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  1. Content type: Research article

    Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DN...

    Authors: Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D. Makova and Dick de Ridder

    Citation: BMC Genomics 2018 19:798

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  2. Content type: Research article

    WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modi...

    Authors: Rui Hu, Jie Xiao, Ting Gu, Xiaofen Yu, Yang Zhang, Junli Chang, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2018 19:803

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    The Correction to this article has been published in BMC Genomics 2018 19:852

  3. Content type: Research article

    A change in the environment may impair development or survival of living organisms leading them to adapt to the change. The resulting adaptation trait may reverse, or become fixed in the population leading to ...

    Authors: Yves Moné, Sandra Nhim, Sylvie Gimenez, Fabrice Legeai, Imène Seninet, Hugues Parrinello, Nicolas Nègre and Emmanuelle d’Alençon

    Citation: BMC Genomics 2018 19:804

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  4. Content type: Research article

    Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest Chin...

    Authors: Chao Hu, Hongxing Yang, Kai Jiang, Ling Wang, Boyun Yang, Tungyu Hsieh, Siren Lan and Weichang Huang

    Citation: BMC Genomics 2018 19:800

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  5. Content type: Research article

    Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the...

    Authors: Suchawan Pornsukarom, Arnoud H M van Vliet and Siddhartha Thakur

    Citation: BMC Genomics 2018 19:801

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  6. Content type: Methodology article

    Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count dat...

    Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli and Héctor Corrada Bravo

    Citation: BMC Genomics 2018 19:799

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  7. Content type: Research article

    Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embry...

    Authors: Yan Chen, Xue Li, Liyao Su, Xu Chen, Shuting Zhang, Xiaoping Xu, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2018 19:805

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  8. Content type: Research article

    Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they...

    Authors: Stacey E. Wahl, Brent H. Wyatt, Stephen D. Turner and Amanda J. G. Dickinson

    Citation: BMC Genomics 2018 19:795

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  9. Content type: Research article

    Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-whi...

    Authors: Juan Carlos Higareda-Almaraz, Michael Karbiener, Maude Giroud, Florian M. Pauler, Teresa Gerhalter, Stephan Herzig and Marcel Scheideler

    Citation: BMC Genomics 2018 19:794

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  10. Content type: Research article

    Dependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products ...

    Authors: Albert Caballero-Solares, Xi Xue, Christopher C. Parrish, Maryam Beheshti Foroutani, Richard G. Taylor and Matthew L. Rise

    Citation: BMC Genomics 2018 19:796

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  11. Content type: Research article

    The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple indivi...

    Authors: Majid Khansefid, Jennie E. Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A. Millen, Amanda J. Chamberlain, Christy J. Vander Jagt and Michael E. Goddard

    Citation: BMC Genomics 2018 19:793

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  12. Content type: Research article

    Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptatio...

    Authors: Billie A. Gould, Juan Diego Palacio-Mejia, Jerry Jenkins, Sujan Mamidi, Kerrie Barry, Jeremy Schmutz, Thomas E. Juenger and David B. Lowry

    Citation: BMC Genomics 2018 19:792

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  13. Content type: Research article

    Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosy...

    Authors: Byoungnam Min, Seunghwan Kim, Youn-Lee Oh, Won-Sik Kong, Hongjae Park, Heejung Cho, Kab-Yeul Jang, Jeong-Gu Kim and In-Geol Choi

    Citation: BMC Genomics 2018 19:789

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  14. Content type: Research article

    Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to ...

    Authors: Justyna Horodyska, Klaus Wimmers, Henry Reyer, Nares Trakooljul, Anne Maria Mullen, Peadar G. Lawlor and Ruth M. Hamill

    Citation: BMC Genomics 2018 19:791

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  15. Content type: Methodology article

    Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) da...

    Authors: Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa and Seiya Imoto

    Citation: BMC Genomics 2018 19:790

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  16. Content type: Methodology article

    Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover...

    Authors: Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang and Yudi Pawitan

    Citation: BMC Genomics 2018 19:786

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  17. Content type: Research article

    The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori ha...

    Authors: Chuan-Zhen Qiu, Qiu-Zhong Zhou, Ting-Ting Liu, Shou-Min Fang, Ya-Wang Wang, Xin Fang, Chun-Li Huang, Quan-You Yu, Chun-Hong Chen and Ze Zhang

    Citation: BMC Genomics 2018 19:788

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  18. Content type: Research article

    Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M....

