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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 22

  1. Content type: Research article

    The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of st...

    Authors: Ran Li, Xiaomeng Tian, Peng Yang, Yingzhi Fan, Ming Li, Hongxiang Zheng, Xihong Wang and Yu Jiang

    Citation: BMC Genomics 2019 20:746

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  2. Content type: Research article

    Heart disease (HD) is the major cause of morbidity and mortality in patients with hypereosinophilic diseases. Due to a lack of adequate animal models, our understanding of the pathophysiology of eosinophil-med...

    Authors: Nives Zimmermann, William J. Gibbons Jr, Shelli M. Homan and Daniel R. Prows

    Citation: BMC Genomics 2019 20:727

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  3. Content type: Research article

    The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study,...

    Authors: Thomas J. Ha, Peter G. Y. Zhang, Remi Robert, Joanna Yeung, Douglas J. Swanson, Anthony Mathelier, Wyeth W. Wasserman, Sujin Im, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest…

    Citation: BMC Genomics 2019 20:718

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  4. Content type: Research article

    Our previous study had proved that nigericin could reduce colorectal cancer cell proliferation in dose- and time-dependent manners by targeting Wnt/β-catenin signaling. To better elucidate its potential anti-c...

    Authors: Zhihua Xu, Jiaqing Shen, Shangbo Hua, Daiwei Wan, Qian Chen, Ye Han, Rui Ren, Fei Liu, Zhiyong Du, Xiaobo Guo, Jianming Shi and Qiaoming Zhi

    Citation: BMC Genomics 2019 20:716

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  6. Content type: Research article

    Infection with Toxoplasma gondii is thought to damage the brain and be a risk factor for neurological and psychotic disorders. The immune response-participating chemokine system has recently been considered vital...

    Authors: Kaoru Kobayashi, Kousuke Umeda, Fumiaki Ihara, Sachi Tanaka, Junya Yamagishi, Yutaka Suzuki and Yoshifumi Nishikawa

    Citation: BMC Genomics 2019 20:705

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  7. Content type: Research article

    It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA ...

    Authors: Rick J. Jansen, Lin Tong, Maria Argos, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md. Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md. Yunus, Muhammad G. Kibriya, John A. Baron, Habibul Ahsan and Brandon L. Pierce

    Citation: BMC Genomics 2019 20:704

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  8. Content type: Research article

    Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity ...

    Authors: Aditya Vijay Bhagwate, Yuanhang Liu, Stacey J. Winham, Samantha J. McDonough, Melody L. Stallings-Mann, Ethan P. Heinzen, Jaime I. Davila, Robert A. Vierkant, Tanya L. Hoskin, Marlene Frost, Jodi M. Carter, Derek C. Radisky, Julie M. Cunningham, Amy C. Degnim and Chen Wang

    Citation: BMC Genomics 2019 20:689

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  9. Content type: Research article

    Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given tha...

    Authors: Anouk M. Olthof, Katery C. Hyatt and Rahul N. Kanadia

    Citation: BMC Genomics 2019 20:686

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  10. Content type: Software

    Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying m...

    Authors: Erik N. Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen and Ludmil B. Alexandrov

    Citation: BMC Genomics 2019 20:685

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  11. Content type: Research article

    Brain-derived neurotrophic factor (BDNF) is a major signaling molecule that the brain uses to control a vast network of intracellular cascades fundamental to properties of learning and memory, and cognition. W...

    Authors: Kathryn M. Hixson, Meaghan Cogswell, Amy R. Brooks-Kayal and Shelley J. Russek

    Citation: BMC Genomics 2019 20:677

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  12. Content type: Research article

    Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several...

    Authors: Qiang Liu, Aisheng Hou, Yongyi Zhang, Ying Guo, Jingjing Li, Yinghao Yao, Kaimeng Niu, Hao Li, Yunlong Ma and Jiangbei Cao

    Citation: BMC Genomics 2019 20:670

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  13. Content type: Research article

    Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. ...

    Authors: Saurabh Belsare, Michal Levy-Sakin, Yulia Mostovoy, Steffen Durinck, Subhra Chaudhuri, Ming Xiao, Andrew S. Peterson, Pui-Yan Kwok, Somasekar Seshagiri and Jeffrey D. Wall

    Citation: BMC Genomics 2019 20:620

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  14. Content type: Methodology article

    Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a wh...

    Authors: Samarth Rangavittal, Natasha Stopa, Marta Tomaszkiewicz, Kristoffer Sahlin, Kateryna D. Makova and Paul Medvedev

    Citation: BMC Genomics 2019 20:641

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  15. Content type: Research article

    The regenerative ability of severed axons in the central nervous system is limited in mammals. However, after central nervous system injury, neural function is partially recovered by the formation of a compens...

    Authors: Hiroshi Tsujioka and Toshihide Yamashita

    Citation: BMC Genomics 2019 20:619

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  16. Content type: Methodology article

    Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enab...

