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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.

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  1. Content type: Research article

    Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The ai...

    Authors: Philip M. M. Ruppert, Jong-Gil Park, Xu Xu, Kyu Yeon Hur, Ann-Hwee Lee and Sander Kersten

    Citation: BMC Genomics 2019 20:199

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  2. Content type: Database Article

    Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with para...

    Authors: Benjamin N. Bimber, Melissa Y. Yan, Samuel M. Peterson and Betsy Ferguson

    Citation: BMC Genomics 2019 20:176

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  3. Content type: Research article

    Altered epigenetic profiles are a feature of intestinal diseases, including ulcerative colitis and Crohn’s disease. DNA methylation studies in these diseases have utilised intestinal mucosal tissue or blood wh...

    Authors: Nerissa L. Hearn, Aaron S. Coleman, Vincent Ho, Christine L. Chiu and Joanne M. Lind

    Citation: BMC Genomics 2019 20:163

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  4. Content type: Research article

    Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well establishe...

    Authors: Kimberly E. Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan and Sean D. Taverna

    Citation: BMC Genomics 2019 20:147

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  5. Content type: Research article

    Heat illness remains a significant cause of morbidity in susceptible populations. Recent research elucidating the cellular mechanism of heat stress leading to heat illness may provide information to develop be...

    Authors: Matthew G. Permenter, Bonna C. McDyre, Danielle L. Ippolito and Jonathan D. Stallings

    Citation: BMC Genomics 2019 20:141

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  6. Content type: Research article

    The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression me...

    Authors: Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2019 20:134

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  7. Content type: Research article

    Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Historically, gene targeting was first done in embryonic stem cells (ESCs) derived from the 129 famil...

    Authors: C. Farkas, F. Fuentes-Villalobos, B. Rebolledo-Jaramillo, F. Benavides, A. F. Castro and R. Pincheira

    Citation: BMC Genomics 2019 20:131

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  8. Content type: Research article

    While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investig...

    Authors: Michael Boettcher, Sergio Covarrubias, Anne Biton, James Blau, Haopeng Wang, Noah Zaitlen and Michael T. McManus

    Citation: BMC Genomics 2019 20:107

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  9. Content type: Methodology article

    In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conse...

    Authors: Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier and Laurent Bréhélin

    Citation: BMC Genomics 2019 20:103

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  10. Content type: Research article

    DNA methylation is involved in the regulation of gene expression. Although bisulfite-sequencing based methods profile DNA methylation at a single CpG resolution, methylation levels are usually averaged over ge...

    Authors: Anna V. Lioznova, Abdullah M. Khamis, Artem V. Artemov, Elizaveta Besedina, Vasily Ramensky, Vladimir B. Bajic, Ivan V. Kulakovskiy and Yulia A. Medvedeva

    Citation: BMC Genomics 2019 20:102

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  11. Content type: Research article

    Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific trans...

    Authors: Alexander Kanitz, Afzal Pasha Syed, Keisuke Kaji and Mihaela Zavolan

    Citation: BMC Genomics 2019 20:100

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  12. Content type: Research article

    Brain sexual differentiation is sculpted by precise coordination of steroid hormones during development. Programming of several brain regions in males depends upon aromatase conversion of testosterone to estro...

    Authors: Madison T. Ortega, Nathan J. Bivens, Takamichi Jogahara, Asato Kuroiwa, Scott A. Givan and Cheryl S. Rosenfeld

    Citation: BMC Genomics 2019 20:87

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  13. Content type: Methodology article

    Hi-C and capture Hi-C (CHi-C) are used to map physical contacts between chromatin regions in cell nuclei using high-throughput sequencing. Analysis typically proceeds considering the evidence for contacts betw...

    Authors: Christiaan Q Eijsbouts, Oliver S Burren, Paul J Newcombe and Chris Wallace

    Citation: BMC Genomics 2019 20:77

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  14. Content type: Research article

    Tuberculosis is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M.tb). M.tb subverts host immune responses to build a favourable niche and survive inside of host macrophages. Macrophag...

    Authors: Elena Denisenko, Reto Guler, Musa Mhlanga, Harukazu Suzuki, Frank Brombacher and Sebastian Schmeier

    Citation: BMC Genomics 2019 20:71

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  15. Content type: Research article

    Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be ben...

    Authors: Hannah Voic, Xiuying Li, Jun-Ho Jang, Chunbin Zou, Prithu Sundd, Jonathan Alder, Mauricio Rojas, Divay Chandra, Scott Randell, Rama K. Mallampalli, Yohannes Tesfaigzi, Tyrone Ryba and Toru Nyunoya

    Citation: BMC Genomics 2019 20:22

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  16. Content type: Research article

    Spalax, the blind mole rat, developed an extraordinary cancer resistance during 40 million years of evolution in a subterranean, hypoxic, thus DNA damaging, habitat. In 50 years of Spalax research, no spontaneous...

