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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

  2. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  16. 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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  17. 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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  18. 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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  19. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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

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  30. The regenerative ability of severed axons in the central nervous system is limited in mammals. However, after central nervous system injury, neural function is partially recovered by the formation of a compens...

    Authors: Hiroshi Tsujioka and Toshihide Yamashita

    Citation: BMC Genomics 2019 20:619

    Content type: Research article

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  31. Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enab...

    Authors: Takashi Shimbo, Machika Kawamura, Edward Wijaya, Eiichi Takaki, Yasufumi Kaneda and Katsuto Tamai

    Citation: BMC Genomics 2019 20:614

    Content type: Methodology article

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  32. Esophageal squamous cell carcinoma (ESCC) cells are heterogeneous, easily develop radioresistance, and recur. Single-cell RNA-seq (scRNA-seq) is a next-generation sequencing method that can delineate diverse g...

    Authors: Ling Yang, Xiaoyan Zhang, Qiang Hou, Ming Huang, Hongfang Zhang, Zhenzhen Jiang, Jing Yue and Shixiu Wu

    Citation: BMC Genomics 2019 20:611

    Content type: Research article

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  33. Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader sp...

    Authors: Isabel Garcia Sousa, Kelly Cristina Rodrigues Simi, Manuela Maragno do Almo, Maryani Andressa Gomes Bezerra, Gero Doose, Tainá Raiol, Peter F. Stadler, Steve Hoffmann, Andréa Queiroz Maranhão and Marcelo Macedo Brigido

    Citation: BMC Genomics 2019 20:593

    Content type: Research article

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  35. Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterizat...

    Authors: Mohamed Doulazmi, Cyril Cros, Isabelle Dusart, Alain Trembleau and Caroline Dubacq

    Citation: BMC Genomics 2019 20:577

    Content type: Research article

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  37. A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, ...

    Authors: Ying Wan, Xiaoyang Liu, Dongwang Zheng, Yuying Wang, Huan Chen, Xiaofeng Zhao, Guoqing Liang, Dongliang Yu and Lin Gan

    Citation: BMC Genomics 2019 20:559

    Content type: Research article

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  38. Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such...

    Authors: Daoshan Zheng, Justyna Trynda, Zhifu Sun and Zhaoyu Li

    Citation: BMC Genomics 2019 20:541

    Content type: Software

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  39. Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effect...

    Authors: Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J. C. Slebos, Christine H. Chung and Xuefeng Wang

    Citation: BMC Genomics 2019 20:539

    Content type: Methodology article

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  41. Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enh...

    Authors: Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka and John A. Capra

    Citation: BMC Genomics 2019 20:511

    Content type: Research article

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  42. Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognosticatio...

    Authors: Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao Saal, Åke Borg, Johan Vallon-Christerson and Carlos Rovira

    Citation: BMC Genomics 2019 20:503

    Content type: Research article

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  43. The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gai...

    Authors: Charlotte R. Feddersen, Lexy S. Wadsworth, Eliot Y. Zhu, Hayley R. Vaughn, Andrew P. Voigt, Jesse D. Riordan and Adam J. Dupuy

    Citation: BMC Genomics 2019 20:497

    Content type: Methodology article

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  44. Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection...

    Authors: Adam Scheidegger, Carissa J. Dunn, Ann Samarakkody, Nii Koney-Kwaku Koney, Danielle Perley, Ramendra N. Saha and Sergei Nechaev

    Citation: BMC Genomics 2019 20:477

    Content type: Research article

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  45. Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of ...

    Authors: Andrii Slonchak, Brian Clarke, Jason Mackenzie, Alberto Anastacio Amarilla, Yin Xiang Setoh and Alexander A. Khromykh

    Citation: BMC Genomics 2019 20:474

    Content type: Research article

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  46. The most widely used human genome reference assembly hg19 harbors minor alleles at 2.18 million positions as revealed by 1000 Genome Phase 3 dataset. Although this is less than 2% of the 89 million variants re...

    Authors: Harsh G. Shukla, Pushpinder Singh Bawa and Subhashini Srinivasan

    Citation: BMC Genomics 2019 20:459

    Content type: Research article

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  47. Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification ag...

    Authors: A. C. Picornell, I. Echavarria, E. Alvarez, S. López-Tarruella, Y. Jerez, K. Hoadley, J. S. Parker, M. del Monte-Millán, R. Ramos-Medina, J. Gayarre, I. Ocaña, M. Cebollero, T. Massarrah, F. Moreno, J. A. García Saenz, H. Gómez Moreno…

    Citation: BMC Genomics 2019 20:452

    Content type: Research article

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  49. Mutations in the transcription factor, KLF1, are common within certain populations of the world. Heterozygous missense mutations in KLF1 mostly lead to benign phenotypes, but a heterozygous mutation in a DNA-bind...

    Authors: Melissa D. Ilsley, Stephen Huang, Graham W. Magor, Michael J. Landsberg, Kevin R. Gillinder and Andrew C. Perkins

    Citation: BMC Genomics 2019 20:417

    Content type: Research article

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  50. Our previous study described the crucial role of Rho-associated coiled-coil containing-kinases (ROCK) in hepatocellular carcinoma (HCC). However, the potential significance of long noncoding RNA downstream of ...

    Authors: He-Ming Zhou, Ji-Gang Zhang, Xue Zhang, Guo-Rong Fan, Gao-Lin Liu and Qin Li

    Citation: BMC Genomics 2019 20:409

    Content type: Research article

    Published on:

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