    Authors: Takashi Shimbo, Machika Kawamura, Edward Wijaya, Eiichi Takaki, Yasufumi Kaneda and Katsuto Tamai

    Citation: BMC Genomics 2019 20:614

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  17. Content type: Research article

    Esophageal squamous cell carcinoma (ESCC) cells are heterogeneous, easily develop radioresistance, and recur. Single-cell RNA-seq (scRNA-seq) is a next-generation sequencing method that can delineate diverse g...

    Authors: Ling Yang, Xiaoyan Zhang, Qiang Hou, Ming Huang, Hongfang Zhang, Zhenzhen Jiang, Jing Yue and Shixiu Wu

    Citation: BMC Genomics 2019 20:611

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  18. Content type: Research article

    Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader sp...

    Authors: Isabel Garcia Sousa, Kelly Cristina Rodrigues Simi, Manuela Maragno do Almo, Maryani Andressa Gomes Bezerra, Gero Doose, Tainá Raiol, Peter F. Stadler, Steve Hoffmann, Andréa Queiroz Maranhão and Marcelo Macedo Brigido

    Citation: BMC Genomics 2019 20:593

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  20. Content type: Research article

    Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterizat...

    Authors: Mohamed Doulazmi, Cyril Cros, Isabelle Dusart, Alain Trembleau and Caroline Dubacq

    Citation: BMC Genomics 2019 20:577

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  22. Content type: Research article

    A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, ...

    Authors: Ying Wan, Xiaoyang Liu, Dongwang Zheng, Yuying Wang, Huan Chen, Xiaofeng Zhao, Guoqing Liang, Dongliang Yu and Lin Gan

    Citation: BMC Genomics 2019 20:559

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  23. Content type: Software

    Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such...

    Authors: Daoshan Zheng, Justyna Trynda, Zhifu Sun and Zhaoyu Li

    Citation: BMC Genomics 2019 20:541

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  24. Content type: Methodology article

    Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effect...

    Authors: Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J. C. Slebos, Christine H. Chung and Xuefeng Wang

    Citation: BMC Genomics 2019 20:539

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  26. Content type: Research article

    Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enh...

    Authors: Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka and John A. Capra

    Citation: BMC Genomics 2019 20:511

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  27. Content type: Research article

    Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognosticatio...

    Authors: Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao Saal, Åke Borg, Johan Vallon-Christerson and Carlos Rovira

    Citation: BMC Genomics 2019 20:503

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  28. Content type: Methodology article

    The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gai...

    Authors: Charlotte R. Feddersen, Lexy S. Wadsworth, Eliot Y. Zhu, Hayley R. Vaughn, Andrew P. Voigt, Jesse D. Riordan and Adam J. Dupuy

    Citation: BMC Genomics 2019 20:497

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  29. Content type: Research article

    Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection...

    Authors: Adam Scheidegger, Carissa J. Dunn, Ann Samarakkody, Nii Koney-Kwaku Koney, Danielle Perley, Ramendra N. Saha and Sergei Nechaev

    Citation: BMC Genomics 2019 20:477

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  30. Content type: Research article

    Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of ...

    Authors: Andrii Slonchak, Brian Clarke, Jason Mackenzie, Alberto Anastacio Amarilla, Yin Xiang Setoh and Alexander A. Khromykh

    Citation: BMC Genomics 2019 20:474

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  31. Content type: Research article

    The most widely used human genome reference assembly hg19 harbors minor alleles at 2.18 million positions as revealed by 1000 Genome Phase 3 dataset. Although this is less than 2% of the 89 million variants re...

    Authors: Harsh G. Shukla, Pushpinder Singh Bawa and Subhashini Srinivasan

    Citation: BMC Genomics 2019 20:459

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  32. Content type: Research article

    Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification ag...

    Authors: A. C. Picornell, I. Echavarria, E. Alvarez, S. López-Tarruella, Y. Jerez, K. Hoadley, J. S. Parker, M. del Monte-Millán, R. Ramos-Medina, J. Gayarre, I. Ocaña, M. Cebollero, T. Massarrah, F. Moreno, J. A. García Saenz, H. Gómez Moreno…

    Citation: BMC Genomics 2019 20:452

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  34. Content type: Research article

    Mutations in the transcription factor, KLF1, are common within certain populations of the world. Heterozygous missense mutations in KLF1 mostly lead to benign phenotypes, but a heterozygous mutation in a DNA-bind...

    Authors: Melissa D. Ilsley, Stephen Huang, Graham W. Magor, Michael J. Landsberg, Kevin R. Gillinder and Andrew C. Perkins

    Citation: BMC Genomics 2019 20:417

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  35. Content type: Research article

    Our previous study described the crucial role of Rho-associated coiled-coil containing-kinases (ROCK) in hepatocellular carcinoma (HCC). However, the potential significance of long noncoding RNA downstream of ...

