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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 3 of 23

  1. 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

    Content type: Research article

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  2. 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

    Content type: Methodology article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Methodology article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Software

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Database

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Methodology article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Software

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

    Published on:

  41. 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

    Content type: Database

    Published on:

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