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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 1 of 24

  1. Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide ...

    Authors: Patrycja Daca-Roszak, Roman Jaksik, Julia Paczkowska, Michał Witt and Ewa Ziętkiewicz

    Citation: BMC Genomics 2020 21:706

    Content type: Research article

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  2. Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and ...

    Authors: Cynthia A. Kelm-Nelson and Stephen Gammie

    Citation: BMC Genomics 2020 21:625

    Content type: Research article

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  3. Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by ...

    Authors: Xiaofeng Guo, Xiaoling Gao, Brendan T. Keenan, Jingxu Zhu, Dimitra Sarantopoulou, Jie Lian, Raymond J. Galante, Gregory R. Grant and Allan I. Pack

    Citation: BMC Genomics 2020 21:633

    Content type: Research article

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  4. Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely relat...

    Authors: Zhenhua Shang, David J. Horovitz, Ronald H. McKenzie, Jessica L. Keisler, Michael R. Felder and Shannon W. Davis

    Citation: BMC Genomics 2020 21:622

    Content type: Research article

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  5. The WD40-repeat containing proteins, including DDB1–CUL4-associated factors (DCAFs), are abundant and conserved proteins that play important roles in different cellular processes including spermatogenesis. DCA...

    Authors: Bhavesh V. Mistry, Maha Alanazi, Hanae Fitwi, Olfat Al-Harazi, Mohamed Rajab, Abdullah Altorbag, Falah Almohanna, Dilek Colak and Abdullah M. Assiri

    Citation: BMC Genomics 2020 21:602

    Content type: Research article

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  6. Statins are widely prescribed to lower plasma low-density lipoprotein cholesterol levels. Though statins reduce cardiovascular disease risk overall, statin efficacy varies, and some people experience adverse s...

    Authors: Elizabeth Theusch, Yii-Der I. Chen, Jerome I. Rotter, Ronald M. Krauss and Marisa W. Medina

    Citation: BMC Genomics 2020 21:555

    Content type: Research article

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  7. Greying of the hair is an obvious sign of human aging. In addition to age, sex- and ancestry-specific patterns of hair greying are also observed and the progression of greying may be affected by environmental ...

    Authors: Ewelina Pośpiech, Magdalena Kukla-Bartoszek, Joanna Karłowska-Pik, Piotr Zieliński, Anna Woźniak, Michał Boroń, Michał Dąbrowski, Magdalena Zubańska, Agata Jarosz, Tomasz Grzybowski, Rafał Płoski, Magdalena Spólnicka and Wojciech Branicki

    Citation: BMC Genomics 2020 21:538

    Content type: Research article

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  8. The gut bacteria-derived metabolite trimethylamine-N-oxide (TMAO) has been discussed in various cardiometabolic diseases. However, evidence characterizing the microbial population responsible for TMAO accumula...

    Authors: Kun Zuo, Xiaoqing Liu, Pan Wang, Jie Jiao, Chunming Han, Zheng Liu, Xiandong Yin, Jing Li and Xinchun Yang

    Citation: BMC Genomics 2020 21:526

    Content type: Research article

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  9. Currently, diabetes has become one of the leading causes of death worldwide. Fasting plasma glucose (FPG) levels that are higher than optimal, even if below the diagnostic threshold of diabetes, can also lead ...

    Authors: Weijing Wang, Caixia Zhang, Hui Liu, Chunsheng Xu, Haiping Duan, Xiaocao Tian and Dongfeng Zhang

    Citation: BMC Genomics 2020 21:491

    Content type: Research article

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  10. Telomeric DNA is typically comprised of G-rich tandem repeat motifs and maintained by telomerase (Greider CW, Blackburn EH; Cell 51:887–898; 1987). In eukaryotes lacking telomerase, a variety of DNA repair and...

    Authors: Heba Z. Abid, Jennifer McCaffrey, Kaitlin Raseley, Eleanor Young, Katy Lassahn, Dharma Varapula, Harold Riethman and Ming Xiao

    Citation: BMC Genomics 2020 21:485

    Content type: Research article

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  11. Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organism...

