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  1. 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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  2. 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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  3. Content type: Research article

    Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasiv...

    Authors: Joaquín Giner-Lamia, Pablo Vinuesa, Laura Betancor, Claudia Silva, Julieta Bisio, Lorena Soleto, José A. Chabalgoity, José Luis Puente and Francisco García-del Portillo

    Citation: BMC Genomics 2019 20:99

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  4. Content type: Research article

    Protein secretion is an essential process in all eukaryotes including organisms belonging to the phylum Apicomplexa, which includes many intracellular parasites. The apicomplexan parasites possess a specialize...

    Authors: K. M. Kaderi Kibria, Jannatul Ferdous, Rahila Sardar, Ashutosh Panda, Dinesh Gupta, Asif Mohmmed and Pawan Malhotra

    Citation: BMC Genomics 2019 20:98

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  5. Content type: Research article

    Toxoplasma gondii is an obligate intracellular parasite that infects humans and other warm-blooded animals. Previous quantitative proteomic analyses of infected host cells revealed that the expression of many hos...

    Authors: Zhaofeng Hou, Dandan Liu, Shijie Su, Lele Wang, Zhenxing Zhao, Yifei Ma, Qiaoqiao Li, Chuanli Jia, Jinjun Xu, Yonghua Zhou and Jianping Tao

    Citation: BMC Genomics 2019 20:97

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  6. Content type: Research article

    Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovari...

    Authors: Manman Shen, Tingting Li, Genxi Zhang, Pengfei Wu, Fuxiang Chen, Qiuhong Lou, Lan Chen, Xuemei Yin, Tao Zhang and Jinyu Wang

    Citation: BMC Genomics 2019 20:96

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  7. Content type: Research article

    RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – ...

    Authors: Per K. I. Wilhelmsson, Jake O. Chandler, Noe Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner-Metzger and Stefan A. Rensing

    Citation: BMC Genomics 2019 20:95

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  8. Content type: Research article

    The SWEET proteins are a group of sugar transporters that play a role in sugar efflux during a range of biological processes, including stress responses. However, there has been no comprehensive analysis of the S...

    Authors: Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Xi Shan, Kan Bao, Li Yu, Hong Wang, Zhangjun Fei and Jianbin Li

    Citation: BMC Genomics 2019 20:93

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  9. Content type: Research article

    Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated ...

    Authors: Zhijuan Ji, Yuxiang Zeng, Yan Liang, Qian Qian and Changdeng Yang

    Citation: BMC Genomics 2019 20:91

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  10. Content type: Research article

    As important female reproductive tissues, the rice (Oryza sativa L.) ovule and female gametophyte is significant in terms of their fertility. Long noncoding RNAs (lncRNAs) play important and wide-ranging roles in...

    Authors: Helian Liu, Ruihua Wang, Bigang Mao, Bingran Zhao and Jianbo Wang

    Citation: BMC Genomics 2019 20:90

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  11. Content type: Research article

    Eggshell formation takes place in the shell gland of the oviduct of laying hens. The eggshell is rich in calcium and various glycoproteins synthesised in the shell gland. Although studies have identified genes...

    Authors: Samiullah Khan, Shu-Biao Wu and Juliet Roberts

    Citation: BMC Genomics 2019 20:89

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  12. Content type: Research article

    The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by you...

    Authors: Clemens Thölken, Markus Thamm, Christoph Erbacher and Marcus Lechner

    Citation: BMC Genomics 2019 20:88

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  13. 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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  14. Content type: Research article

    Nicotine-degrading microorganisms (NDMs) have recently received much attention since they can consume nicotine as carbon and nitrogen source for growth. In our previous work, we isolated an efficient nicotine-...

    Authors: Chunjuan He, Yougui Huang, Peng Liu, Jianhuan Wei, Yirui Yang, Li Xu and Min Xiao

    Citation: BMC Genomics 2019 20:86

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  15. Content type: Research article

    Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynth...

