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Non-human and non-rodent vertebrate genomics

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

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  1. The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soun...

    Authors: Maria K. Rosengren, Heiðrún Sigurðardóttir, Susanne Eriksson, Rakan Naboulsi, Ahmad Jouni, Miguel Novoa-Bravo, Elsa Albertsdóttir, Þorvaldur Kristjánsson, Marie Rhodin, Åsa Viklund, Brandon D. Velie, Juan J. Negro, Marina Solé and Gabriella Lindgren

    Citation: BMC Genomics 2021 22:267

    Content type: Research article

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  2. Increases in ocean temperatures and in the frequency and severity of hypoxic events are expected with climate change, and may become a challenge for cultured Atlantic salmon and negatively affect their growth,...

    Authors: Anne Beemelmanns, Fábio S. Zanuzzo, Xi Xue, Rebeccah M. Sandrelli, Matthew L. Rise and A. Kurt Gamperl

    Citation: BMC Genomics 2021 22:261

    Content type: Research article

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  3. Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have b...

    Authors: Joanna Malukiewicz, Reed A. Cartwright, Nelson H. A. Curi, Jorge A. Dergam, Claudia S. Igayara, Silvia B. Moreira, Camila V. Molina, Patricia A. Nicola, Angela Noll, Marcello Passamani, Luiz C. M. Pereira, Alcides Pissinatti, Carlos R. Ruiz-Miranda, Daniel L. Silva, Anne C. Stone, Dietmar Zinner…

    Citation: BMC Genomics 2021 22:239

    Content type: Research article

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  4. The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradi...

    Authors: Matyas Cserhati

    Citation: BMC Genomics 2021 22:228

    Content type: Research article

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  5. Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reprod...

    Authors: Ran Di, Qiu-Yue Liu, Shu-Hui Song, Dong-Mei Tian, Jian-Ning He, Ying Ge, Xiang-Yu Wang, Wen-Ping Hu, Joram-Mwashigadi Mwacharo, Zhang-Yuan Pan, Jian-Dong Wang, Qing Ma, Gui-Ling Cao, Hui-Hui Jin, Xiao-Jun Liang and Ming-Xing Chu

    Citation: BMC Genomics 2021 22:217

    Content type: Research article

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  6. Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal mod...

    Authors: Yang Dong, Morgan Newman, Stephen M. Pederson, Karissa Barthelson, Nhi Hin and Michael Lardelli

    Citation: BMC Genomics 2021 22:211

    Content type: Research article

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  7. Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and per...

    Authors: Valérie Ducret, Adam J. Richards, Mathieu Videlier, Thibault Scalvenzi, Karen A. Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet and Anthony Herrel

    Citation: BMC Genomics 2021 22:204

    Content type: Research article

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  8. Tilapia (Oreochromis niloticus) cultures are frequently infected by Vibrio vulnificus, causing major economic losses to production units. Previously, tilapia expressing recombinant delta-5 desaturase and delta-6 ...

    Authors: Pin-Yang Tu, Shin-Jie Huang, Venugopal Rajanbabu, Jen-Leih Wu and Jyh-Yih Chen

    Citation: BMC Genomics 2021 22:200

    Content type: Research article

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  9. Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant...

    Authors: Trent M. Prall, Emma K. Neumann, Julie A. Karl, Cecilia G. Shortreed, David A. Baker, Hailey E. Bussan, Roger W. Wiseman and David H. O’Connor

    Citation: BMC Genomics 2021 22:182

    Content type: Methodology article

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  10. Long noncoding RNA (lncRNA) is highly associated with inflammatory response and virus-induced interferon production. By far the majority of studies have focused on the immune-related lncRNAs of mice and humans...

    Authors: Junxin Gao, Yu Pan, Yunfei Xu, Wenli Zhang, Lin Zhang, Xi Li, Zhijun Tian, Hongyan Chen and Yue Wang

    Citation: BMC Genomics 2021 22:177

    Content type: Research article

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  11. Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne’s disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple ...