    Authors: He-Ming Zhou, Ji-Gang Zhang, Xue Zhang, Guo-Rong Fan, Gao-Lin Liu and Qin Li

    Citation: BMC Genomics 2019 20:409

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  36. Content type: Research article

    Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusin...

    Authors: Azam Yazdani, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol and Ahmad Samiei

    Citation: BMC Genomics 2019 20:395

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  38. Content type: Research article

    Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly ...

    Authors: Alltalents T. Murahwa, Fredrick Nindo, Harris Onywera, Tracy L. Meiring, Darren P. Martin and Anna-Lise Williamson

    Citation: BMC Genomics 2019 20:368

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  39. Content type: Research article

    There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study de...

    Authors: Georgina Mansell, Tyler J. Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S. Schalkwyk, Jonathan Mill and Eilis Hannon

    Citation: BMC Genomics 2019 20:366

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  40. Content type: Research article

    Blood flow restoration is a definitive therapy for salvaging the myocardium following ischemic injury. Nevertheless, the sudden restoration of blood flow to the ischemic myocardium can induce ischemia-reperfus...

    Authors: Zanxin Wang, Junmin Wen, Chuzhi Zhou, Zhiwei Wang and Minxin Wei

    Citation: BMC Genomics 2019 20:361

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  41. Content type: Research article

    Ionizing Radiation (IR) is a known pro-inflammatory agent and in the process of development of biomarkers for radiation biodosimetry, a chronic inflammatory disease condition could act as a confounding factor....

    Authors: Sanjay Mukherjee, Evagelia C. Laiakis, Albert J. Fornace Jr and Sally A. Amundson

    Citation: BMC Genomics 2019 20:329

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  42. Content type: Research article

    During decidualization in endometrial stromal cells (ESCs), expressions of a number of genes and epigenetic modifications of histones are altered. However, there is little information about whether DNA methyla...

    Authors: Ryo Maekawa, Isao Tamura, Masahiro Shinagawa, Yumiko Mihara, Shun Sato, Maki Okada, Toshiaki Taketani, Hiroshi Tamura and Norihiro Sugino

    Citation: BMC Genomics 2019 20:324

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  43. Content type: Research article

    Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence gene expression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices wit...

    Authors: Alexander G. Foote, Ziyue Wang, Christina Kendziorski and Susan L. Thibeault

    Citation: BMC Genomics 2019 20:308

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  44. Content type: Research article

    DNA methylation plays an important role in multiple biological processes that are closely related to human health. The study of DNA methylation can provide an insight into the mechanism behind human health and...

    Authors: Limin Jiang, Chongqing Wang, Jijun Tang and Fei Guo

    Citation: BMC Genomics 2019 20:306

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    The Correction to this article has been published in BMC Genomics 2019 20:365

  45. Content type: Research article

    Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or th...

    Authors: Ding Wu, Brett Pepowski, Satoe Takahashi and Stephen J. Kron

    Citation: BMC Genomics 2019 20:290

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  46. Content type: Research article

    In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical ste...

    Authors: Hua Li, Ling Bai, Hongmei Li, Xinhui Li, Yani Kang, Ningbo Zhang, Jielin Sun and Zhifeng Shao

    Citation: BMC Genomics 2019 20:282

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  47. Content type: Research article

    Ketamine ester analogs, SN 35210 and SN 35563, demonstrate different pharmacological profiles to ketamine in animal models. Both confer hypnosis with predictably rapid offset yet, paradoxically, SN35563 induce...

    Authors: Gregory M. Jacobson, Logan J. Voss, Anica Klockars, Steve Bird, Ivo Dimitrov, William A. Denny, Pawel K. Olszewski, James W. Sleigh and Martyn G. Harvey

    Citation: BMC Genomics 2019 20:281

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  48. Content type: Methodology article

    Large-scale genetic screening using CRISPR-Cas9 technology has emerged as a powerful approach to uncover and validate gene functions. The ability to control the timing of genetic perturbation during CRISPR scr...

    Authors: Ning Sun, Sakina Petiwala, Rui Wang, Charles Lu, Mufeng Hu, Sujana Ghosh, Yan Hao, Christopher P. Miller and Namjin Chung

    Citation: BMC Genomics 2019 20:225

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  49. Content type: Research article

    Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination be...

    Authors: Isabela Tiemy Pereira, Lucia Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya and Bruno Dallagiovanna

    Citation: BMC Genomics 2019 20:219

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  50. Content type: Database Article

    Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can ob...

    Authors: Tong Liu, Jacob Porter, Chenguang Zhao, Hao Zhu, Nan Wang, Zheng Sun, Yin-Yuan Mo and Zheng Wang

    Citation: BMC Genomics 2019 20:217

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