

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

    Citation: BMC Genomics 2017 18:326

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  15. Content type: Research article

    High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays comb...

    Authors: Rajini R. Haraksingh, Alexej Abyzov and Alexander Eckehart Urban

    Citation: BMC Genomics 2017 18:321

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  16. Content type: Research article

    Numerous studies have highlighted the elevated degree of comorbidity associated with autism spectrum disorder (ASD). These comorbid conditions may add further impairments to individuals with autism and are sub...

    Authors: Leticia Diaz-Beltran, Francisco J. Esteban, Maya Varma, Alp Ortuzk, Maude David and Dennis P. Wall

    Citation: BMC Genomics 2017 18:315

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  17. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:305

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  18. Content type: Research article

    Krüppel-like factor 9 (Klf9) is a zinc finger transcription factor that functions in neural cell differentiation, but little is known about its genomic targets or mechanism of action in neurons.

    Authors: Joseph R. Knoedler, Arasakumar Subramani and Robert J. Denver

    Citation: BMC Genomics 2017 18:299

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  19. Content type: Research article

    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 ...

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

    Citation: BMC Genomics 2017 18:270

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  20. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:254

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  21. Content type: Research article

    Vitamin C (vit C) is an essential dietary nutrient, which is a potent antioxidant, a free radical scavenger and functions as a cofactor in many enzymatic reactions. Vit C is also considered to enhance the immu...

    Authors: Sakshi Dhingra Batra, Malobi Nandi, Kriti Sikri and Jaya Sivaswami Tyagi

    Citation: BMC Genomics 2017 18:252

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  22. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:250

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  23. Content type: Research article

    Genetic studies of human lung function and Chronic Obstructive Pulmonary Disease have identified a highly significant and reproducible signal on 4q24. It remains unclear which of the two candidate genes within...

    Authors: Alexander K. Kheirallah, Cornelia H. de Moor, Alen Faiz, Ian Sayers and Ian P. Hall

    Citation: BMC Genomics 2017 18:248

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  24. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:202

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  25. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:185

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  26. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:184

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  27. Content type: Research article

    Skeletal muscle is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is ...

    Authors: Chia-Ling Wu, Yoshinori Satomi and Kenneth Walsh

    Citation: BMC Genomics 2017 18:181

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  28. Content type: Research article

    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...

    Authors: 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

    Citation: BMC Genomics 2017 18:173

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  29. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:169

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  30. Content type: Research article

    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...

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

    Citation: BMC Genomics 2017 18:161

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  31. Content type: Research article

    Among the different tobacco products that are available on the US market, cigarette smoking is shown to be the most harmful and the effects of cigarette smoking have been well studied. US epidemiological studi...

    Authors: Subhashini Arimilli, Behrouz Madahian, Peter Chen, Kristin Marano and G. L. Prasad

    Citation: BMC Genomics 2017 18:156

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  32. Content type: Software

    Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family...

    Authors: Alessia Visconti, Mashael Al-Shafai, Wadha A. Al Muftah, Shaza B. Zaghlool, Massimo Mangino, Karsten Suhre and Mario Falchi

    Citation: BMC Genomics 2017 18:150

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  33. Content type: Research article

    Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab...

    Authors: Andreas R. Gschwind, Anjali Singh, Ulrich Certa, Alexandre Reymond and Tobias Heckel

    Citation: BMC Genomics 2017 18:144

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  34. Content type: Research article

    Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined...

    Authors: David D. McManus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane E. Freedman and Daniel Levy

    Citation: BMC Genomics 2017 18:139

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  35. Content type: Research article

    We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. However, recognizing tumors that have inactivation of the NF1 tumor suppressor ...

    Authors: Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez and Casey S. Greene

    Citation: BMC Genomics 2017 18:127

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  36. Content type: Research article

    Alternative mRNA isoform usage is an important source of protein diversity in mammalian cells. This phenomenon has been extensively studied in bulk tissues, however, it remains unclear how this diversity is re...

    Authors: Kasper Karlsson and Sten Linnarsson

    Citation: BMC Genomics 2017 18:126

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  37. Content type: Research article

    Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. I...

    Authors: Elizabeth L. Johnson, David G. Robinson and Hilary A. Coller

    Citation: BMC Genomics 2017 18:123

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  38. Content type: Research article

    High-protein diets (HPD) alter the large intestine microbiota composition in association with a metabolic shift towards protein degradation. Some amino acid-derived metabolites produced by the colon bacteria a...

    Authors: Martin Beaumont, Mireille Andriamihaja, Lucie Armand, Marta Grauso, Florence Jaffrézic, Denis Laloë, Marco Moroldo, Anne-Marie Davila, Daniel Tomé, François Blachier and Annaïg Lan

    Citation: BMC Genomics 2017 18:116

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  39. Content type: Research article

    Significant gaps remain regarding the pathomechanisms underlying the autoimmune response in vitiligo (VL), where the loss of self-tolerance leads to the targeted killing of melanocytes. Specifically, there is ...

    Authors: Rama Dey-Rao and Animesh A. Sinha

    Citation: BMC Genomics 2017 18:109

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