    Authors: Olivier Ariel, Jean-Simon Brouard, Andrew Marete, Filippo Miglior, Eveline Ibeagha-Awemu and Nathalie Bissonnette

    Citation: BMC Genomics 2021 22:162

    Content type: Research article

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  12. Maternal hormones, like testosterone, can strongly influence developing offspring, even generating long-term organizational effects on adult behavior; yet, the mechanisms facilitating these effects are still u...

    Authors: Alexandra B. Bentz, Chad E. Niederhuth, Laura L. Carruth and Kristen J. Navara

    Citation: BMC Genomics 2021 22:158

    Content type: Research article

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  13. Growth performance is significant in broiler production. In the growth process of broilers, gene expression varies at different growth stages. However, limited research has been conducted on the molecular mech...

    Authors: Genxi Zhang, Pengfei Wu, Kaizhi Zhou, Mingliang He, Xinchao Zhang, Cong Qiu, Tingting Li, Tao Zhang, Kaizhou Xie, Guojun Dai and Jinyu Wang

    Citation: BMC Genomics 2021 22:157

    Content type: Research article

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  14. China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characte...

    Authors: Qing-bo Zhao, Favour Oluwapelumi Oyelami, Qamar Raza Qadri, Hao Sun, Zhong Xu, Qi-shan Wang and Yu-chun Pan

    Citation: BMC Genomics 2021 22:151

    Content type: Research article

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  15. Retinol (RO) and its active metabolite retinoic acid (RA) are major regulators of gene expression in vertebrates and influence various processes like organ development, cell differentiation, and immune respons...

    Authors: Clemens Falker-Gieske, Andrea Mott, Sören Franzenburg and Jens Tetens

    Citation: BMC Genomics 2021 22:146

    Content type: Research article

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  16. The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can...

    Authors: Haibo Shen, Caiwu Li, Ming He, Yan Huang, Jing Wang, Minglei Wang, Bisong Yue and Xiuyue Zhang

    Citation: BMC Genomics 2021 22:143

    Content type: Research article

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  17. The transcriptional changes around the time of embryonic genome activation in pre-implantation embryos indicate that this process is highly dynamic. In vitro produced porcine blastocysts are known to be less c...

    Authors: Vera A. van der Weijden, Meret Schmidhauser, Mayuko Kurome, Johannes Knubben, Veronika L. Flöter, Eckhard Wolf and Susanne E. Ulbrich

    Citation: BMC Genomics 2021 22:139

    Content type: Research article

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  18. Bone marrow mesenchymal stem cells are a potential resource for the clinical therapy of certain diseases. Canine, as a companion animal, living in the same space with human, is an ideal new model for human dis...

    Authors: Jinglu Wang, Pengxiu Dai, Tong Zou, Yangou Lv, Wen Zhao, Xinke Zhang and Yihua Zhang

    Citation: BMC Genomics 2021 22:134

    Content type: Research article

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  19. As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chua...

    Authors: Shan He, Jun-Jie You, Xu-Fang Liang, Zhi-Lu Zhang and Yan-Peng Zhang

    Citation: BMC Genomics 2021 22:129

    Content type: Research article

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  20. The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In thi...

    Authors: Hongchang Zhao, Tingting Guo, Zengkui Lu, Jianbin Liu, Shaohua Zhu, Guoyan Qiao, Mei Han, Chao Yuan, Tianxiang Wang, Fanwen Li, Yajun Zhang, Fujun Hou, Yaojing Yue and Bohui Yang

    Citation: BMC Genomics 2021 22:127

    Content type: Research article

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  21. The homologous recombination (HR) pathway is largely inactive in early embryos prior to the first cell division, making it difficult to achieve targeted gene knock-ins. The homology-mediated end joining (HMEJ)...

    Authors: Joseph R. Owen, Sadie L. Hennig, Bret R. McNabb, Tamer A. Mansour, Justin M. Smith, Jason C. Lin, Amy E. Young, Josephine F. Trott, James D. Murray, Mary E. Delany, Pablo J. Ross and Alison L. Van Eenennaam

    Citation: BMC Genomics 2021 22:118

    Content type: Research article

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  22. In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived...

