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  1. Content type: Research article

    Phytophthora nicotianae Breda de Haan (Phytophthora parasitica Dastur) causes severe damage to citrus crops worldwide. A population of citrandarins was created from the cross between the susceptible parent Citrus...

    Authors: Rômulo P. M. Lima, Maiara Curtolo, Marcus V. Merfa, Mariângela Cristofani-Yaly and Marcos A. Machado

    Citation: BMC Genomics 2018 19:516

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  2. Content type: Research article

    Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify small RNAs as a...

    Authors: Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz and Claus O. Wilke

    Citation: BMC Genomics 2018 19:510

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  3. Content type: Research article

    Cis-regulatory elements control gene expression over large distances through the formation of chromatin loops, which allow contact between enhancers and gene promoters. Alterations in cis-acting regulatory system...

    Authors: Stéphanie Moisan, Stéphanie Levon, Emilie Cornec-Le Gall, Yannick Le Meur, Marie-Pierre Audrézet, Josée Dostie and Claude Férec

    Citation: BMC Genomics 2018 19:515

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  4. Content type: Research article

    Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely...

    Authors: Dongwei Xie, Zhigang Dai, Zemao Yang, Qing Tang, Jian Sun, Xue Yang, Xixia Song, Ying Lu, Debao Zhao, Liguo Zhang and Jianguang Su

    Citation: BMC Genomics 2018 19:512

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  5. Content type: Research article

    Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that has been associated with cancer cell proliferation in vitro and with survival in vivo. NAT1 expression has been associated with the est...

    Authors: Rodney F. Minchin and Neville J. Butcher

    Citation: BMC Genomics 2018 19:513

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  6. Content type: Research article

    The hemibiotrophic pathogens Moniliophthora perniciosa (witches’ broom disease) and Moniliophthora roreri (frosty pod rot disease) are among the most important pathogens of cacao. Moniliophthora perniciosa has a ...

    Authors: Ceslaine Santos Barbosa, Rute R. da Fonseca, Thiago Mafra Batista, Mariana Araújo Barreto, Caio Suzart Argolo, Mariana Rocha de Carvalho, Daniel Oliveira Jordão do Amaral, Edson Mário de Andrade Silva, Enrique Arévalo-Gardini, Karina Solis Hidalgo, Glória Regina Franco, Carlos Priminho Pirovani, Fabienne Micheli and Karina Peres Gramacho

    Citation: BMC Genomics 2018 19:509

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  7. Content type: Methodology article

    RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...

    Authors: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen

    Citation: BMC Genomics 2018 19:511

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  8. Content type: Research article

    Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation...

    Authors: Wuhui Li, Junmei Liu, Hui Tan, Lingling Luo, Jialin Cui, Jie Hu, Shi Wang, Qingfeng Liu, Fangzhou Hu, Chenchen Tang, Li Ren, Conghui Yang, Rurong Zhao, Min Tao, Chun Zhang, Qinbo Qin…

    Citation: BMC Genomics 2018 19:517

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  9. Content type: Research article

    The medicinal plant, Catharanthus roseus (C. roseus), accumulates a wide range of terpenoid indole alkaloids (TIAs). Ethylene (ET) and methyl-jasmonate (MeJA) were previously reported as effective elicitors for t...

    Authors: Ya-jie Pan, Ying-chao Lin, Bo-fan Yu, Yuan-gang Zu, Fang Yu and Zhong-Hua Tang

    Citation: BMC Genomics 2018 19:508

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  10. Content type: Methodology article

    To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding light on the genetic architecture of complex dise...

    Authors: Yi Yang, Mingwei Dai, Jian Huang, Xinyi Lin, Can Yang, Min Chen and Jin Liu

    Citation: BMC Genomics 2018 19:503

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  11. Content type: Research article

    Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental stu...

    Authors: Suyu Mei, Erik K. Flemington and Kun Zhang

    Citation: BMC Genomics 2018 19:505

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  12. Content type: Research article

    Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs...

    Authors: Hao Bai, Yanyan Sun, Nian Liu, Fuguang Xue, Yunlei Li, Songshan Xu, Jianhua Ye, Lei Zhang, Yu Chen and Jilan Chen

    Citation: BMC Genomics 2018 19:501

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  13. Content type: Research article

    Anuran metamorphosis, which is obligatorily initiated and sustained by thyroid hormone (TH), is a dramatic example of extensive morphological, biochemical and cellular changes occurring during post-embryonic d...

    Authors: Lusha Liu, Wei Zhu, Jiongyu Liu, Shouhong Wang and Jianping Jiang

    Citation: BMC Genomics 2018 19:507

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  14. Content type: Research article

    Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will mak...

    Authors: Constantinos G. Broustas, Andrew D. Harken, Guy Garty and Sally A. Amundson

    Citation: BMC Genomics 2018 19:504

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  15. Content type: Methodology article

    Cronobacter species are associated with severe foodborne infections in neonates and infants, with particular pathovars associated with specific clinical presentations. However, before 2008 the genus was regarded ...

    Authors: Qingyan Guo, Jielin Yang, S. J. Forsythe, Yuan Jiang, Wei Han, Yuping He and Bing Niu

    Citation: BMC Genomics 2018 19:506

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  16. Content type: Research article

    Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is uncle...

    Authors: James Buckley, Eric B. Holub, Marcus A. Koch, Philippine Vergeer and Barbara K. Mable

    Citation: BMC Genomics 2018 19:496

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  17. Content type: Research article

    The evolutionarily conserved Sonic Hedgehog (Shh) signaling pathway is essential for embryogenesis and orofacial development. SHH ligand secreted from the surface ectoderm activates pathway activity in the und...

    Authors: Joshua L. Everson, Dustin M. Fink, Hannah M. Chung, Miranda R. Sun and Robert J. Lipinski

    Citation: BMC Genomics 2018 19:497

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  18. Content type: Research article

    Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breedi...

    Authors: Xuewen Wang, Shuai Yang, Yongdui Chen, Shumeng Zhang, Qingshi Zhao, Meng Li, Yulong Gao, Long Yang and Jeffrey L. Bennetzen

    Citation: BMC Genomics 2018 19:500

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  19. Content type: Research article

    The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding...

    Authors: Shengru Wu, Yanli Liu, Wei Guo, Xi Cheng, Xiaochun Ren, Si Chen, Xueyuan Li, Yongle Duan, Qingzhu Sun and Xiaojun Yang

    Citation: BMC Genomics 2018 19:498

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  20. Content type: Research article

    Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a who...

    Authors: Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. de Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão…

    Citation: BMC Genomics 2018 19:499

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  21. Content type: Research article

    Long intergenic noncoding RNAs (lincRNAs) have been recognized in recent years as key regulators of biological processes. However, lincRNAs in goat remain poorly characterized both across various tissues and d...

    Authors: Shen Song, Min Yang, Yefang Li, Marhaba Rouzi, Qianjun Zhao, Yabin Pu, Xiaohong He, Joram M. Mwacharo, Ning Yang, Yuehui Ma and Lin Jiang

    Citation: BMC Genomics 2018 19:495

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  22. Content type: Research article

    Gossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reductio...

    Authors: Liping Fan, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hongwei Geng, Quanjia Chen and Yanying Qu

    Citation: BMC Genomics 2018 19:489

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  23. Content type: Software

    Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Altho...

    Authors: Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:493

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