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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 23

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  7. 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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  9. 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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  10. 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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  11. 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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  12. 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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  14. 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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  15. 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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  16. 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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  17. 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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  20. 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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  21. 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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  23. The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory ger...

    Authors: Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Liu, Xun Xu, Achim Klug and Elizabeth A. McCullagh

    Citation: BMC Genomics 2019 20:903

    Content type: Research article

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  25. Previous study reported that patients who suffered coronary heart disease (CHD) complicated with non-alcoholic fatty liver disease (NAFLD) had worse cardiac function and clinical outcomes than patients with CH...

    Authors: Yiwen Zhang, Jun Xu, Xuemei Wang, Xinhua Ren and Yulan Liu

    Citation: BMC Genomics 2019 20:862

    Content type: Research article

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  26. The incidence of dementia and cognitive decline is increasing with no therapy or cure. One of the reasons treatment remains elusive is because there are various pathologies that contribute to age-related cogni...

    Authors: Kate E. Foley, Hongtian Stanley Yang, Leah C. Graham and Gareth R. Howell

    Citation: BMC Genomics 2019 20:860

    Content type: Research article

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  27. Cleft lip (CL), one of the most common congenital birth defects, shows considerable geographic and ethnic variation, with contribution of both genetic and environmental factors. Mouse genetic studies have iden...

    Authors: Akiko Suzuki, Hiroki Yoshioka, Dima Summakia, Neha G. Desai, Goo Jun, Peilin Jia, David S. Loose, Kenichi Ogata, Mona V. Gajera, Zhongming Zhao and Junichi Iwata

    Citation: BMC Genomics 2019 20:852

    Content type: Research article

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  28. Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thor...

    Authors: Hong Zeng, Bao-fu Yu, Nan Liu, Yan-yan Yang, Hua-yi Xing, Xiao-xie Liu and Mou-wang Zhou

    Citation: BMC Genomics 2019 20:851

    Content type: Research article

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  29. micro RNA (miRNA) are important regulators of gene expression and may influence phenotypes and disease traits. The connection between genetics and miRNA expression can be determined through expression quantita...

    Authors: Gordon Kordas, Pratyaydipta Rudra, Audrey Hendricks, Laura Saba and Katerina Kechris

    Citation: BMC Genomics 2019 20:849

    Content type: Research article

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  30. Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous popul...

    Authors: Lian Deng, Haiyi Lou, Xiaoxi Zhang, Bhooma Thiruvahindrapuram, Dongsheng Lu, Christian R. Marshall, Chang Liu, Bo Xie, Wanxing Xu, Lai-Ping Wong, Chee-Wei Yew, Aghakhanian Farhang, Rick Twee-Hee Ong, Mohammad Zahirul Hoque, Abdul Rahman Thuhairah, Bhak Jong…

    Citation: BMC Genomics 2019 20:842

    Content type: Research article

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  31. Machine learning can effectively nominate novel genes for various research purposes in the laboratory. On a genome-wide scale, we implemented multiple databases and algorithms to predict and prioritize the human

    Authors: Masoud Arabfard, Mina Ohadi, Vahid Rezaei Tabar, Ahmad Delbari and Kaveh Kavousi

    Citation: BMC Genomics 2019 20:832

    Content type: Research article

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  32. Formalin-fixed and paraffin-embedded (FFPE) blocks held in clinical laboratories are an invaluable resource for clinical research, especially in the era of personalized medicine. It is important to accurately ...

    Authors: Xiaojing Lin, Lihong Qiu, Xue Song, Junyan Hou, Weizhi Chen and Jun Zhao

    Citation: BMC Genomics 2019 20:831

    Content type: Methodology article

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  33. As one of the most described epigenetic marks in human cancers, DNA methylation plays essential roles in gene expression regulation and has been implicated in the prognosis and therapeutics of many cancers. We...

    Authors: Xiao Chen, Jianying Zhang and Xiaofeng Dai

    Citation: BMC Genomics 2019 20:823

    Content type: Research article

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  34. The growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinic...

    Authors: Jacob J. Hughey, Seth D. Rhoades, Darwin Y. Fu, Lisa Bastarache, Joshua C. Denny and Qingxia Chen

    Citation: BMC Genomics 2019 20:805

    Content type: Research article

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  35. In the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars. Understanding the genetic architecture and detecting genetic markers asso...

    Authors: Ning Gao, Yilong Chen, Xiaohong Liu, Yunxiang Zhao, Lin Zhu, Ali Liu, Wei Jiang, Xing Peng, Conglin Zhang, Zhenshuang Tang, Xinyun Li and Yaosheng Chen

    Citation: BMC Genomics 2019 20:797

    Content type: Research article

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  37. The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of st...

