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Human and rodent genomics

This section covers the genome structure and function in humans, primates and rodents.

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  1. Genetic aberrations in hepatocellular carcinoma (HCC) are well known, but the functional consequences of such aberrations remain poorly understood.

    Authors: Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Marco Colombi, Dritan Liko, Charlotte K. Y. Ng, Salvatore Piscuoglio, Jonas Behr, Ariane L. Moore, Jochen Singer, Hans-Joachim Ruscheweyh, Matthias S. Matter, Dirk Mossmann, Luigi M. Terracciano, Michael N. Hall and Niko Beerenwinkel

    Citation: BMC Genomics 2021 22:592

    Content type: Research article

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  2. Single cell Strand-seq is a unique tool for the discovery and phasing of genomic inversions. Conventional methods to discover inversions with Strand-seq data are blind to known inversion locations, limiting th...

    Authors: Vincent C. T. Hanlon, Carl-Adam Mattsson, Diana C. J. Spierings, Victor Guryev and Peter M. Lansdorp

    Citation: BMC Genomics 2021 22:582

    Content type: Methodology article

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  3. Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the Adenomatous polyposis coli (Apc) gene. Mice carrying a nonsense mu...

    Authors: Alexandra Dorman, Ilona Binenbaum, Hanifa J. Abu-Toamih Atamni, Aristotelis Chatziioannou, Ian Tomlinson, Richard Mott and Fuad A. Iraqi

    Citation: BMC Genomics 2021 22:566

    Content type: Research article

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  4. Preterm birth, defined as parturition before 37 completed weeks of gestation, is associated with an increased risk of neonatal complications and death, as well as poor health and disease later in life. Epigene...

    Authors: Young-Ah You, Eun Jin Kwon, Han-Sung Hwang, Suk-Joo Choi, Sae Kyung Choi and Young Ju Kim

    Citation: BMC Genomics 2021 22:528

    Content type: Research article

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  5. Brown adipose tissue (BAT) is specialized to dissipate energy in the form of heat. BAT-mediated heat production in rodents and humans is critical for effective temperature adaptation of newborns to the extraut...

    Authors: Sujoy Ghosh, Chul-Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jennifer Sones, Heike Münzberg, Leanne Redman and Ji Suk Chang

    Citation: BMC Genomics 2021 22:500

    Content type: Research article

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  6. Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and...

    Authors: Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas and Jonas Paulsen

    Citation: BMC Genomics 2021 22:499

    Content type: Research article

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  7. Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression ...

    Authors: Yucheng Wang, Eilis Hannon, Olivia A. Grant, Tyler J. Gorrie-Stone, Meena Kumari, Jonathan Mill, Xiaojun Zhai, Klaus D. McDonald-Maier and Leonard C. Schalkwyk

    Citation: BMC Genomics 2021 22:484

    Content type: Methodology article

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  8. Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression pa...

    Authors: Ruining Liu, Gang Li, Haoli Ma, Xianlong Zhou, Pengcheng Wang and Yan Zhao

    Citation: BMC Genomics 2021 22:472

    Content type: Research article

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  9. Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic muta...

    Authors: Xue Lin, Yingying Hua, Shuanglin Gu, Li Lv, Xingyu Li, Pin Chen, Peng Dai, Yunyun Hu, Anna Liu and Jian Li

    Citation: BMC Genomics 2021 22:440

    Content type: Software

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  10. Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these...

    Authors: Yao Hu, Stephanie A. Bien, Katherine K. Nishimura, Jeffrey Haessler, Chani J. Hodonsky, Antoine R. Baldassari, Heather M. Highland, Zhe Wang, Michael Preuss, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Mariaelisa Graff, Laura M. Huckins, Quan Sun, Ming-Huei Chen…

    Citation: BMC Genomics 2021 22:432

    Content type: Research article

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  11. Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretati...

    Authors: Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S. Cram and Yu Zhang

    Citation: BMC Genomics 2021 22:407

    Content type: Software

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  12. Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array ...

    Authors: Kimberly R. Andrews, Samuel S. Hunter, Brandi K. Torrevillas, Nora Céspedes, Sarah M. Garrison, Jessica Strickland, Delaney Wagers, Gretchen Hansten, Daniel D. New, Matthew W. Fagnan and Shirley Luckhart

    Citation: BMC Genomics 2021 22:378

    Content type: Methodology article

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  13. Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is kn...

    Authors: Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka J. Lund, Asta Laiho and Laura L. Elo

    Citation: BMC Genomics 2021 22:357

    Content type: Research article

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  14. Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerab...

    Authors: Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh and Soumyadeep Nandi

    Citation: BMC Genomics 2021 22:336

    Content type: Research article

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  15. RNA sequencing analysis focus on the detection of differential gene expression changes that meet a two-fold minimum change between groups. The variability present in RNA sequencing data may obscure the detecti...

