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Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

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

Page 1 of 20

  1. Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the abs...

    Authors: Diego Robledo, Alastair Hamilton, Alejandro P. Gutiérrez, James E. Bron and Ross D. Houston

    Citation: BMC Genomics 2020 21:271

    Content type: Research article

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  2. Polydactyly is one of the most common congenital limb dysplasia in many animal species. Although preaxial polydactyly (PPD) has been comprehensively studied in humans as a common abnormality, the genetic varia...

    Authors: Cheng Ma, Saber Khederzadeh, Adeniyi C. Adeola, Xu-Man Han, Hai-Bing Xie and Ya-Ping Zhang

    Citation: BMC Genomics 2020 21:268

    Content type: Research article

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  3. Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play crit...

    Authors: Xian Zou, Tingting Lu, Zhifeng Zhao, Guangbin Liu, Zhiquan Lian, Yongqing Guo, Baoli Sun, Dewu Liu and Yaokun Li

    Citation: BMC Genomics 2020 21:267

    Content type: Research article

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  4. Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integ...

    Authors: Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Sihai Zhao, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan and Enqi Liu

    Citation: BMC Genomics 2020 21:266

    Content type: Database

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  5. The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental period...

    Authors: Zhibin Ji, Tianle Chao, Zhaohua Liu, Lei Hou, Jin Wang, Aili Wang, Jie Zhou, Rong Xuan, Guizhi Wang and Jianmin Wang

    Citation: BMC Genomics 2020 21:254

    Content type: Research article

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  6. The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to ...

    Authors: Andrew S. Lang, Suzanne H. Austin, Rayna M. Harris, Rebecca M. Calisi and Matthew D. MacManes

    Citation: BMC Genomics 2020 21:251

    Content type: Research article

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  7. Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals.

    Authors: Tinghua Huang, Min Yang, Kaihui Dong, Mingjiang Xu, Jinhui Liu, Zhi Chen, Shijia Zhu, Wang Chen, Jun Yin, Kai Jin, Yu Deng, Zhou Guan, Xiali Huang, Jun Yang, Rongxun Han and Min Yao

    Citation: BMC Genomics 2020 21:229

    Content type: Research article

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  8. Cope’s gray treefrog, Dryophytes chrysoscelis, withstands the physiological challenges of corporeal freezing, partly by accumulating cryoprotective compounds of hepatic origin, including glycerol, urea, and gluco...

    Authors: M. Clara F. do Amaral, James Frisbie, Raphael J. Crum, David L. Goldstein and Carissa M. Krane

    Citation: BMC Genomics 2020 21:226

    Content type: Research article

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  9. Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully expl...

    Authors: Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney and Mohamed Salem

    Citation: BMC Genomics 2020 21:209

    Content type: Research article

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  10. Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-estab...

    Authors: Hoi Man Ng, Jeff Cheuk Hin Ho, Wenyan Nong, Jerome Ho Lam Hui, Keng Po Lai and Chris Kong Chu Wong

    Citation: BMC Genomics 2020 21:208

    Content type: Research article

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  11. The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. T...

    Authors: Pierce Rafter, Isobel Claire Gormley, Andrew C. Parnell, John Francis Kearney and Donagh P. Berry

    Citation: BMC Genomics 2020 21:205

    Content type: Research article

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  12. The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population ...

    Authors: Yu Wang, Haoyang Cai, Xiaolin Luo, Yi Ai, Mingfeng Jiang and Yongli Wen

    Citation: BMC Genomics 2020 21:201

    Content type: Research article

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  13. Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool ...

    Authors: Ranran Zhao, Nan Liu, Fuhui Han, Hegang Li, Jifeng Liu, Lanlan Li, Guoyi Wang and Jianning He

    Citation: BMC Genomics 2020 21:187

    Content type: Research article

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  14. Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate wheth...