    Authors: Robert Altwasser, Arnon Paz, Abraham Korol, Irena Manov, Aaron Avivi and Imad Shams

    Citation: BMC Genomics 2019 20:17

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  17. Content type: Research article

    Heart development is a relatively fragile process in which many transcription factor genes show dose-sensitive characteristics such as haploinsufficiency and lower penetrance. Despite efforts to unravel the ge...

    Authors: Yutaro Hori, Yoko Tanimoto, Satoru Takahashi, Tetsushi Furukawa, Kazuko Koshiba-Takeuchi and Jun K. Takeuchi

    Citation: BMC Genomics 2018 19:967

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  18. Content type: Software

    Studies that aim at explaining phenotypes or disease susceptibility by genetic or epigenetic variants often rely on clustering methods to stratify individuals or samples. While statistical associations may poi...

    Authors: Jiangning Gao, Görel Sundström, Behrooz Torabi Moghadam, Neda Zamani and Manfred G. Grabherr

    Citation: BMC Genomics 2018 19:964

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  19. Content type: Research article

    A-to-I RNA editing is a co−/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, ...

    Authors: Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Alice Filippini, Jessica Mingardi, Chiara Magri and Alessandro Barbon

    Citation: BMC Genomics 2018 19:963

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  20. Content type: Research article

    Swine streptococcosis has caused great economic loss in the swine industry, and the major pathogen responsible for this disease is Streptococcus Suis serotype 2 (SS2). Disease resistance breeding is a fundamental...

    Authors: Zhe Ma, Haodan Zhu, Yiqi Su, Yu Meng, Huixing Lin, Kongwang He and Hongjie Fan

    Citation: BMC Genomics 2018 19:907

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  21. Content type: Research article

    Subterranean rodents have evolved many features to adapt to their hypoxic environment. The brain is an organ that is particularly vulnerable to damage caused by exposure to hypoxic conditions. To investigate t...

    Authors: Qianqian Dong, Luye Shi, Yangwei Li, Mengwan Jiang, Hong Sun, Baishi Wang, Han Cheng, Yifeng Zhang, Tian Shao, Yuhua Shi and Zhenlong Wang

    Citation: BMC Genomics 2018 19:901

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  22. Content type: Research article

    While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and express...

    Authors: Madeline Rose Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang and James M. Cheverud

    Citation: BMC Genomics 2018 19:888

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  23. Content type: Research article

    Copy number variants (CNVs) have been shown to increase risk for physical anomalies, developmental, psychiatric and medical disorders. Some of them have been associated with changes in weight, height, and othe...

    Authors: David Owen, Mathew Bracher-Smith, Kimberley M. Kendall, Elliott Rees, Mark Einon, Valentina Escott-Price, Michael J. Owen, Michael C. O’Donovan and George Kirov

    Citation: BMC Genomics 2018 19:867

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  24. Content type: Research article

    The CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders. While the non-synonymous CHRNA5 variant rs16969968 appears to be the main risk factor, linkage disequilibriu...

    Authors: Sung-Ha Lee, Woo-Young Ahn, Michał Seweryn and Wolfgang Sadee

    Citation: BMC Genomics 2018 19:826

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  25. Content type: Database

    MicroRNAs (miRNAs) regulate gene expression and have been targeted as indicators of environmental/toxicologic stressors. Using the data from our deep sequencing of miRNAs in an extensive sampling of rat tissue...

    Authors: Pierre R. Bushel, Florian Caiment, Han Wu, Raegan O’Lone, Frank Day, John Calley, Aaron Smith and Jianying Li

    Citation: BMC Genomics 2018 19:825

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  26. Content type: Research article

    PAX6 is a homeodomain transcription factor that acts in a highly dosage-sensitive manner to regulate the development and function of the eyes, nose, central nervous system, gut, and endocrine pancreas. Several...

    Authors: Bridget C. Ryan, Kieran Lowe, Laura Hanson, Talveen Gil, Lauren Braun, Perry L. Howard and Robert L. Chow

    Citation: BMC Genomics 2018 19:820

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  27. Content type: Research article

    The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regu...

    Authors: Katarzyna Szołtysek, Patryk Janus, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Simon Cockell, Neil D. Perkins, Marek Kimmel and Piotr Widlak

    Citation: BMC Genomics 2018 19:813

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  28. Content type: Research article

    Current heart failure (HF) treatment is based on targeting symptoms and left ventricle dysfunction severity, relying on a common HF pathway paradigm to justify common treatments for HF patients. This common st...

