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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 21

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. Content type: Research article

    Human perception of bitter substances is partially genetically determined. Previously we discovered a single nucleotide polymorphism (SNP) within the cluster of bitter taste receptor genes on chromosome 12 tha...

    Authors: Liang-Dar Hwang, Puya Gharahkhani, Paul A. S. Breslin, Scott D. Gordon, Gu Zhu, Nicholas G. Martin, Danielle R. Reed and Margaret J. Wright

    Citation: BMC Genomics 2018 19:678

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  20. Content type: Research article

    The current literature on single cell genomic analyses on the DNA level is conflicting regarding requirements for cell quality, amplification success rates, allelic dropouts and resolution, lacking a systemati...

    Authors: Anita T. Simonsen, Marcus C. Hansen, Eigil Kjeldsen, Peter L. Møller, Johnny J. Hindkjær, Peter Hokland and Anni Aggerholm

    Citation: BMC Genomics 2018 19:681

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  21. Content type: Research article

    To explore long non-coding RNA (lncRNA), mRNA and circular RNA (circRNA) expression profiles and their biological functions in the pathogenesis of kidney stones in ethylene glycol-induced urolithiasis rats.

    Authors: Yanan Cao, Xiaowei Gao, Yue Yang, Zhi Ye, E. Wang and Zhitao Dong

    Citation: BMC Genomics 2018 19:660

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  22. Content type: Research article

    Intermittent fasting and time-restricted diets are associated with lower risk biomarkers for cardio-metabolic disease. The shared mechanisms underpinning the similar physiological response to these events is n...

    Authors: Alexessander Couto Alves, Craig A. Glastonbury, Julia S. El-Sayed Moustafa and Kerrin S. Small

    Citation: BMC Genomics 2018 19:659

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  23. Content type: Research article

    The transient middle cerebral artery occlusion (tMCAO) model is used for studying the molecular mechanisms of ischemic damage and neuroprotection. Numerous studies have demonstrated the role of individual gene...

    Authors: Lyudmila V. Dergunova, Ivan B. Filippenkov, Vasily V. Stavchansky, Alina E. Denisova, Vadim V. Yuzhakov, Sergey A. Mozerov, Leonid V. Gubsky and Svetlana A. Limborska

    Citation: BMC Genomics 2018 19:655

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  24. Content type: Research article

    MicroRNAs (miRNAs) are small non-coding RNAs that bind messenger RNAs and promote their degradation or repress their translation. There is increasing evidence of miRNAs playing an important role in alcohol rel...

    Authors: Pratyaydipta Rudra, Wen J. Shi, Pamela Russell, Brian Vestal, Boris Tabakoff, Paula Hoffman, Katerina Kechris and Laura Saba

    Citation: BMC Genomics 2018 19:639

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  25. Content type: Research article

    Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivota...

    Authors: Eduardo Larriba, Eduardo Rial and Jesús del Mazo

    Citation: BMC Genomics 2018 19:634

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  26. Content type: Research article

    Although most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the gen...

    Authors: Shamsuddin A. Bhuiyan, Sophia Ly, Minh Phan, Brandon Huntington, Ellie Hogan, Chao Chun Liu, James Liu and Paul Pavlidis

    Citation: BMC Genomics 2018 19:637

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  27. Content type: Database

    Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modificati...

    Authors: Fengrui Wu, Yong Liu, Qingqing Wu, Dengkun Li, Ling Zhang, Xiaoqing Wu, Rong Wang, Di Zhang, Shaorong Gao and Wenyong Li

    Citation: BMC Genomics 2018 19:631

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  28. Content type: Research article

    Long-term exposure to elevated levels of free fatty acids (FFAs) is deleterious for beta-cell function and may contribute to development of type 2 diabetes mellitus (T2DM). Whereas mechanisms of impaired gluco...

    Authors: Ernest Sargsyan, Jing Cen, Kirsten Roomp, Reinhard Schneider and Peter Bergsten

    Citation: BMC Genomics 2018 19:629

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  29. Content type: Research article

    The emergence of fully antimicrobial resistant Neisseria gonorrhoeae has led global public health agencies to identify a critical need for next generation anti-gonococcal pharmaceuticals. The development and succ...