    Authors: Yongjun Wang, Xiuting Hua, Jingsheng Xu, Zhichang Chen, Tianqu Fan, Zhaohui Zeng, Hengbo Wang, Ai-Ling Hour, Qingyi Yu, Ray Ming and Jisen Zhang

    Citation: BMC Genomics 2019 20:83

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  16. 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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  17. Content type: Research article

    Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flo...

    Authors: Chakkree Lekklar, Monnat Pongpanich, Duangjai Suriya-arunroj, Aumnart Chinpongpanich, Helen Tsai, Luca Comai, Supachitra Chadchawan and Teerapong Buaboocha

    Citation: BMC Genomics 2019 20:76

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  18. Content type: Methodology article

    Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data fr...

    Authors: Wenbin Ye, Yuqi Long, Guoli Ji, Yaru Su, Pengchao Ye, Hongjuan Fu and Xiaohui Wu

    Citation: BMC Genomics 2019 20:75

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  19. Content type: Research article

    G-protein coupled receptors (GPCRs) are ancient, ubiquitous, constitute the largest family of transducing cell surface proteins, and are integral to cell communication via an array of ligands/neuropeptides. Mo...

    Authors: Nhut M. Tran, Donald L. Mykles, Abigail Elizur and Tomer Ventura

    Citation: BMC Genomics 2019 20:74

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  20. Content type: Research article

    Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it...

    Authors: David L. J. Vendrami, Jaume Forcada and Joseph I. Hoffman

    Citation: BMC Genomics 2019 20:72

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  21. 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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  22. Content type: Research article

    The genus Anaplasma is made up of organisms characterized by small genomes that are undergoing reductive evolution. Anaplasma ovis, one of the seven recognized species in this genus, is an understudied pathogen o...

    Authors: Zhijie Liu, Austin M. Peasley, Jifei Yang, Youquan Li, Guiquan Guan, Jianxun Luo, Hong Yin and Kelly A. Brayton

    Citation: BMC Genomics 2019 20:69

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  23. Content type: Research article

    The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genom...

    Authors: Xue Zhao, Haipeng Jiang, Lei Feng, Yingfan Qu, Weili Teng, Lijuan Qiu, Hongkun Zheng, Yingpeng Han and Wenbin Li

    Citation: BMC Genomics 2019 20:68

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  24. Content type: Research article

    The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and th...

    Authors: Macarena Ruger-Herreros, Obdulia Parra-Rivero, Javier Pardo-Medina, Francisco J. Romero-Campero, M. Carmen Limón and Javier Avalos

    Citation: BMC Genomics 2019 20:67

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  25. Content type: Research article

    The diversity of avian eggshell colour plays important biological roles in ensuring successful reproduction. Eggshell colour is also an important trait in poultry, but the mechanisms underlying it are poorly u...

    Authors: Ding-Ping Bai, Xin-Yu Lin, Yan Wu, Shi-Ye Zhou, Zhong-bin Huang, Yi-Fan Huang, Ang Li and Xiao-Hong Huang

    Citation: BMC Genomics 2019 20:66

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  26. Content type: Research article

    Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antib...

    Authors: Bart J. F. Keijser, Valeria Agamennone, Tim J. van den Broek, Martien Caspers, Adri van de Braak, Richard Bomers, Mieke Havekes, Eric Schoen, Martin van Baak, Daniël Mioch, Lonneke Bomers and Roy C. Montijn

    Citation: BMC Genomics 2019 20:65

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  27. Content type: Research article

    Many small peptides regulate eukaryotic cell biology. In fungi, some of these peptides are produced after KEX2 protease activity on proteins displaying repetitions of identical or nearly identical motifs. Foll...

    Authors: Morgane Le Marquer, Hélène San Clemente, Christophe Roux, Bruno Savelli and Nicolas Frei dit Frey

    Citation: BMC Genomics 2019 20:64

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    The Correction to this article has been published in BMC Genomics 2019 20:94

  28. Content type: Research article

    Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria...