    Authors: William W. Wilfinger, Robert Miller, Hamid R. Eghbalnia, Karol Mackey and Piotr Chomczynski

    Citation: BMC Genomics 2021 22:322

    Content type: Methodology article

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  16. Analysis of lymphocyte cell lines revealed substantial differences in the expression of mRNA and microRNA (miRNA) among human populations. The extent of such population-associated differences in actual human t...

    Authors: Song Guo, Shuyun Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve L. Fairbrother, David A. Hughes, Mark Stoneking and Philipp Khaitovich

    Citation: BMC Genomics 2021 22:286

    Content type: Research article

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  17. Mammalian centromeres are satellite-rich chromatin domains that execute conserved roles in kinetochore assembly and chromosome segregation. Centromere satellites evolve rapidly between species, but little is k...

    Authors: Uma P. Arora, Caleigh Charlebois, Raman Akinyanju Lawal and Beth L. Dumont

    Citation: BMC Genomics 2021 22:279

    Content type: Research article

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  18. Prior work demonstrated that female rats (but not their male littermates) exposed to methamphetamine become hypersensitive to myocardial ischemic injury. Importantly, this sex-dependent effect persists followi...

    Authors: Hasitha Chavva, Daniel A. Brazeau, James Denvir, Donald A. Primerano, Jun Fan, Sarah L. Seeley and Boyd R. Rorabaugh

    Citation: BMC Genomics 2021 22:259

    Content type: Research article

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  19. Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial ...

    Authors: B. Dnate’ Baxter, Eric D. Larson, Laetitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N. Bubak, Christy S. Niemeyer, James Hassell Jr, Doug Shepherd, Vijay R. Ramakrishnan, Maria A. Nagel and Diego Restrepo

    Citation: BMC Genomics 2021 22:224

    Content type: Research article

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  21. Low pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has re...

    Authors: Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King and Charles Cox

    Citation: BMC Genomics 2021 22:197

    Content type: Research article

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  22. MicroRNAs play an important role in many fundamental biological and pathological processes. Defining the microRNAs profile underlying the processes by beneficial and detrimental lifestyles, including caloric r...

    Authors: Huan Gong, Ming Zhang, Yiwen Han, Ying Zhang, Jing Pang, Yanyang Zhao, Beidong Chen, Wei Wu, Ruomei Qi and Tiemei Zhang

    Citation: BMC Genomics 2021 22:196

    Content type: Research article

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  23. Aging is a multifactorial process that affects multiple tissues and is characterized by changes in homeostasis over time, leading to increased morbidity. Whole blood gene expression signatures have been associ...

    Authors: Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra and Lude Franke

    Citation: BMC Genomics 2021 22:184

    Content type: Research article

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  24. It is still challenging to predict interacting enhancer-promoter pairs (IEPs), partially because of our limited understanding of their characteristics. To understand IEPs better, here we studied the IEPs in ni...

    Authors: Amlan Talukder, Haiyan Hu and Xiaoman Li

    Citation: BMC Genomics 2021 22:163

    Content type: Research article

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  25. Bi-specific T-cell engager (BiTE) antibody is a class of bispecific antibodies designed for cancer immunotherapy. Blinatumomab is the first approved BiTE to treat acute B cell lymphoblastic leukemia (B-ALL). I...

    Authors: Yi Huo, Zhen Sheng, Daniel R. Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Yin and Ruibao Ren

    Citation: BMC Genomics 2021 22:145

    Content type: Research article

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  26. Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individua...

    Authors: Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman and Hakon Hakonarson

    Citation: BMC Genomics 2021 22:133

    Content type: Software

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  27. Toxoplasma gondii is a globally distributed protozoan parasite that establishes life-long asymptomatic infection in humans, often emerging as a life-threatening opportunistic pathogen during immunodeficiency. As ...

    Authors: Kayla L. Menard, Lijing Bu and Eric Y. Denkers

    Citation: BMC Genomics 2021 22:130

    Content type: Research article

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  28. Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by trans...

    Authors: Jinhuan Dou, Flavio Schenkel, Lirong Hu, Adnan Khan, Muhammad Zahoor Khan, Ying Yu, Yajing Wang and Yachun Wang

    Citation: BMC Genomics 2021 22:122

    Content type: Research article

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  29. Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps wer...

    Authors: Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi, Heping Zheng, Yousong Peng and Zhongyang Tan

    Citation: BMC Genomics 2021 22:76

    Content type: Research article

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  31. DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epi...

    Authors: Victor Yuan, Desmond Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain and Wendy P. Robinson

    Citation: BMC Genomics 2021 22:6

    Content type: Research article

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  32. Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood fol...