    Authors: Mary E. Sweet, Andrea Cocciolo, Dobromir Slavov, Kenneth L. Jones, Joseph R. Sweet, Sharon L. Graw, T. Brett Reece, Amrut V. Ambardekar, Michael R. Bristow, Luisa Mestroni and Matthew R. G. Taylor

    Citation: BMC Genomics 2018 19:812

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  29. Content type: Research article

    Epithelial–mesenchymal transition (EMT) is regarded as a critical event during tumor metastasis. Recent studies have revealed changes and the contributions of proteins in/on exosomes during EMT. Besides protei...

    Authors: Yue-Ting Tang, Yi-Yao Huang, Jing-Huan Li, Si-Hua Qin, Yong Xu, Tai-Xue An, Chun-Chen Liu, Qian Wang and Lei Zheng

    Citation: BMC Genomics 2018 19:802

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  30. Content type: Research article

    Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-whi...

    Authors: Juan Carlos Higareda-Almaraz, Michael Karbiener, Maude Giroud, Florian M. Pauler, Teresa Gerhalter, Stephan Herzig and Marcel Scheideler

    Citation: BMC Genomics 2018 19:794

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  31. Content type: Methodology article

    Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) da...

    Authors: Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa and Seiya Imoto

    Citation: BMC Genomics 2018 19:790

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  32. Content type: Research article

    Our previous study showed that (+)-cholesten-3-one (CN) has the potential to induce the osteoblastic differentiation of mesenchymal stem cells (MSCs). However, the roles of CN in targeting miRNA-mRNA-lncRNA in...

    Authors: Qiuke Hou, Yongquan Huang, Yamei Liu, Yiwen Luo, Bin Wang, Rudong Deng, Saixia Zhang, Fengbin Liu and Dongfeng Chen

    Citation: BMC Genomics 2018 19:783

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  33. Content type: Research article

    The relationship between aging and epigenetic profiles has been highlighted in many recent studies. Models using somatic cell methylomes to predict age have been successfully constructed. However, gamete aging...

    Authors: Timothy G. Jenkins, Kenneth I. Aston, Bradley Cairns, Andrew Smith and Douglas T. Carrell

    Citation: BMC Genomics 2018 19:763

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  34. Content type: Research article

    Mitochondrial DNA (mtDNA) copy number has been found associated with multiple diseases, including cancers, diabetes and so on. Both environmental and genetic factors could affect the copy number of mtDNA. Howe...

    Authors: Zhihua Li, Meng Zhu, Jiangbo Du, Hongxia Ma, Guangfu Jin and Juncheng Dai

    Citation: BMC Genomics 2018 19:752

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  35. Content type: Research article

    Long noncoding RNAs (lncRNAs) are known to play important roles in different cell contexts, including cancers. However, little is known about lncRNAs in cholangiocarcinoma (CCA), a cholangiocyte malignancy wit...

    Authors: Bo-Wei Han, Hua Ye, Pan-Pan Wei, Bo He, Cai Han, Zhen-Hua Chen, Yue-Qin Chen and Wen-Tao Wang

    Citation: BMC Genomics 2018 19:735

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  36. Content type: Research article

    Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their gene transcription profile. This technology is widely used in medicine, animal husbandry and other industries. Ho...

    Authors: Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Jing Xin, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao and Wenyong Li

    Citation: BMC Genomics 2018 19:734

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  37. Content type: Research article

    The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interf...

    Authors: Nicolás Santander, Carlos Lizama, Leandro Murgas, Sebastián Contreras, Alberto J. M. Martin, Paz Molina, Alonso Quiroz, Katherine Rivera, Francisca Salas-Pérez, Alejandro Godoy, Attilio Rigotti and Dolores Busso

    Citation: BMC Genomics 2018 19:731

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  38. Content type: Research article

    Transposome-based technologies have enabled the streamlined production of sequencer-ready DNA libraries; however, current methods are highly sensitive to the amount and quality of input nucleic acid.

    Authors: Stephen Bruinsma, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, Lee Brady, Anupama Khanna, Lindsay Freeberg, Rosamond G Jackson, Pascale Mathonet, Susan C Verity, Andrew F Slatter, Rooz Golshani, Haiying Grunenwald…

    Citation: BMC Genomics 2018 19:722

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  39. Content type: Software

    Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the ...

    Authors: Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh and Hiroaki Kitano

    Citation: BMC Genomics 2018 19:715

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