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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. Branch points (BPs) map within short motifs upstream of acceptor splice sites (3’ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, B...

    Authors: Raphaël Leman, Hélène Tubeuf, Sabine Raad, Isabelle Tournier, Céline Derambure, Raphaël Lanos, Pascaline Gaildrat, Gaia Castelain, Julie Hauchard, Audrey Killian, Stéphanie Baert-Desurmont, Angelina Legros, Nicolas Goardon, Céline Quesnelle, Agathe Ricou, Laurent Castera…

    Citation: BMC Genomics 2020 21:86

    Content type: Research article

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  34. Increasing evidence has shown that circular RNAs (circRNAs) are involved in neurodegenerative disorders, but their roles in neurological toxoplasmosis are yet to know. This study examined miRNA and circRNA exp...

    Authors: Chun-Xue Zhou, Kang Ai, Cui-Qin Huang, Jing-Jing Guo, Hua Cong, Shen-Yi He and Xing-Quan Zhu

    Citation: BMC Genomics 2020 21:46

    Content type: Research article

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  35. Hypoxia mediated pulmonary hypertension (HPH) is a lethal disease and lacks effective therapy. CircRNAs play significant roles in physiological process. Recently, circRNAs are found to be m6A-modified. The abunda...

    Authors: Hua Su, Guowen Wang, Lingfang Wu, Xiuqing Ma, Kejing Ying and Ruifeng Zhang

    Citation: BMC Genomics 2020 21:39

    Content type: Research article

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  36. DNA double-stranded breaks (DSBs) are potentially deleterious events in a cell. The end structures (blunt, 3′- and 5′-overhangs) at DSB sites contribute to the fate of their repair and provide critical informa...

    Authors: Karol Szlachta, Heather M. Raimer, Laurey D. Comeau and Yuh-Hwa Wang

    Citation: BMC Genomics 2020 21:25

    Content type: Methodology article

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  37. Myopia is one of the most common vision defects worldwide. microRNAs can regulate the target gene expression, influencing the development of diseases.

    Authors: Dadong Guo, Meihua Ding, Xiaoli Song, Yuanyuan Sun, Guoping Li, Zonghong Li, Huixia Wei, Jianfeng Wu, Wenjun Jiang and Hongsheng Bi

    Citation: BMC Genomics 2020 21:13

    Content type: Research article

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  38. The clinical success of immune checkpoint inhibitors demonstrates that reactivation of the human immune system delivers durable responses for some patients and represents an exciting approach for cancer treatm...

    Authors: Wenyan Zhong, Jeremy S. Myers, Fang Wang, Kai Wang, Justin Lucas, Edward Rosfjord, Judy Lucas, Andrea T. Hooper, Sharon Yang, Lu Anna Lemon, Magali Guffroy, Chad May, Jadwiga R. Bienkowska and Paul A. Rejto

    Citation: BMC Genomics 2020 21:2

    Content type: Research article

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  39. The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we perfor...

    Authors: Nirupama Benis, Jerry M. Wells, Mari A. Smits, Soumya Kanti Kar, Bart van der Hee, Vitor A. P. Martins dos Santos, Maria Suarez-Diez and Dirkjan Schokker

    Citation: BMC Genomics 2019 20:1028

    Content type: Research article

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  40. Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic ana...

    Authors: Christopher J. Troll, Joshua Kapp, Varsha Rao, Kelly M. Harkins, Charles Cole, Colin Naughton, Jessica M. Morgan, Beth Shapiro and Richard E. Green

    Citation: BMC Genomics 2019 20:1023

    Content type: Methodology article

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  41. Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacterium that causes serious life threatening and nosocomial infections including pneumonia. PA has the ability to alter host genome to facilitate it...

    Authors: David L. Ebenezer, Panfeng Fu, Yashaswin Krishnan, Mark Maienschein-Cline, Hong Hu, Segun Jung, Ravi Madduri, Zarema Arbieva, Anantha Harijith and Viswanathan Natarajan

    Citation: BMC Genomics 2019 20:984

    Content type: Research article

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  42. Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices base...

    Authors: Yanling Hu, Aihua Tan, Lei Yu, Chenyang Hou, Haofa Kuang, Qunying Wu, Jinghan Su, Qingniao Zhou, Yuanyuan Zhu, Chenqi Zhang, Wei Wei, Lianfeng Li, Weidong Li, Yuanjie Huang, Hongli Huang, Xing Xie…

    Citation: BMC Genomics 2019 20:983

    Content type: Research article

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