    Authors: Dekang Zhu, Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Yu You, Xiaoyue Chen…

    Citation: BMC Genomics 2019 20:63

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  29. Content type: Research article

    MicroRNAs (miRNAs) are short endogenous, single-stranded, noncoding small RNA molecules of approximately 22 nucleotides in length. They regulate gene expression posttranscriptionally by silencing mRNA expressi...

    Authors: Martin Bilbao-Arribas, Naiara Abendaño, Endika Varela-Martínez, Ramsés Reina, Damián de Andrés and Begoña M. Jugo

    Citation: BMC Genomics 2019 20:62

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  30. Content type: Research article

    Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a...

    Authors: Hui Wang, Zhixin Chai, Dan Hu, Qiumei Ji, Jinwei Xin, Chengfu Zhang and Jincheng Zhong

    Citation: BMC Genomics 2019 20:61

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  31. Content type: Research article

    Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. sal...

    Authors: Rui Pan, Dongli He, Le Xu, Meixue Zhou, Chengdao Li, Chu Wu, Yanhao Xu and Wenying Zhang

    Citation: BMC Genomics 2019 20:60

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  32. Content type: Research article

    Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. ...

    Authors: Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad and Youxiong Que

    Citation: BMC Genomics 2019 20:57

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  33. Content type: Software

    Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is oft...

    Authors: Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin and Charles Pineau

    Citation: BMC Genomics 2019 20:56

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  34. Content type: Research article

    The gram-negative Xanthomonas genus contains a large group of economically important plant pathogens, which cause severe diseases on many crops worldwide. The diffusible signal factor (DSF) - mediated quorum sens...

    Authors: Lei Li, Jinyun Li, Yunzeng Zhang and Nian Wang

    Citation: BMC Genomics 2019 20:55

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  35. Content type: Methodology article

    Chromatin-immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for mapping genome-wide binding of chromatin-associated factors. However, broadly applicable methods for between-sample c...

    Authors: Luis A. Vale-Silva, Tovah E. Markowitz and Andreas Hochwagen

    Citation: BMC Genomics 2019 20:54

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  36. Content type: Research article

    Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January–March and a period of low temperature is neces...

    Authors: Fengxi Yang, Genfa Zhu, Yonglu Wei, Jie Gao, Gang Liang, Lingyuan Peng, Chuqiao Lu and Jianpeng Jin

    Citation: BMC Genomics 2019 20:53

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  37. Content type: Research article

    Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adap...

    Authors: Rahul V. Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Goujie Zhang, Siu F. Lee, Ary A. Hoffmann and John G. Oakeshott

    Citation: BMC Genomics 2019 20:52

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  38. Content type: Research article

    Aging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, liver shows age-related dysregulation of lipid metabolism, impaired detoxif...

    Authors: Kerui Huang, Wenhao Chen, Fang Zhu, Patrick Wai-Lun Li, Pankaj Kapahi and Hua Bai

    Citation: BMC Genomics 2019 20:50

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  39. Content type: Research article

    Red-fleshed papaya is a good material to study the different carotenoids accumulation mechanism in the peel and flesh. Although the peel and flesh of papaya closely integrated into one body, the flesh colorati...

    Authors: Yan Hong Shen, Fei Ying Yang, Bing Guo Lu, Wan Wan Zhao, Tao Jiang, Li Feng, Xiao Jing Chen and Ray Ming

    Citation: BMC Genomics 2019 20:49

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  40. Content type: Research article

    Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and acceler...

    Authors: Chen Huang, Dongliang Leng, Shixue Sun and Xiaohua Douglas Zhang

    Citation: BMC Genomics 2019 20:48

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  41. Content type: Research article

    Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilizat...

    Authors: Liana Apolis, Joanna Olivas, Prakash Srinivasan, Ambuj K. Kushwaha and Sanjay A. Desai

    Citation: BMC Genomics 2019 20:47

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  42. Content type: Research article

    The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood. To explain the role of miRNAs in this process we applied a r...

    Authors: Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik and Ewa Borzym

    Citation: BMC Genomics 2019 20:46

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