    Authors: Erin Kathleen McClelland, Michelle T. T. Chan, Xiang Lin, Dionne Sakhrani, Felicia Vincelli, Jin-Hyoung Kim, Daniel D. Heath and Robert H. Devlin

    Citation: BMC Genomics 2020 21:185

    Content type: Research article

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  15. Gang goose is a native species with gray plumage in Sichuan, China. As a result of overhunting, the number of gray Gang geese has decreased dramatically. To keep the species from extinction, conservation work ...

    Authors: Yang Xi, Lei Wang, Hehe Liu, Shengchao Ma, Yanying Li, Liang Li, Jiwen Wang, Han Chunchun, Lili Bai, Ahsan Mustafa and Hua He

    Citation: BMC Genomics 2020 21:162

    Content type: Research article

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  16. Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption...

    Authors: Madhu Sudhana Saddala, Anton Lennikov, Adam Bouras and Hu Huang

    Citation: BMC Genomics 2020 21:132

    Content type: Research article

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  17. Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings remains poorly understood. To study t...

    Authors: Fengyao Wu, Fengying Lu, Xin Fan, Jin Chao, Chuanmin Liu, Qunxing Pan, Huawei Sun and Xiaofei Zhang

    Citation: BMC Genomics 2020 21:123

    Content type: Research article

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  18. Osmotic stress is a widespread phenomenon in aquatic animal. The ability to cope with salinity stress and alkaline stress is quite important for the survival of aquatic species under natural conditions. Tilapi...

    Authors: Huanhuan Su, Dongmei Ma, Huaping Zhu, Zhigang Liu and Fengying Gao

    Citation: BMC Genomics 2020 21:110

    Content type: Research article

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  19. The fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refe...

    Authors: Larry A. Cogburn, Nares Trakooljul, Xiaofei Wang, Laura E. Ellestad and Tom E. Porter

    Citation: BMC Genomics 2020 21:109

    Content type: Research article

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  20. Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuab...

    Authors: Li Yi, Menggen Dalai, Rina Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang and Surong Hasi

    Citation: BMC Genomics 2020 21:108

    Content type: Research article

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  22. Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenet...

    Authors: Zhihua Ju, Qiang Jiang, Jinpeng Wang, Xiuge Wang, Chunhong Yang, Yan Sun, Yaran Zhang, Changfa Wang, Yaping Gao, Xiaochao Wei, Minghai Hou and Jinming Huang

    Citation: BMC Genomics 2020 21:102

    Content type: Research article

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  23. Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild popula...

    Authors: Lene Kleppe, Rolf Brudvik Edvardsen, Tomasz Furmanek, Eva Andersson, Kai Ove Skaftnesmo, Frida Thyri Segafredo and Anna Wargelius

    Citation: BMC Genomics 2020 21:99

    Content type: Research article

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  25. PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art metho...

    Authors: R. Meyermans, W. Gorssen, N. Buys and S. Janssens

    Citation: BMC Genomics 2020 21:94

    Content type: Methodology article

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  26. Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Je...

    Authors: Young-Lim Lee, Mirte Bosse, Erik Mullaart, Martien A. M. Groenen, Roel F. Veerkamp and Aniek C. Bouwman

    Citation: BMC Genomics 2020 21:89

    Content type: Research article

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  27. Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al.

    Authors: Sara R. Selitsky, David Marron, Daniel Hollern, Lisle E. Mose, Katherine A. Hoadley, Corbin Jones, Joel S. Parker, Dirk P. Dittmer and Charles M. Perou

    Citation: BMC Genomics 2020 21:79

    Content type: Research article

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  28. This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneou...

    Authors: Nicholas J. Hudson, Antonio Reverter, William J. Griffiths, Eylan Yutuc, Yuqin Wang, Angela Jeanes, Sean McWilliam, David W. Pethick and Paul L. Greenwood

    Citation: BMC Genomics 2020 21:77

    Content type: Research article

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  29. Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the regulatory mechanism of its spermat...

