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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. Prior work demonstrated that female rats (but not their male littermates) exposed to methamphetamine become hypersensitive to myocardial ischemic injury. Importantly, this sex-dependent effect persists followi...

    Authors: Hasitha Chavva, Daniel A. Brazeau, James Denvir, Donald A. Primerano, Jun Fan, Sarah L. Seeley and Boyd R. Rorabaugh

    Citation: BMC Genomics 2021 22:259

    Content type: Research article

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  2. Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial ...

    Authors: B. Dnate’ Baxter, Eric D. Larson, Laetitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N. Bubak, Christy S. Niemeyer, James Hassell Jr, Doug Shepherd, Vijay R. Ramakrishnan, Maria A. Nagel and Diego Restrepo

    Citation: BMC Genomics 2021 22:224

    Content type: Research article

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  3. Low pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has re...

    Authors: Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King and Charles Cox

    Citation: BMC Genomics 2021 22:197

    Content type: Research article

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  4. MicroRNAs play an important role in many fundamental biological and pathological processes. Defining the microRNAs profile underlying the processes by beneficial and detrimental lifestyles, including caloric r...

    Authors: Huan Gong, Ming Zhang, Yiwen Han, Ying Zhang, Jing Pang, Yanyang Zhao, Beidong Chen, Wei Wu, Ruomei Qi and Tiemei Zhang

    Citation: BMC Genomics 2021 22:196

    Content type: Research article

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  5. Aging is a multifactorial process that affects multiple tissues and is characterized by changes in homeostasis over time, leading to increased morbidity. Whole blood gene expression signatures have been associ...

    Authors: Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra and Lude Franke

    Citation: BMC Genomics 2021 22:184

    Content type: Research article

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  6. It is still challenging to predict interacting enhancer-promoter pairs (IEPs), partially because of our limited understanding of their characteristics. To understand IEPs better, here we studied the IEPs in ni...

    Authors: Amlan Talukder, Haiyan Hu and Xiaoman Li

    Citation: BMC Genomics 2021 22:163

    Content type: Research article

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  7. Bi-specific T-cell engager (BiTE) antibody is a class of bispecific antibodies designed for cancer immunotherapy. Blinatumomab is the first approved BiTE to treat acute B cell lymphoblastic leukemia (B-ALL). I...

    Authors: Yi Huo, Zhen Sheng, Daniel R. Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Yin and Ruibao Ren

    Citation: BMC Genomics 2021 22:145

    Content type: Research article

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  8. Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individua...

    Authors: Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman and Hakon Hakonarson

    Citation: BMC Genomics 2021 22:133

    Content type: Software

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  9. Toxoplasma gondii is a globally distributed protozoan parasite that establishes life-long asymptomatic infection in humans, often emerging as a life-threatening opportunistic pathogen during immunodeficiency. As ...

    Authors: Kayla L. Menard, Lijing Bu and Eric Y. Denkers

    Citation: BMC Genomics 2021 22:130

    Content type: Research article

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  10. Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by trans...

    Authors: Jinhuan Dou, Flavio Schenkel, Lirong Hu, Adnan Khan, Muhammad Zahoor Khan, Ying Yu, Yajing Wang and Yachun Wang

    Citation: BMC Genomics 2021 22:122

    Content type: Research article

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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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

  42. 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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