    Authors: Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu and Dan Xie

    Citation: BMC Genomics 2018 19:787

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  19. Content type: Research article

    The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is pred...

    Authors: Lin-sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-gang Sun, Irfan Ullah and Yin-cang Han

    Citation: BMC Genomics 2018 19:785

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  21. Content type: Research article

    Heterosis, a multigenic complex trait extrapolated as sum total of many phenotypic features, is widely utilized phenomenon in agricultural crops for about a century. It is mainly focused on establishing vigoro...

    Authors: Zareen Sarfraz, Muhammad Shahid Iqbal, Zhaoe Pan, Yinhua Jia, Shoupu He, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Zhiying Ma, Dongyong Xu, Jinlong Yang, Jinbiao Zhang, Wenfang Gong, Xiaoli Geng…

    Citation: BMC Genomics 2018 19:776

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  22. Content type: Research article

    MicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for ...

    Authors: Mingkun Luo, Lanmei Wang, Wenbin Zhu, Jianjun Fu, Feibiao Song, Min Fang, Juanjuan Dong and Zaijie Dong

    Citation: BMC Genomics 2018 19:779

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  23. Content type: Research article

    Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only...

    Authors: Jingxin Zhang, John Hu, Huifang Shen, Yucheng Zhang, Dayuan Sun, Xiaoming Pu, Qiyun Yang, Qiurong Fan and Birun Lin

    Citation: BMC Genomics 2018 19:782

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  24. Content type: Research article

    Disrupted diurnal rhythms cause accelerated aging and an increased incidence in age-related disease and morbidity. The circadian clock governs cell physiology and metabolism by controlling transcription and ch...

    Authors: Jinhee Park and William J. Belden

    Citation: BMC Genomics 2018 19:777

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  25. Content type: Methodology article

    Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved o...

    Authors: Zoltán Maróti, Zsolt Boldogkői, Dóra Tombácz, Michael Snyder and Tibor Kalmár

    Citation: BMC Genomics 2018 19:778

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  26. Content type: Research article

    The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with ...

    Authors: Yung-Chih Lai, Ya-Chen Liang, Ting-Xin Jiang, Randall B. Widelitz, Ping Wu and Cheng-Ming Chuong

    Citation: BMC Genomics 2018 19:780

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  27. Content type: Research article

    Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich f...

    Authors: Daniel G. Mediati, Catherine M. Burke, Shirin Ansari, Elizabeth J. Harry and Iain G. Duggin

    Citation: BMC Genomics 2018 19:781

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  28. Content type: Research article

    Our previous study showed that (+)-cholesten-3-one (CN) has the potential to induce the osteoblastic differentiation of mesenchymal stem cells (MSCs). However, the roles of CN in targeting miRNA-mRNA-lncRNA in...

    Authors: Qiuke Hou, Yongquan Huang, Yamei Liu, Yiwen Luo, Bin Wang, Rudong Deng, Saixia Zhang, Fengbin Liu and Dongfeng Chen

    Citation: BMC Genomics 2018 19:783

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  29. Content type: Research article

    The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitocho...

    Authors: Shuangshuang Li, Zhiwen Chen, Nan Zhao, Yumei Wang, Hushuai Nie and Jinping Hua

    Citation: BMC Genomics 2018 19:775

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  31. Content type: Research article

    Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has ...

    Authors: Dan Zhang, Xiuyu Lou, Hao Yan, Junhang Pan, Haiyan Mao, Hongfeng Tang, Yan Shu, Yun Zhao, Lei Liu, Junping Li, Jiang Chen, Yanjun Zhang and Xuejun Ma

    Citation: BMC Genomics 2018 19:773

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  32. Content type: Research article

    Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli

    Authors: Katie R Bradwell, Vishal N Koparde, Andrey V Matveyev, Myrna G Serrano, João M P Alves, Hardik Parikh, Bernice Huang, Vladimir Lee, Oneida Espinosa-Alvarez, Paola A Ortiz, André G Costa-Martins, Marta M G Teixeira and Gregory A Buck

    Citation: BMC Genomics 2018 19:770

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  34. Content type: Research article

    Wheat (Triticum aestivum L.) is one of the world’s most important grain crops. The amyloplast, a specialized organelle, is the major site for starch synthesis and storage in wheat grain. Understanding the metabol...

