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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 23

  1. TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes...

    Authors: Yongcheng Dong, Ziyan Huang, Qifan Kuang, Zhining Wen, Zhibin Liu, Yizhou Li, Yi Yang and Menglong Li

    Citation: BMC Genomics 2017 18:666

    Content type: Research article

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  2. The human oral microbiome is formed early in development. Its composition is influenced by environmental factors including diet, substance use, oral health, and overall health and disease. The influence of hum...

    Authors: Brittany A. Demmitt, Robin P. Corley, Brooke M. Huibregtse, Matthew C. Keller, John K. Hewitt, Matthew B. McQueen, Rob Knight, Ivy McDermott and Kenneth S. Krauter

    Citation: BMC Genomics 2017 18:659

    Content type: Research article

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  3. Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of ...

    Authors: Zhiwen Jiang, Jiaqi Yang, Aimei Dai, Yuming Wang, Wei Li and Zhi Xie

    Citation: BMC Genomics 2017 18:638

    Content type: Research article

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  4. DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid c...

    Authors: David P. Astling, Ilea E. Heft, Kenneth L. Jones and James M. Sikela

    Citation: BMC Genomics 2017 18:614

    Content type: Methodology article

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  5. 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...

    Authors: 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

    Citation: BMC Genomics 2017 18:591

    Content type: Research article

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  6. Human polymorphisms with derived alleles that are protective against disease may provide powerful translational opportunities. Here we report a method to identify such candidate polymorphisms and apply it to c...

    Authors: Joe M. Butler, Neil Hall, Niro Narendran, Yit C. Yang and Luminita Paraoan

    Citation: BMC Genomics 2017 18:575

    Content type: Research Article

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  7. 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...

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

    Citation: BMC Genomics 2017 18:552

    Content type: Methodology Article

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  8. 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 ...

    Authors: Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M. Earl and Carlos Caldas

    Citation: BMC Genomics 2017 18:526

    Content type: Research article

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  9. The placenta is the principal organ regulating intrauterine growth and development, performing critical functions on behalf of the developing fetus. The delineation of functional networks and pathways driving ...

    Authors: Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J. Marsit and Jia Chen

    Citation: BMC Genomics 2017 18:520

    Content type: Research article

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  10. 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...

    Authors: Daniela Esser, Niklas Holze, Jochen Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel and Christoph Röcken

    Citation: BMC Genomics 2017 18:517

    Content type: Research article

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  11. 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. ...

    Authors: Justin M. Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John R. Hoidal and Namakkal S. Rajasekaran

    Citation: BMC Genomics 2017 18:509

    Content type: Research article

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  12. Human endogenous retroviruses (HERVs) belong to the LTR-retrotransposon family, where the complete HERV sequence contains two long terminal repeats (LTRs) located at each end. Intact LTRs possess highly conser...

    Authors: Tomoaki Kahyo, Hidetaka Yamada, Hong Tao, Nobuya Kurabe and Haruhiko Sugimura

    Citation: BMC Genomics 2017 18:487

    Content type: Research article

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  13. The understanding of genomic and physiological mechanisms related to how organisms living in extreme environments survive and reproduce is an outstanding question facing evolutionary and organismal biologists....

    Authors: Lauren Kordonowy and Matthew MacManes

    Citation: BMC Genomics 2017 18:473

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Methodology article

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  16. 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

    Content type: Research Article

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  17. 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

    Content type: Software

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Methodology article

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  21. 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

    Content type: Research Article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Methodology article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Methodology article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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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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