    Authors: Madoka Vera Krick, Erick Desmarais, Athanasios Samaras, Elise Guéret, Arkadios Dimitroglou, Michalis Pavlidis, Costas Tsigenopoulos and Bruno Guinand

    Citation: BMC Genomics 2021 22:111

    Content type: Research article

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  23. Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, wh...

    Authors: Shinji Sasaki, Youko Miki, Takayuki Ibi, Hiroyuki Wakaguri, Yuichi Yoshida, Yoshikazu Sugimoto and Yutaka Suzuki

    Citation: BMC Genomics 2021 22:107

    Content type: Research article

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  24. Dissolved oxygen (DO) in the water is a vital abiotic factor in aquatic animal farming. A hypoxic environment affects the growth, metabolism, and immune system of fish. Glycolipid metabolism is a vital energy ...

    Authors: Jun-Lei Ma, Jun Qiang, Yi-Fan Tao, Jing-Wen Bao, Hao-Jun Zhu, Lian-Ge Li and Pao Xu

    Citation: BMC Genomics 2021 22:105

    Content type: Research article

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  25. Cataracts are defects of the lens that cause progressive visual impairment and ultimately blindness in many vertebrate species. Most cataracts are age-related, but up to one third have an underlying genetic ca...

    Authors: Chao Bai, Yuyan You, Xuefeng Liu, Maohua Xia, Wei Wang, Ting Jia, Tianchun Pu, Yan Lu, Chenglin Zhang, Xiaoguang Li, Yanqiang Yin, Liqin Wang, Jun Zhou and Lili Niu

    Citation: BMC Genomics 2021 22:100

    Content type: Research article

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  26. Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed ...

    Authors: Fuhui Han, Jing Li, Ranran Zhao, Lirong Liu, Lanlan Li, Qian Li, Jianning He and Nan Liu

    Citation: BMC Genomics 2021 22:98

    Content type: Research article

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  27. Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity a...

    Authors: Ligang Wang, Zhong-Yin Zhou, Tian Zhang, Longchao Zhang, Xinhua Hou, Hua Yan and Lixian Wang

    Citation: BMC Genomics 2021 22:95

    Content type: Research article

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  28. One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality. Previously, we showed that a 50 K transcribed-SNP chip can be used to detect quantitati...

    Authors: Rafet Al-Tobasei, Ali Ali, Andre L. S. Garcia, Daniela Lourenco, Tim Leeds and Mohamed Salem

    Citation: BMC Genomics 2021 22:92

    Content type: Research article

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  29. Hair follicle density influences wool fibre production, which is one of the most important traits of the Wan Strain Angora rabbit. However, molecular mechanisms regulating hair follicle density have remained e...

    Authors: Haisheng Ding, Huiling Zhao, Xiaowei Zhao, Yunxia Qi, Xiaofei Wang and Dongwei Huang

    Citation: BMC Genomics 2021 22:89

    Content type: Research article

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  30. Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this s...

    Authors: Chao Yuan, Zengkui Lu, Tingting Guo, Yaojing Yue, Xijun Wang, Tianxiang Wang, Yajun Zhang, Fujun Hou, Chune Niu, Xiaopin Sun, Hongchang Zhao, Shaohua Zhu, Jianbin Liu and Bohui Yang

    Citation: BMC Genomics 2021 22:78

    Content type: Research article

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  31. Canine hip dysplasia (CHD) is a common disease, with a complex genetic background. Dogs with severe CHD sometimes also suffer from osteoarthritis (OA), an inflammatory, often painful and incurable condition. P...

    Authors: Lea Mikkola, Kaisa Kyöstilä, Jonas Donner, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2021 22:68

    Content type: Research article

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  32. Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 n...

    Authors: Hao Li, Pengfei Cui, Xue Fu, Lan Zhang, Wenjun Yan, Yaru Zhai, Changwei Lei, Hongning Wang and Xin Yang

    Citation: BMC Genomics 2021 22:67

    Content type: Research article

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  33. miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, littl...

    Authors: Jie Liu, Fuwei Li, Xin Hu, Dingguo Cao, Wei Liu, Haixia Han, Yan Zhou and Qiuxia Lei

    Citation: BMC Genomics 2021 22:64

    Content type: Research article

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  34. Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutan...