    Authors: Axelle Brulport, Daniel Vaiman, Elias Bou-Maroun, Marie-Christine Chagnon and Ludovic Le Corre

    Citation: BMC Genomics 2020 21:881

    Content type: Research article

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  33. The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improv...

    Authors: M. Heath Farris, Pamela A. Texter, Agustin A. Mora, Michael V. Wiles, Ellen F. Mac Garrigle, Sybil A. Klaus and Kristine Rosfjord

    Citation: BMC Genomics 2020 21:856

    Content type: Methodology article

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  35. Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important comp...

    Authors: Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang and San Ming Wang

    Citation: BMC Genomics 2020 21:842

    Content type: Research article

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  37. Malonylation is a recently discovered post-translational modification that is associated with a variety of diseases such as Type 2 Diabetes Mellitus and different types of cancers. Compared with experimental i...

    Authors: Xin Liu, Liang Wang, Jian Li, Junfeng Hu and Xiao Zhang

    Citation: BMC Genomics 2020 21:812

    Content type: Methodology article

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  38. Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughpu...

    Authors: Bronte Wen, Hyun Jun Jung, Lihe Chen, Fahad Saeed and Mark A. Knepper

    Citation: BMC Genomics 2020 21:806

    Content type: Software

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  39. Birth weight is determined by the interplay between infant genetics and the intrauterine environment and is associated with several health outcomes in later life. Many studies have reported an association betw...

    Authors: Pontus Henriksson, Antonio Lentini, Signe Altmäe, David Brodin, Patrick Müller, Elisabet Forsum, Colm E. Nestor and Marie Löf

    Citation: BMC Genomics 2020 21:769

    Content type: Research article

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  40. Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 i...

    Authors: Daniela Kajihara, Chung-Chau Hon, Aimi Naim Abdullah, João Wosniak Jr, Ana Iochabel S. Moretti, Joice F. Poloni, Diego Bonatto, Kosuke Hashimoto, Piero Carninci and Francisco R. M. Laurindo

    Citation: BMC Genomics 2020 21:766

    Content type: Research article

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  41. Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gol...

    Authors: Wesley J. Delage, Julien Thevenon and Claire Lemaitre

    Citation: BMC Genomics 2020 21:762

    Content type: Research article

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  42. The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, u...

    Authors: Ilona Binenbaum, Hanifa Abu-Toamih Atamni, Georgios Fotakis, Georgia Kontogianni, Theodoros Koutsandreas, Eleftherios Pilalis, Richard Mott, Heinz Himmelbauer, Fuad A. Iraqi and Aristotelis A. Chatziioannou

    Citation: BMC Genomics 2020 21:761

    Content type: Research article

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  43. Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematic...

    Authors: Siddharth Sethi, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Simon Greenaway, John Williams, Vsevolod J. Makeev, Steve D. M. Brown, Michelle M. Simon and Ann-Marie Mallon

    Citation: BMC Genomics 2020 21:754

    Content type: Research article

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  45. Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMeth...

    Authors: Yunsung Lee, Kristine L. Haftorn, William R. P. Denault, Haakon E. Nustad, Christian M. Page, Robert Lyle, Sindre Lee-Ødegård, Gunn-Helen Moen, Rashmi B. Prasad, Leif C. Groop, Line Sletner, Christine Sommer, Maria C. Magnus, Håkon K. Gjessing, Jennifer R. Harris, Per Magnus…

    Citation: BMC Genomics 2020 21:747

    Content type: Methodology article

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  46. In diploid cells, it is important to construct maternal and paternal Hi-C contact maps respectively since the two homologous chromosomes can differ in chromatin three-dimensional (3D) organization. Though prev...

    Authors: Han Luo, Xinxin Li, Haitao Fu and Cheng Peng

    Citation: BMC Genomics 2020 21:746

    Content type: Software

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  47. Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide ...

    Authors: Patrycja Daca-Roszak, Roman Jaksik, Julia Paczkowska, Michał Witt and Ewa Ziętkiewicz

    Citation: BMC Genomics 2020 21:706

    Content type: Research article

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  48. Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and ...

    Authors: Cynthia A. Kelm-Nelson and Stephen Gammie

    Citation: BMC Genomics 2020 21:625

    Content type: Research article

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  49. Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by ...

    Authors: Xiaofeng Guo, Xiaoling Gao, Brendan T. Keenan, Jingxu Zhu, Dimitra Sarantopoulou, Jie Lian, Raymond J. Galante, Gregory R. Grant and Allan I. Pack

    Citation: BMC Genomics 2020 21:633

    Content type: Research article

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  50. Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely relat...

    Authors: Zhenhua Shang, David J. Horovitz, Ronald H. McKenzie, Jessica L. Keisler, Michael R. Felder and Shannon W. Davis

    Citation: BMC Genomics 2020 21:622

    Content type: Research article

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