    Authors: Xumin Ni, Mengshi Zhou, Heming Wang, Karen Y. He, Uli Broeckel, Craig Hanis, Sharon Kardia, Susan Redline, Richard S. Cooper, Hua Tang and Xiaofeng Zhu

    Citation: BMC Genomics 2020 21:476

    Content type: Research article

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  12. Female infertility is a worldwide concern and the etiology of infertility has not been thoroughly demonstrated. Although the mouse is a good model system to perform functional studies, the differences between ...

    Authors: Zheng-Hui Zhao, Tie-Gang Meng, Ang Li, Heide Schatten, Zhen-Bo Wang and Qing-Yuan Sun

    Citation: BMC Genomics 2020 21:475

    Content type: Research article

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  13. Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer di...

    Authors: Juntang Guo, Kefeng Ma, Hua Bao, Xiangyuan Ma, Yang Xu, Xue Wu, Yang W. Shao, Mei Jiang and Jin Huang

    Citation: BMC Genomics 2020 21:473

    Content type: Research article

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  14. Mesangial cells play an important role in the glomerulus to provide mechanical support and maintaine efficient ultrafiltration of renal plasma. Loss of mesangial cells due to pathologic conditions may lead to ...

    Authors: Chee-Yin Wong, Yao-Ming Chang, Yu-Shuen Tsai, Wailap Victor Ng, Soon-Keng Cheong, Ting-Yu Chang, I-Fang Chung and Yang-Mooi Lim

    Citation: BMC Genomics 2020 21:467

    Content type: Research article

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  15. One of the health risks posed to astronauts during deep space flights is exposure to high charge, high-energy (HZE) ions (Z > 13), which can lead to the induction of hepatocellular carcinoma (HCC). However, li...

    Authors: Anna M. Nia, Kamil Khanipov, Brooke L. Barnette, Robert L. Ullrich, George Golovko and Mark R. Emmett

    Citation: BMC Genomics 2020 21:453

    Content type: Research article

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  16. Approximately 5% of the human genome shows common structural variation, which is enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural...

    Authors: Sandra Louzada, Walid Algady, Eleanor Weyell, Luciana W. Zuccherato, Paulina Brajer, Faisal Almalki, Marilia O. Scliar, Michel S. Naslavsky, Guilherme L. Yamamoto, Yeda A. O. Duarte, Maria Rita Passos-Bueno, Mayana Zatz, Fengtang Yang and Edward J. Hollox

    Citation: BMC Genomics 2020 21:446

    Content type: Research article

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  17. Multipotent mesenchymal stromal cells (MSCs) can be isolated from numerous tissues and are attractive candidates for therapeutic clinical applications due to their immunomodulatory and pro-regenerative capacit...

    Authors: Satoru Onizuka, Yasuharu Yamazaki, Sung-Joon Park, Takayuki Sugimoto, Yumiko Sone, Sebastian Sjöqvist, Michihiko Usui, Akira Takeda, Kenta Nakai, Keisuke Nakashima and Takanori Iwata

    Citation: BMC Genomics 2020 21:417

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:551

  18. Protein supplementation improves physiological adaptations to endurance training, but the impact on adaptive changes in the skeletal muscle transcriptome remains elusive. The present analysis was executed to d...

    Authors: Pim Knuiman, Roland Hangelbroek, Mark Boekschoten, Maria Hopman and Marco Mensink

    Citation: BMC Genomics 2020 21:397

    Content type: Research article

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  19. There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physica...

    Authors: Sarah Rose Moore, Kathryn Leigh Humphreys, Natalie Lisanne Colich, Elena Goetz Davis, David Tse Shen Lin, Julia Lynn MacIsaac, Michael Steffen Kobor and Ian Henry Gotlib

    Citation: BMC Genomics 2020 21:389

    Content type: Research article

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  20. Inflammation has been considered to be central to the onset, progression, and outcome of infectious diseases, especially as one of the hallmarks of cancer. Non-coding RNAs (ncRNAs), such as miRNAs and lncRNAs,...

    Authors: Shuyuan Wang, Shunheng Zhou, Haizhou Liu, Qianqian Meng, Xueyan Ma, Hui Liu, Lihong Wang and Wei Jiang

    Citation: BMC Genomics 2020 21:380

    Content type: Database

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  21. The computational prediction of methylation levels at single CpG resolution is promising to explore the methylation levels of CpGs uncovered by existing array techniques, especially for the 450 K beadchip arra...