    Authors: Dongyun Ma, Xin Huang, Junfeng Hou, Ying Ma, Qiaoxia Han, Gege Hou, Chenyang Wang and Tiancai Guo

    Citation: BMC Genomics 2018 19:768

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  36. Content type: Research article

    The cattle gastrointestinal tract (GIT) is the main enterohemorrhagic Escherichia coli (EHEC) reservoir. In order to identify nutrients required for the survival or multiplication of EHEC in the bovine GIT, we co...

    Authors: Audrey Segura, Marine Bertoni, Pauline Auffret, Christophe Klopp, Olivier Bouchez, Clémence Genthon, Alexandra Durand, Yolande Bertin and Evelyne Forano

    Citation: BMC Genomics 2018 19:766

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  37. Content type: Research article

    Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of p...

    Authors: Tiago Ebert Fritsch, Franciele Maboni Siqueira and Irene Silveira Schrank

    Citation: BMC Genomics 2018 19:767

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  38. Content type: Research article

    Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even th...

    Authors: Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori and Satoshi Nagai

    Citation: BMC Genomics 2018 19:765

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  39. Content type: Research article

    The relationship between aging and epigenetic profiles has been highlighted in many recent studies. Models using somatic cell methylomes to predict age have been successfully constructed. However, gamete aging...

    Authors: Timothy G. Jenkins, Kenneth I. Aston, Bradley Cairns, Andrew Smith and Douglas T. Carrell

    Citation: BMC Genomics 2018 19:763

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  40. Content type: Research article

    A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here ai...

    Authors: Koryu Kin, Gillian Forbes, Andrew Cassidy and Pauline Schaap

    Citation: BMC Genomics 2018 19:764

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  41. Content type: Research article

    Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and o...

    Authors: Viacheslav Sinkov, Oleg Ogarkov, Igor Mokrousov, Yuri Bukin, Svetlana Zhdanova and Scott K. Heysell

    Citation: BMC Genomics 2018 19:762

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  42. Content type: Research article

    Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their allev...

    Authors: Luis M Avila, Wisam Obeidat, Hugh Earl, Xiaomu Niu, William Hargreaves and Lewis Lukens

    Citation: BMC Genomics 2018 19:761

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  43. Content type: Research article

    An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to extern...

    Authors: Gaurav Sharma, Rebecca Parales and Mitchell Singer

    Citation: BMC Genomics 2018 19:757

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  44. Content type: Research article

    In the past years, our laboratory successfully generated transgenic rainbow trout bearing cecropin P1 transgene. These fish exhibited resistant characteristic to infection by Aeromonas salmonicida, Infectious Hem...

    Authors: Yueh-Chiang Han, Chun-Mean Lin and Thomas T. Chen

    Citation: BMC Genomics 2018 19:760

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  45. Content type: Research article

    In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partition...

    Authors: Long Zhao, Lei Han, Chaoxia Xiao, Xiuyun Lin, Chunming Xu and Chunwu Yang

    Citation: BMC Genomics 2018 19:756

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  46. Content type: Research article

    Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates. These databases combine interactions across...

    Authors: R. Greg Stacey, Michael A. Skinnider, Jenny H. L. Chik and Leonard J. Foster

    Citation: BMC Genomics 2018 19:758

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  48. Content type: Software

    Previous studies demonstrate the usefulness of using multiple tools and methods for improving the accuracy of motif detection. Over the past years, numerous motif discovery pipelines have been developed. Howev...

    Authors: Ngoc Tam L. Tran and Chun-Hsi Huang

    Citation: BMC Genomics 2018 19:755

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  49. Content type: Research article

    COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCFCOI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown ...

    Authors: Jian-fang Bai, Yu-kun Wang, Peng Wang, Shao-hua Yuan, Jian-gang Gao, Wen-jing Duan, Na Wang, Feng-ting Zhang, Wen-jie Zhang, Meng-ying Qin, Chang-ping Zhao and Li-ping Zhang

    Citation: BMC Genomics 2018 19:754

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  50. Content type: Research article

    Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range ...

    Authors: Filipe P Matteoli, Hemanoel Passarelli-Araujo, Régis Josué A Reis, Letícia O da Rocha, Emanuel M de Souza, L Aravind, Fabio L Olivares and Thiago M Venancio

    Citation: BMC Genomics 2018 19:750

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