    Authors: Dawei Zhang, Wenjing Wu, Xin Huang, Ke Xu, Cheng Zheng and Jin Zhang

    Citation: BMC Genomics 2021 22:61

    Content type: Research article

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  35. The mechanism of body growth in mammals is poorly understood. Here, we investigated the regulatory networks involved in body growth through transcriptomic analysis of pituitary and epiphyseal tissues of smalle...

    Authors: Jun Fang, Dong Zhang, Jun Wei Cao, Li Zhang, Chun Xia Liu, Yan Ping Xing, Feng Wang, Hong Yang Xu, Shi Chao Wang, Yu Ling, Wei Wang, Yan Ru Zhang and Huan Min Zhou

    Citation: BMC Genomics 2021 22:58

    Content type: Research article

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  36. Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by ...

    Authors: Grazyella M. Yoshida and José M. Yáñez

    Citation: BMC Genomics 2021 22:57

    Content type: Research article

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  37. With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture....

    Authors: Jinqiang Quan, Yujun Kang, Zhicheng Luo, Guiyan Zhao, Lanlan Li and Zhe Liu

    Citation: BMC Genomics 2021 22:48

    Content type: Research article

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  38. Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GW...

    Authors: Gabriele Flossmann, Christine Wurmser, Hubert Pausch, Amabel Tenghe, Jörg Dodenhoff, Günther Dahinten, Kay-Uwe Götz, Ingolf Russ and Ruedi Fries

    Citation: BMC Genomics 2021 22:38

    Content type: Research article

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  39. Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resol...

    Authors: Sonia Rey, Xingkun Jin, Børge Damsgård, Marie-Laure Bégout and Simon Mackenzie

    Citation: BMC Genomics 2021 22:33

    Content type: Research article

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  40. The use of sex-sorted sperm in cattle assisted reproduction is constantly increasing. However, sperm fertility can substantially differ between unsorted (conventional) and sex-sorted semen batches of the same ...

    Authors: Esin Keles, Eleni Malama, Siyka Bozukova, Mathias Siuda, Sarah Wyck, Ulrich Witschi, Stefan Bauersachs and Heinrich Bollwein

    Citation: BMC Genomics 2021 22:30

    Content type: Research article

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  41. Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of...

    Authors: Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. Louise Cosby and Sinéad M. Waters

    Citation: BMC Genomics 2021 22:14

    Content type: Research article

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  42. Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome...

    Authors: Shenping Zhou, Rongrong Ding, Fanming Meng, Xingwang Wang, Zhanwei Zhuang, Jianping Quan, Qian Geng, Jie Wu, Enqin Zheng, Zhenfang Wu, Jianhui Yang and Jie Yang

    Citation: BMC Genomics 2021 22:12

    Content type: Research article

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  43. DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Here...

    Authors: Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2021 22:8

    Content type: Research article

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  44. Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examina...

    Authors: Marina Braun, Annika Lehmbecker, Deborah Eikelberg, Maren Hellige, Andreas Beineke, Julia Metzger and Ottmar Distl

    Citation: BMC Genomics 2021 22:1

    Content type: Research article

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  45. Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowl...

    Authors: Zhengzheng Hu, Yuchen Li, Heng Du, Junxiao Ren, Xianrui Zheng, Kejian Wei and Jianfeng Liu

    Citation: BMC Genomics 2020 21:891

    Content type: Research article

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  46. Voice disorders are a worldwide problem impacting human health, particularly for occupational voice users. Avoidance of surface dehydration is commonly prescribed as a protective factor against the development...

    Authors: Taylor W. Bailey, Andrea Pires dos Santos, Naila Cannes do Nascimento, Shaojun Xie, Jyothi Thimmapuram, M. Preeti Sivasankar and Abigail Cox

    Citation: BMC Genomics 2020 21:888

    Content type: Research article

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  47. The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these...

    Authors: Jian Wang, Chengcheng Lu, Yifan Zhao, Zhijiao Tang, Jiakun Song and Chunxin Fan

    Citation: BMC Genomics 2020 21:875

    Content type: Research article

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