    Authors: Ran Li, Xiaomeng Tian, Peng Yang, Yingzhi Fan, Ming Li, Hongxiang Zheng, Xihong Wang and Yu Jiang

    Citation: BMC Genomics 2019 20:746

    Content type: Research article

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  38. Heart disease (HD) is the major cause of morbidity and mortality in patients with hypereosinophilic diseases. Due to a lack of adequate animal models, our understanding of the pathophysiology of eosinophil-med...

    Authors: Nives Zimmermann, William J. Gibbons Jr, Shelli M. Homan and Daniel R. Prows

    Citation: BMC Genomics 2019 20:727

    Content type: Research article

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  39. The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study,...

    Authors: Thomas J. Ha, Peter G. Y. Zhang, Remi Robert, Joanna Yeung, Douglas J. Swanson, Anthony Mathelier, Wyeth W. Wasserman, Sujin Im, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest…

    Citation: BMC Genomics 2019 20:718

    Content type: Research article

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  40. Our previous study had proved that nigericin could reduce colorectal cancer cell proliferation in dose- and time-dependent manners by targeting Wnt/β-catenin signaling. To better elucidate its potential anti-c...

    Authors: Zhihua Xu, Jiaqing Shen, Shangbo Hua, Daiwei Wan, Qian Chen, Ye Han, Rui Ren, Fei Liu, Zhiyong Du, Xiaobo Guo, Jianming Shi and Qiaoming Zhi

    Citation: BMC Genomics 2019 20:716

    Content type: Research article

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  42. Infection with Toxoplasma gondii is thought to damage the brain and be a risk factor for neurological and psychotic disorders. The immune response-participating chemokine system has recently been considered vital...

    Authors: Kaoru Kobayashi, Kousuke Umeda, Fumiaki Ihara, Sachi Tanaka, Junya Yamagishi, Yutaka Suzuki and Yoshifumi Nishikawa

    Citation: BMC Genomics 2019 20:705

    Content type: Research article

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  43. It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA ...

    Authors: Rick J. Jansen, Lin Tong, Maria Argos, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md. Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md. Yunus, Muhammad G. Kibriya, John A. Baron, Habibul Ahsan and Brandon L. Pierce

    Citation: BMC Genomics 2019 20:704

    Content type: Research article

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  44. Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity ...

    Authors: Aditya Vijay Bhagwate, Yuanhang Liu, Stacey J. Winham, Samantha J. McDonough, Melody L. Stallings-Mann, Ethan P. Heinzen, Jaime I. Davila, Robert A. Vierkant, Tanya L. Hoskin, Marlene Frost, Jodi M. Carter, Derek C. Radisky, Julie M. Cunningham, Amy C. Degnim and Chen Wang

    Citation: BMC Genomics 2019 20:689

    Content type: Research article

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  45. Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given tha...

    Authors: Anouk M. Olthof, Katery C. Hyatt and Rahul N. Kanadia

    Citation: BMC Genomics 2019 20:686

    Content type: Research article

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  46. Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying m...

    Authors: Erik N. Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen and Ludmil B. Alexandrov

    Citation: BMC Genomics 2019 20:685

    Content type: Software

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  47. Brain-derived neurotrophic factor (BDNF) is a major signaling molecule that the brain uses to control a vast network of intracellular cascades fundamental to properties of learning and memory, and cognition. W...

    Authors: Kathryn M. Hixson, Meaghan Cogswell, Amy R. Brooks-Kayal and Shelley J. Russek

    Citation: BMC Genomics 2019 20:677

    Content type: Research article

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  48. Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several...

    Authors: Qiang Liu, Aisheng Hou, Yongyi Zhang, Ying Guo, Jingjing Li, Yinghao Yao, Kaimeng Niu, Hao Li, Yunlong Ma and Jiangbei Cao

    Citation: BMC Genomics 2019 20:670

    Content type: Research article

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  49. Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. ...

    Authors: Saurabh Belsare, Michal Levy-Sakin, Yulia Mostovoy, Steffen Durinck, Subhra Chaudhuri, Ming Xiao, Andrew S. Peterson, Pui-Yan Kwok, Somasekar Seshagiri and Jeffrey D. Wall

    Citation: BMC Genomics 2019 20:620

    Content type: Research article

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  50. Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a wh...

    Authors: Samarth Rangavittal, Natasha Stopa, Marta Tomaszkiewicz, Kristoffer Sahlin, Kateryna D. Makova and Paul Medvedev

    Citation: BMC Genomics 2019 20:641

    Content type: Methodology article

    Published on:

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