    Authors: Jianxiong Tang, Jianxiao Zou, Xiaoran Zhang, Mei Fan, Qi Tian, Shuyao Fu, Shihong Gao and Shicai Fan

    Citation: BMC Genomics 2020 21:364

    Content type: Methodology article

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  22. The thymus is a highly specialized organ of the immune system where T cell precursors develop and differentiate into self-tolerant CD4+ or CD8+ T cells. No studies to date have investigated how the human trans...

    Authors: Hanna Helgeland, Ingvild Gabrielsen, Helle Akselsen, Arvind Y. M. Sundaram, Siri Tennebø Flåm and Benedicte Alexandra Lie

    Citation: BMC Genomics 2020 21:350

    Content type: Research article

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  23. DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle develo...

    Authors: Yixuan Fan, Yaxu Liang, Kaiping Deng, Zhen Zhang, Guomin Zhang, Yanli Zhang and Feng Wang

    Citation: BMC Genomics 2020 21:327

    Content type: Research article

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  24. Balanced complex chromosome rearrangements (BCCR) are balanced chromosomal structural aberrations that involve two or more chromosomes and at least three breakpoints. It is very rare in the population. The obj...

    Authors: Gang Li, Weiyi Shi, Wenbin Niu, Jiawei Xu, Yihong Guo, Yingchun Su and Yingpu Sun

    Citation: BMC Genomics 2020 21:326

    Content type: Research article

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  25. Copy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have i...

    Authors: Oscar A. Nyangiri, Harry Noyes, Julius Mulindwa, Hamidou Ilboudo, Justin Windingoudi Kabore, Bernardin Ahouty, Mathurin Koffi, Olivier Fataki Asina, Dieudonne Mumba, Elvis Ofon, Gustave Simo, Magambo Phillip Kimuda, John Enyaru, Vincent Pius Alibu, Kelita Kamoto, John Chisi…

    Citation: BMC Genomics 2020 21:289

    Content type: Research article

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  26. Histological grade (HG) is commonly adopted as a prognostic factor for ER-positive breast cancer patients. However, HG evaluation methods, such as the pathological Nottingham grading system, are highly subject...

    Authors: Jing Li, Wenbin Jiang, Qirui Liang, Guanghao Liu, Yupeng Dai, Hailong Zheng, Jing Yang, Hao Cai and Guo Zheng

    Citation: BMC Genomics 2020 21:283

    Content type: Research article

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  27. Graph-based reference genomes have become popular as they allow read mapping and follow-up analyses in settings where the exact haplotypes underlying a high-throughput sequencing experiment are not precisely k...

    Authors: Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt and Geir K. Sandve

    Citation: BMC Genomics 2020 21:282

    Content type: Methodology Article

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  28. The C:G > T:A substitution at the CpG dinucleotide contexts is the most frequent substitution type in genome evolution. The mutational process is obviously ongoing in the human germline; however, its impact on...

    Authors: Jeonghwan Youk, Yohan An, Seongyeol Park, June-Koo Lee and Young Seok Ju

    Citation: BMC Genomics 2020 21:270

    Content type: Research article

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  29. Marine endophytic fungi (MEF) are good sources of structurally unique and biologically active secondary metabolites. Due to the increase in antimicrobial resistance, the secondary metabolites from MEF ought to...

    Authors: Ethel Juliet Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur and James Adjaye

    Citation: BMC Genomics 2020 21:265

    Content type: Research article

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  30. Identifying nuclease-induced double-stranded breaks in DNA on a genome-wide scale is critical for assessing the safety and efficacy of genome editing therapies. We previously demonstrated that after administer...

    Authors: Camilo Breton, Peter M. Clark, Lili Wang, Jenny A. Greig and James M. Wilson

    Citation: BMC Genomics 2020 21:239

    Content type: Methodology article

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  31. DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web app...

    Authors: Tobias Rausch, Markus Hsi-Yang Fritz, Andreas Untergasser and Vladimir Benes

    Citation: BMC Genomics 2020 21:230

    Content type: Software

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  32. Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asia...

