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Human and rodent genomics

This section covers the genome structure and function in humans, primates and rodents.

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  1. Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps wer...

    Authors: Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi, Heping Zheng, Yousong Peng and Zhongyang Tan

    Citation: BMC Genomics 2021 22:76

    Content type: Research article

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  3. DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epi...

    Authors: Victor Yuan, Desmond Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain and Wendy P. Robinson

    Citation: BMC Genomics 2021 22:6

    Content type: Research article

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  4. Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood fol...

    Authors: Axelle Brulport, Daniel Vaiman, Elias Bou-Maroun, Marie-Christine Chagnon and Ludovic Le Corre

    Citation: BMC Genomics 2020 21:881

    Content type: Research article

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  5. The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improv...

    Authors: M. Heath Farris, Pamela A. Texter, Agustin A. Mora, Michael V. Wiles, Ellen F. Mac Garrigle, Sybil A. Klaus and Kristine Rosfjord

    Citation: BMC Genomics 2020 21:856

    Content type: Methodology article

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  7. Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important comp...

    Authors: Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang and San Ming Wang

    Citation: BMC Genomics 2020 21:842

    Content type: Research article

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  9. Malonylation is a recently discovered post-translational modification that is associated with a variety of diseases such as Type 2 Diabetes Mellitus and different types of cancers. Compared with experimental i...

    Authors: Xin Liu, Liang Wang, Jian Li, Junfeng Hu and Xiao Zhang

    Citation: BMC Genomics 2020 21:812

    Content type: Methodology article

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  10. Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughpu...

    Authors: Bronte Wen, Hyun Jun Jung, Lihe Chen, Fahad Saeed and Mark A. Knepper

    Citation: BMC Genomics 2020 21:806

    Content type: Software

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  11. Birth weight is determined by the interplay between infant genetics and the intrauterine environment and is associated with several health outcomes in later life. Many studies have reported an association betw...

    Authors: Pontus Henriksson, Antonio Lentini, Signe Altmäe, David Brodin, Patrick Müller, Elisabet Forsum, Colm E. Nestor and Marie Löf

    Citation: BMC Genomics 2020 21:769

    Content type: Research article

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  12. Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 i...

    Authors: Daniela Kajihara, Chung-Chau Hon, Aimi Naim Abdullah, João Wosniak Jr, Ana Iochabel S. Moretti, Joice F. Poloni, Diego Bonatto, Kosuke Hashimoto, Piero Carninci and Francisco R. M. Laurindo

    Citation: BMC Genomics 2020 21:766

    Content type: Research article

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  13. Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gol...

    Authors: Wesley J. Delage, Julien Thevenon and Claire Lemaitre

    Citation: BMC Genomics 2020 21:762

    Content type: Research article

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  14. The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, u...

    Authors: Ilona Binenbaum, Hanifa Abu-Toamih Atamni, Georgios Fotakis, Georgia Kontogianni, Theodoros Koutsandreas, Eleftherios Pilalis, Richard Mott, Heinz Himmelbauer, Fuad A. Iraqi and Aristotelis A. Chatziioannou

    Citation: BMC Genomics 2020 21:761

    Content type: Research article

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  15. Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematic...

    Authors: Siddharth Sethi, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Simon Greenaway, John Williams, Vsevolod J. Makeev, Steve D. M. Brown, Michelle M. Simon and Ann-Marie Mallon

    Citation: BMC Genomics 2020 21:754

    Content type: Research article

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  17. Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMeth...

    Authors: Yunsung Lee, Kristine L. Haftorn, William R. P. Denault, Haakon E. Nustad, Christian M. Page, Robert Lyle, Sindre Lee-Ødegård, Gunn-Helen Moen, Rashmi B. Prasad, Leif C. Groop, Line Sletner, Christine Sommer, Maria C. Magnus, Håkon K. Gjessing, Jennifer R. Harris, Per Magnus…

    Citation: BMC Genomics 2020 21:747

    Content type: Methodology article

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  18. In diploid cells, it is important to construct maternal and paternal Hi-C contact maps respectively since the two homologous chromosomes can differ in chromatin three-dimensional (3D) organization. Though prev...

    Authors: Han Luo, Xinxin Li, Haitao Fu and Cheng Peng

    Citation: BMC Genomics 2020 21:746

    Content type: Software

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  19. 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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  20. 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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  21. 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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  22. 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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  24. 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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  25. 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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  27. 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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  28. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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

  39. 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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  40. 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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  41. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  49. 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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  50. 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

    Published on:

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