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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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

  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. Content type: Research article

    Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or...

    Authors: Jongsuk Chung, Ki-Wook Lee, Chung Lee, Seung-Ho Shin, Sungkyu Kyung, Hyo-Jeong Jeon, Sook-Young Kim, Eunjung Cho, Chang Eun Yoo, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Citation: BMC Genomics 2019 20:216

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  25. Content type: Research article

    Massively-parallel-sequencing, coupled with sample multiplexing, has made genetic tests broadly affordable. However, intractable index mis-assignments (commonly exceeds 1%) were repeatedly reported on some wid...

    Authors: Qiaoling Li, Xia Zhao, Wenwei Zhang, Lin Wang, Jingjing Wang, Dongyang Xu, Zhiying Mei, Qiang Liu, Shiyi Du, Zhanqing Li, Xinming Liang, Xiaman Wang, Hanmin Wei, Pengjuan Liu, Jing Zou, Hanjie Shen…

    Citation: BMC Genomics 2019 20:215

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  26. Content type: Methodology article

    Massively parallel reporter assays (MPRAs) have emerged as a popular means for understanding noncoding variation in a variety of conditions. While a large number of experiments have been described in the liter...

    Authors: Leslie Myint, Dimitrios G. Avramopoulos, Loyal A. Goff and Kasper D. Hansen

    Citation: BMC Genomics 2019 20:209

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  27. Content type: Research article

    Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanyin...

    Authors: Benjamín Planells, Isabel Gómez-Redondo, Eva Pericuesta, Patrick Lonergan and Alfonso Gutiérrez-Adán

    Citation: BMC Genomics 2019 20:202

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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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