    Authors: Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Shuisheng Li, Haoran Lin and Xiaochun Liu

    Citation: BMC Genomics 2020 21:73

    Content type: Research article

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  30. Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model orga...

    Authors: Haipeng Bai, Lijun Liu, Ke An, Xiaochan Lu, Michael Harrison, Yanqiu Zhao, Ruibin Yan, Zhijie Lu, Song Li, Shuo Lin, Fang Liang and Wei Qin

    Citation: BMC Genomics 2020 21:67

    Content type: Methodology article

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  31. Reproductive capacity can be altered by challenges experienced during critical periods of development, including fetal development and early neonatal life. Gossypol is a polyphenolic compound, commonly found i...

    Authors: Helder Louvandini, Patricia S. Corrêa, Rocío Amorín, Lihe Liu, Egon H. Ieda, Carolina R. Jimenez, Siu M. Tsai, Concepta M. McManus and Francisco Peñagaricano

    Citation: BMC Genomics 2020 21:59

    Content type: Research article

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  32. Fatty acid composition contributes greatly to the quality and nutritional value of meat. However, the molecular regulatory mechanisms underlying fatty acid accumulation in poultry have not yet been cleared. Th...

    Authors: Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou and Shuisheng Hou

    Citation: BMC Genomics 2020 21:58

    Content type: Research article

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  33. Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, tra...

    Authors: Ehsan Pashay Ahi, Laurène A. Lecaudey, Angelika Ziegelbecker, Oliver Steiner, Ronald Glabonjat, Walter Goessler, Victoria Hois, Carina Wagner, Achim Lass and Kristina M. Sefc

    Citation: BMC Genomics 2020 21:54

    Content type: Research article

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  34. The Tibial dyschondroplasia (TD) in fast-growing chickens is mainly caused by improper blood circulation. The exact mechanism underlying angiogenesis and vascularization in tibial growth plate of broiler chick...

    Authors: Ali Raza Jahejo, Ding Zhang, Sheng Niu, Raza Ali Mangi, Afrasyab Khan, Muhammad Farhan Qadir, Ajab Khan, Huan-chun Chen and Wen-xia Tian

    Citation: BMC Genomics 2020 21:50

    Content type: Research article

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  35. Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to iden...

    Authors: Ellen Freebern, Daniel J. A. Santos, Lingzhao Fang, Jicai Jiang, Kristen L. Parker Gaddis, George E. Liu, Paul M. VanRaden, Christian Maltecca, John B. Cole and Li Ma

    Citation: BMC Genomics 2020 21:41

    Content type: Research article

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  36. Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits ...

    Authors: Yining Wang, Feng Zhang, Robert Mukiibi, Liuhong Chen, Michael Vinsky, Graham Plastow, John Basarab, Paul Stothard and Changxi Li

    Citation: BMC Genomics 2020 21:38

    Content type: Research article

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  37. Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted i...

    Authors: Feng Zhang, Yining Wang, Robert Mukiibi, Liuhong Chen, Michael Vinsky, Graham Plastow, John Basarab, Paul Stothard and Changxi Li

    Citation: BMC Genomics 2020 21:36

    Content type: Research article

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  38. Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local ...

    Authors: Meenu Bhati, Naveen Kumar Kadri, Danang Crysnanto and Hubert Pausch

    Citation: BMC Genomics 2020 21:27

    Content type: Research article

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  39. Early sex differentiation genes of zebrafish remain an unsolved mystery due to the difficulty to distinguish the sex of juvenile zebrafish. However, aromatase inhibitors (AIs) could direct juvenile zebrafish s...

    Authors: Lu Chen, Li Wang, Qiwei Cheng, Yi-Xuan Tu, Zhuang Yang, Run-Ze Li, Zhi-Hui Luo and Zhen-Xia Chen

    Citation: BMC Genomics 2020 21:22

    Content type: Research article

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  40. The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack...