    Authors: Ian P. Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik-Dasthagirisaheb, Scott D. Gray-Owen and Lee M. Wetzler

    Citation: BMC Genomics 2018 19:627

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  30. Content type: Review

    The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majori...

    Authors: K. Blighe, L. DeDionisio, K. A. Christie, B. Chawes, S. Shareef, T. Kakouli-Duarte, C. Chao-Shern, V. Harding, R. S. Kelly, L. Castellano, J. Stebbing, J. A. Lasky-Su, M. A. Nesbit and C. B. T. Moore

    Citation: BMC Genomics 2018 19:595

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  31. Content type: Research article

    Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4...

    Authors: Weijing Cai, Dapeng Zhou, Weibo Wu, Wen Ling Tan, Jiaqian Wang, Caicun Zhou and Yanyan Lou

    Citation: BMC Genomics 2018 19:582

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  32. Content type: Research article

    3,4-methylenedioxymethamphetamine (MDMA, “ecstasy”) is a widely used entactogenic drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cortical regions have well established r...

    Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D. Ando, Laszlo Tothfalusi and Gyorgy Bagdy

    Citation: BMC Genomics 2018 19:580

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  33. Content type: Research article

    N6-methyladenosine (m6A) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify m6A in a large scale, machine learni...

    Authors: Zhixun Zhao, Hui Peng, Chaowang Lan, Yi Zheng, Liang Fang and Jinyan Li

    Citation: BMC Genomics 2018 19:574

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  34. Content type: Research article

    Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and a leading model for cell motility and chemotaxis. However, primary neutrophils are short-lived, limiti...

    Authors: Esther Rincón, Briana L. Rocha-Gregg and Sean R. Collins

    Citation: BMC Genomics 2018 19:573

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  35. Content type: Methodology article

    Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of mole...

    Authors: Thomas J. F. Pranzatelli, Drew G. Michael and John A. Chiorini

    Citation: BMC Genomics 2018 19:563

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  36. Content type: Research article

    Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify ...

    Authors: Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa…

    Citation: BMC Genomics 2018 19:551

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  37. Content type: Research article

    Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberran...

    Authors: Yuhong Dou, Yong Zhu, Junmei Ai, Hankui Chen, Helu Liu, Jeffrey A. Borgia, Xiao Li, Fan Yang, Bin Jiang, Jun Wang and Youping Deng

    Citation: BMC Genomics 2018 19:545

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  38. Content type: Research article

    Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are ...

    Authors: Seong Hyeon Hong, Jun Tae Kwon, Jihye Kim, Juri Jeong, Jaehwan Kim, Seonhee Lee and Chunghee Cho

    Citation: BMC Genomics 2018 19:539

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  39. Content type: Research article

    Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the tru...

    Authors: Jintao Guo, Jiankun Huang, Ying Zhou, Yulin Zhou, Liying Yu, Huili Li, Lingyun Hou, Liuwei Zhu, Dandan Ge, Yuanyuan Zeng, Bayasi Guleng and Qiyuan Li

    Citation: BMC Genomics 2018 19:538

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  40. Content type: Methodology article

    Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome...

    Authors: John Cologne, Lenora Loo, Yurii B. Shvetsov, Munechika Misumi, Philip Lin, Christopher A. Haiman, Lynne R. Wilkens and Loïc Le Marchand

    Citation: BMC Genomics 2018 19:524

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  41. Content type: Research article

    Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to ...

    Authors: Marine Mommert, Olivier Tabone, Guy Oriol, Elisabeth Cerrato, Audrey Guichard, Magali Naville, Paola Fournier, Jean-Nicolas Volff, Alexandre Pachot, Guillaume Monneret, Fabienne Venet, Karen Brengel-Pesce, Julien Textoris and François Mallet

    Citation: BMC Genomics 2018 19:522

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  42. Content type: Research article

    Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that has been associated with cancer cell proliferation in vitro and with survival in vivo. NAT1 expression has been associated with the est...

    Authors: Rodney F. Minchin and Neville J. Butcher

    Citation: BMC Genomics 2018 19:513

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  43. Content type: Methodology article

    RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...

    Authors: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen

    Citation: BMC Genomics 2018 19:511

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