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  1. Content type: Research article

    Tree peony (Paeonia suffruticosa Andrews) is a globally famous ornamental flower, with large and colorful flowers and abundant flower types. However, a relatively short and uniform flowering period hinders the ap...

    Authors: Shunli Wang, Jie Gao, Jingqi Xue, Yuqian Xue, Dandan Li, Yanren Guan and Xiuxin Zhang

    Citation: BMC Genomics 2019 20:572

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  2. Content type: Research

    Purpose of study is revealing significant differences in serum proteomes in schizophrenia and bipolar disorder (BD).

    Authors: Liudmila Smirnova, Alexander Seregin, Irina Boksha, Elena Dmitrieva, German Simutkin, Elena Kornetova, Olga Savushkina, Anastasia Letova, Nikolay Bokhan, Svetlana Ivanova and Victor Zgoda

    Citation: BMC Genomics 2019 20(Suppl 7):535

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    This article is part of a Supplement: Volume 20 Supplement 7

  3. Content type: Research article

    Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increas...

    Authors: Xiao-Qing Huang, Xiao-Hong Lu, Man-Hong Sun, Rong-Jun Guo, Anne D. van Diepeningen and Shi-Dong Li

    Citation: BMC Genomics 2019 20:570

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  4. Content type: Research article

    To illuminate the mechanisms underlying the high-altitude tolerance of Tibetan pig spermatozoa, proteomes of spermatozoa from Tibetan pigs raised in high and low altitudes were compared using a tandem mass tag...

    Authors: Yanling Zhao, Xiaoli Lu, Zhipeng Cheng, Mengfang Tian, Yangzong Qiangba, Qiang Fu and Zili Ren

    Citation: BMC Genomics 2019 20:569

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    The Correction to this article has been published in BMC Genomics 2019 20:626

  5. Content type: Research article

    The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube (Ziziphus juju...

    Authors: Hongtai Li, Weilin Gao, Chaoling Xue, Yao Zhang, Zhiguo Liu, Yu Zhang, Xianwei Meng, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:568

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  6. Content type: Research article

    The σ54 factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ54 is present in many Clostridiales species that have ...

    Authors: Xiaoqun Nie, Wenyue Dong and Chen Yang

    Citation: BMC Genomics 2019 20:565

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  7. Content type: Research article

    Anthocyanins perform diverse biological functions in plants and are beneficial to human health. Leaf color is the most important trait of ornamental kale and the characteristics of changes in leaf color make i...

    Authors: Ning Guo, Shuo Han, Mei Zong, Guixiang Wang, Shuning Zheng and Fan Liu

    Citation: BMC Genomics 2019 20:564

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  8. Content type: Research article

    T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large ...

    Authors: Xin Wen, Yadong Hu, Xinyu Zhang, Xiaozhen Wei, Tao Wang and Shaowu Yin

    Citation: BMC Genomics 2019 20:563

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  9. Content type: Research article

    The production of foam nests is one of the strategies that has evolved to allow some anuran species to protect their eggs and larvae. Despite considerable knowledge of the biochemical components of and constru...

    Authors: Wei Zhang, Li Huang, Jun Li, Yinghua Li, Shichao Wei, Ling Cai and Hua Wu

    Citation: BMC Genomics 2019 20:562

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  10. Content type: Research article

    Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tok...

    Authors: Katlyn Borgers, Jheng-Yang Ou, Po-Xing Zheng, Petra Tiels, Annelies Van Hecke, Evelyn Plets, Gitte Michielsen, Nele Festjens, Nico Callewaert and Yao-Cheng Lin

    Citation: BMC Genomics 2019 20:561

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  11. Content type: Research article

    Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size ...

    Authors: Marco Meola, Etienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud and Christophe Chassard

    Citation: BMC Genomics 2019 20:560

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  12. Content type: Research article

    A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, ...

    Authors: Ying Wan, Xiaoyang Liu, Dongwang Zheng, Yuying Wang, Huan Chen, Xiaofeng Zhao, Guoqing Liang, Dongliang Yu and Lin Gan

    Citation: BMC Genomics 2019 20:559

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  13. Content type: Research article

    Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing...