    Authors: Chani J. Hodonsky, Antoine R. Baldassari, Stephanie A. Bien, Laura M. Raffield, Heather M. Highland, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Marielisa Graff, Weihong Tang, Bharat Thyagarajan, Steve Buyske, Myriam Fornage, Lucia A. Hindorff, Yun Li, Danyu Lin…

    Citation: BMC Genomics 2020 21:228

    Content type: Research article

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  33. Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and i...

    Authors: Saman Khakmardan, Mohsen Rezvani, Ali Akbar Pouyan, Mansoor Fateh and Hamid Alinejad-Rokny

    Citation: BMC Genomics 2020 21:225

    Content type: Software

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  34. The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene...

    Authors: Huan Li, Shiyao Zhang, Wenxiang Zhang, Siyu Chen, Anjara Rabearivony, Yujie Shi, Jie Liu, Christopher J. Corton and Chang Liu

    Citation: BMC Genomics 2020 21:224

    Content type: Research article

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  35. Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages w...

    Authors: Yinghui Ling, Qi Zheng, Lu Zhu, Lina Xu, Menghua Sui, Yunhai Zhang, Ya Liu, Fugui Fang, Mingxing Chu, Yuehui Ma and Xiaorong Zhang

    Citation: BMC Genomics 2020 21:220

    Content type: Research article

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  36. Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred t...

    Authors: If H. A. Barnes, Ximena Ibarra-Soria, Stephen Fitzgerald, Jose M. Gonzalez, Claire Davidson, Matthew P. Hardy, Deepa Manthravadi, Laura Van Gerven, Mark Jorissen, Zhen Zeng, Mona Khan, Peter Mombaerts, Jennifer Harrow, Darren W. Logan and Adam Frankish

    Citation: BMC Genomics 2020 21:196

    Content type: Research article

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  37. Vaccines have greatly reduced the burden of infectious disease, ranking in their impact on global health second only after clean water. Most vaccines confer protection by the production of antibodies with bind...

    Authors: Anna Fowler, Jacob D. Galson, Johannes Trück, Dominic F. Kelly and Gerton Lunter

    Citation: BMC Genomics 2020 21:176

    Content type: Methodology Article

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  38. Proximity ligation based techniques, like Hi-C, involve restriction digestion followed by ligation of formaldehyde cross-linked chromatin. Distinct chromatin states can impact the restriction digestion, and he...

    Authors: Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, Srinivas Kethavath, Monika Dass, Harpreet Singh, Rakhee Nayak, Sreenivasulu Kurukuti and Kuljeet Singh Sandhu

    Citation: BMC Genomics 2020 21:175

    Content type: Research article

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  39. MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total m...

    Authors: Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiangdong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang and Xiaoxi Sun

    Citation: BMC Genomics 2020 21:165

    Content type: Research article

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  40. Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalia...

    Authors: Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W. Davis, Mitchell V. Finnegan, Matthew Geniza, David A. Hendrix, Christiane V. Löhr, Vanessa M. Petro, Thomas J. Sharpton, Jackson Wells, Clinton W. Epps, Pankaj Jaiswal, Brett M. Tyler…

    Citation: BMC Genomics 2020 21:153

    Content type: Research article

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  41. The consensus on how to choose a reference gene for serum or plasma miRNA expression qPCR studies has not been reached and none of the potential candidates have yet been convincingly validated. We proposed a n...

    Authors: Konrad Pagacz, Przemyslaw Kucharski, Urszula Smyczynska, Szymon Grabia, Dipanjan Chowdhury and Wojciech Fendler

    Citation: BMC Genomics 2020 21:111

    Content type: Methodology article

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  42. Luman is a member of CREB3 (cAMP responsive element-binding) subfamily of the basic leucine-zipper (bZIP) transcription factors. It may play an important regulatory role during the decidualization process sinc...

    Authors: Fan Zhao, Huan Liu, Nan Wang, Lijun Yu, Aihua Wang, Yanglei Yi and Yaping Jin

    Citation: BMC Genomics 2020 21:103

    Content type: Research article

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