    Authors: Araya Radtanakatikanon, Stefan M. Keller, Nikos Darzentas, Peter F. Moore, Géraldine Folch, Viviane Nguefack Ngoune, Marie-Paule Lefranc and William Vernau

    Citation: BMC Genomics 2020 21:20

    Content type: Research article

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  41. Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to bette...

    Authors: F. Jehl, C. Désert, C. Klopp, M. Brenet, A. Rau, S. Leroux, M. Boutin, L. Lagoutte, K. Muret, Y. Blum, D. Esquerré, D. Gourichon, T. Burlot, A. Collin, F. Pitel, A. Benani…

    Citation: BMC Genomics 2019 20:1033

    Content type: Research article

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  42. The proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis...

    Authors: Jane de Oliveira Peixoto, Igor Ricardo Savoldi, Adriana Mércia Guaratini Ibelli, Maurício Egídio Cantão, Fátima Regina Ferreira Jaenisch, Poliana Fernanda Giachetto, Matthew Lee Settles, Ricardo Zanella, Jorge Augusto Petroli Marchesi, José Rodrigo Pandolfi, Luiz Lehmann Coutinho and Mônica Corrêa Ledur

    Citation: BMC Genomics 2019 20:1031

    Content type: Research article

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  43. Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can ...

    Authors: Lea Mikkola, Saila Holopainen, Tiina Pessa-Morikawa, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2019 20:1027

    Content type: Research article

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  44. Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising ei...

    Authors: Jin-Hyoung Kim, Daniel J. Macqueen, James R. Winton, John D. Hansen, Hyun Park and Robert H. Devlin

    Citation: BMC Genomics 2019 20:1024

    Content type: Research article

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  45. Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of ...

    Authors: Roni Tadmor-Levi, Adi Doron-Faigenboim, Evgeniya Marcos-Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, Geert F. Wiegertjes and Lior David

    Citation: BMC Genomics 2019 20:1019

    Content type: Research article

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  46. As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate...

    Authors: Haojie Zhang, Baoyu Hu, Jiali Xiong, Ting Chen, Qianyun Xi, Junyi Luo, Qingyan Jiang, Jiajie Sun and Yongliang Zhang

    Citation: BMC Genomics 2019 20:1013

    Content type: Research article

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  47. Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated...

    Authors: Daniela D. Moré, Fernando F. Cardoso, Maurício A. Mudadu, Wilson Malagó-Jr, Claudia C. Gulias-Gomes, Bruna P. Sollero, Adriana M. G. Ibelli, Luiz L. Coutinho and Luciana C. A. Regitano

    Citation: BMC Genomics 2019 20:998

    Content type: Research article

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  48. The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential ro...

    Authors: Wei-wei Wang, Jing Wang, Hai-jun Zhang, Shu-geng Wu and Guang-hai Qi

    Citation: BMC Genomics 2019 20:970

    Content type: Research article

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  49. Melanocytes are derived from neural crest stem cells in the embryonic stage. In mature melanocytes, a series of complex enzyme-catalyzed reactions leads to the production of melanins, which determine the hair ...

    Authors: Xuexian Liu, Bin Du, Pengqian Zhang, Junzhen Zhang, Zhiwei Zhu, Bo Liu and Ruiwen Fan

    Citation: BMC Genomics 2019 20:962

    Content type: Research article

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  50. Sperm epigenetics is an emerging area of study supported by observations reporting that abnormal sperm DNA methylation patterns are associated with infertility. Here, we explore cytosine-guanine dinucleotides ...

    Authors: Emanuele Capra, Barbara Lazzari, Federica Turri, Paola Cremonesi, Antônia Moemia Rodrigues Portela, Paolo Ajmone-Marsan, Alessandra Stella and Flavia Pizzi

    Citation: BMC Genomics 2019 20:940

    Content type: Research article

    Published on:

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