    Authors: Huiru Sun, Hengling Wei, Hantao Wang, Pengbo Hao, Lijiao Gu, Guoyuan Liu, Liang Ma, Zhengzheng Su and Shuxun Yu

    Citation: BMC Genomics 2019 20:558

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  14. Content type: Research article

    National genetic evaluations for disease resistance do not exist, precluding the genetic improvement of cattle for these traits. We imputed BovineHD genotypes to whole genome sequence for 2703 Holsteins that w...

    Authors: Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel, Christopher M. Seabury, Holly L. Neibergs and Jeremy F. Taylor

    Citation: BMC Genomics 2019 20:555

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  15. Content type: Research article

    Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that...

    Authors: Carolina Munari Rodrigues, Marco Aurélio Takita, Nicholas Vinicius Silva, Marcelo Ribeiro-Alves and Marcos Antonio Machado

    Citation: BMC Genomics 2019 20:554

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  16. Content type: Research article

    SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family...

    Authors: Hongfeng Wang, Zhichao Lu, Yiteng Xu, Lingcui Kong, Jianjun Shi, Yafei Liu, Chunxiang Fu, Xiaoshan Wang, Zeng-Yu Wang, Chuanen Zhou and Lu Han

    Citation: BMC Genomics 2019 20:552

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  17. Content type: Correction

    Following the publication of this article [1], the authors reported that the link to Additional file 11 linked to the wrong set of data. The correct supplementary data is provided in this Correction article (A...

    Authors: Shrikant Patil, Sara Moeys, Peter von Dassow, Marie J. J. Huysman, Daniel Mapleson, Lieven De Veylder, Remo Sanges, Wim Vyverman, Marina Montresor and Maria Immacolata Ferrante

    Citation: BMC Genomics 2019 20:544

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    The original article was published in BMC Genomics 2015 16:930

  18. Content type: Research article

    Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these pa...

    Authors: Álvaro Polonio, Pedro Seoane, M. Gonzalo Claros and Alejandro Pérez-García

    Citation: BMC Genomics 2019 20:543

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  19. Content type: Research article

    Viruses have evolved to create a cellular environment permissive for viral replication in susceptible hosts. Possibly both enabling and resulting from these virus-triggered changes, infected hosts undergo a dr...

    Authors: Mengshi Wu, Xue Ding, Xing Fu and Rosa Lozano-Duran

    Citation: BMC Genomics 2019 20:542

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  20. Content type: Software

    Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such...

    Authors: Daoshan Zheng, Justyna Trynda, Zhifu Sun and Zhaoyu Li

    Citation: BMC Genomics 2019 20:541

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  21. Content type: Methodology article

    Transcriptomic profiles can improve our understanding of the phenotypic molecular basis of biological research, and many statistical methods have been proposed to identify differentially expressed genes (DEGs)...

    Authors: Kyungtaek Park, Jaehoon An, Jungsoo Gim, Minseok Seo, Woojoo Lee, Taesung Park and Sungho Won

    Citation: BMC Genomics 2019 20:540

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  22. Content type: Methodology article

    Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effect...

    Authors: Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J. C. Slebos, Christine H. Chung and Xuefeng Wang

    Citation: BMC Genomics 2019 20:539

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  23. Content type: Research article

    Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. T...

    Authors: Weixi Li, Dayong Zhang, Guozhong Zhu, Xinyue Mi and Wangzhen Guo

    Citation: BMC Genomics 2019 20:538

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  24. Content type: Methodology article

    Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miR...

    Authors: Rui Wang, Zhongyi Yang, Yuhan Fei, Jiejie Feng, Hui Zhu, Fang Huang, Hongsheng Zhang and Ji Huang

    Citation: BMC Genomics 2019 20:534

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  25. Content type: Research article

    Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and a...

    Authors: Yong Huang, Ling Jiang, Bo-Yu Liu, Cheng-Fang Tan, Dong-Hong Chen, Wen-Hui Shen and Ying Ruan

    Citation: BMC Genomics 2019 20:533

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  26. Content type: Software

    MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for...

    Authors: Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, Mohcen Benmounah and Hélène Touzet

    Citation: BMC Genomics 2019 20:532

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  27. Content type: Research article

    The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far...

    Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura

    Citation: BMC Genomics 2019 20:531

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    The Correction to this article has been published in BMC Genomics 2019 20:622

  28. Content type: Research article

    Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicr...

    Authors: Nicholas Costa Barroso Lima, Arif M. Tanmoy, Emilie Westeel, Luiz Gonzaga Paula de Almeida, Alain Rajoharison, Maksuda Islam, Hubert P. Endtz, Samir K. Saha, Ana Tereza Ribeiro de Vasconcelos and Florence Komurian-Pradel

    Citation: BMC Genomics 2019 20:530

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  29. Content type: Research article

    The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an ...

    Authors: Anja Striberny, Even H. Jørgensen, Christophe Klopp and Elodie Magnanou

    Citation: BMC Genomics 2019 20:529

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  30. Content type: Research article

    Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. As...

    Authors: Teshale Assefa, Paul I. Otyama, Anne V. Brown, Scott R. Kalberer, Roshan S. Kulkarni and Steven B. Cannon

    Citation: BMC Genomics 2019 20:527

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  31. Content type: Research article

    Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susc...

    Authors: Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli and Elisa Angelini

    Citation: BMC Genomics 2019 20:526

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  32. Content type: Research article

    Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar prod...

    Authors: Marc G. Higgins, David A. Kenny, Claire Fitzsimons, Gordon Blackshields, Séan Coyle, Clare McKenna, Mark McGee, Derek W. Morris and Sinéad M. Waters

    Citation: BMC Genomics 2019 20:525

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  33. Content type: Correction

    Following the publication of this article [1], the authors reported that the Fig. 2 described in the article had a mistake that two grey blocks in S. moellendorffii was not placed as background color, and in the ...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang

    Citation: BMC Genomics 2019 20:523

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    The original article was published in BMC Genomics 2019 20:484

  34. Content type: Research article

    Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, ...

    Authors: Valeria Petrella, Serena Aceto, Vincenza Colonna, Giuseppe Saccone, Remo Sanges, Nikola Polanska, Petr Volf, Luigi Gradoni, Gioia Bongiorno and Marco Salvemini

    Citation: BMC Genomics 2019 20:522

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  35. Content type: Research article

    Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related dise...

    Authors: Fernando Carazo, Marian Gimeno, Juan A. Ferrer-Bonsoms and Angel Rubio

    Citation: BMC Genomics 2019 20:521

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  36. Content type: Research article

    The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed...

    Authors: Danielly Beraldo dos Santos Silva, Larissa Fernanda Simielli Fonseca, Daniel Guariz Pinheiro, Maria Malane Magalhães Muniz, Ana Fabrícia Braga Magalhães, Fernando Baldi, Jesus Aparecido Ferro, Luis Artur Loyola Chardulo and Lucia Galvão de Albuquerque

    Citation: BMC Genomics 2019 20:520

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  37. Content type: Research article

    Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng

    Citation: BMC Genomics 2019 20:519

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  38. Content type: Research article

    The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we...

    Authors: Rayner González-Prendes, Emilio Mármol-Sánchez, Raquel Quintanilla, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Tainã Figueiredo Cardoso, Arianna Manunza, Ángela Cánovas and Marcel Amills

    Citation: BMC Genomics 2019 20:518

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  39. Content type: Research article

    Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV...

    Authors: Wenliang Li, Li Mao, Xin Shu, Runxia Liu, Fei Hao, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Chunyan Zhong and Jieyuan Jiang

    Citation: BMC Genomics 2019 20:516

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  40. Content type: Research article

    Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish s...

    Authors: Mingkun Luo, Lanmei Wang, Haoran Yin, Wenbin Zhu, Jianjun Fu and Zaijie Dong

    Citation: BMC Genomics 2019 20:515

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  41. Content type: Research article

    Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan

    Citation: BMC Genomics 2019 20:514

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  42. Content type: Methodology article

    RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapt...

    Authors: Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger and Joo Heon Shin

    Citation: BMC Genomics 2019 20:513

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