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  1. Avian reovirus (ARV) is an important poultry pathogen that can cause immunosuppression. In this study, RNA-Seq technology was applied to investigate the transcriptome-wide changes of DF-1 cells upon ARV infect...

    Authors: Xiaosai Niu, Yuyang Wang, Min Li, Xiaorong Zhang and Yantao Wu
    Citation: BMC Genomics 2017 18:911
    Content type: Research article Published on:

  2. The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic ...

    Authors: Mirjam Frischknecht, Beat Bapst, Franz R. Seefried, Heidi Signer-Hasler, Dorian Garrick, Christian Stricker, Ruedi Fries, Ingolf Russ, Johann Sölkner, Anna Bieber, Maria G. Strillacci, Birgit Gredler-Grandl and Christine Flury
    Citation: BMC Genomics 2017 18:910
    Content type: Research article Published on:

  3. Sugarcane is a major crop of the tropics cultivated mainly for its high sucrose content. The crop is genetically less explored due to its complex polyploid genome. Sucrose synthesis and accumulation are comple...

    Authors: Prathima P. Thirugnanasambandam, Nam V. Hoang, Agnelo Furtado, Frederick C. Botha and Robert J. Henry
    Citation: BMC Genomics 2017 18:909
    Content type: Research article Published on:

  4. Crustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of c...

    Authors: Jing Qin, Yaohua Hu, Ka Yan Ma, Xiaosen Jiang, Ching Hei Ho, Ling Ming Tsang, Lefei Yi, Ricky Wai Tak Leung and Ka Hou Chu
    Citation: BMC Genomics 2017 18:908
    Content type: Database Published on:

  5. Streptomyces clavuligerus ATCC 27064, the industrial producer of the β-lactamase inhibitor clavulanic acid, carries 49 putative secondary metabolite gene clusters. These secondary meta...

    Authors: Rubén Álvarez-Álvarez, Yolanda Martínez-Burgo, Antonio Rodríguez-García and Paloma Liras
    Citation: BMC Genomics 2017 18:907
    Content type: Research article Published on:

  6. As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a l...

    Authors: Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst and Joel A. Schick
    Citation: BMC Genomics 2017 18:905
    Content type: Software Published on:

  8. Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae i...

    Authors: Christine Marie George, Mahamud Rashid, Mathieu Almeida, K. M. Saif-Ur-Rahman, Shirajum Monira, Md. Sazzadul Islam Bhuyian, Khaled Hasan, Toslim T. Mahmud, Shan Li, Jessica Brubaker, Jamie Perin, Zillur Rahman, Munshi Mustafiz, David A. Sack, R. Bradley Sack, Munirul Alam…
    Citation: BMC Genomics 2017 18:903
    Content type: Research article Published on:

  9. Epigenetic alterations are strongly associated with the development of cancer. The aim of this study was to identify epigenetic pattern in squamous cell lung cancer (LUSC) on a genome-wide scale.

    Authors: Yuan-Xiang Shi, Ying Wang, Xi Li, Wei Zhang, Hong-Hao Zhou, Ji-Ye Yin and Zhao-Qian Liu
    Citation: BMC Genomics 2017 18:901
    Content type: Research article Published on:

  10. The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of ...

    Authors: Birgit S. Gruben, Miia R. Mäkelä, Joanna E. Kowalczyk, Miaomiao Zhou, Isabelle Benoit-Gelber and Ronald P. De Vries
    Citation: BMC Genomics 2017 18:900
    Content type: Research article Published on:

  11. Lily is an economically important plant, with leaves and bulbs consisting of overlapping scales, large ornamental flowers and a very large genome. Although it is recognized that flowers and bulb scales are mod...

    Authors: Fang Du, Junmiao Fan, Ting Wang, Yun Wu, Donald Grierson, Zhongshan Gao and Yiping Xia
    Citation: BMC Genomics 2017 18:899
    Content type: Research article Published on:

  12. Cowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input...

    Authors: Vikram A. Misra, Yu Wang and Michael P. Timko
    Citation: BMC Genomics 2017 18:898
    Content type: Research article Published on:

  13. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are g...

    Authors: Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun and Ryohei Terauchi
    Citation: BMC Genomics 2017 18:897
    Content type: Research article Published on:

  14. Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recogniz...

    Authors: Ji Li, Jian Xu, Qin-Wei Guo, Zhe Wu, Ting Zhang, Kai-Jing Zhang, Chun-yan Cheng, Pin-yu Zhu, Qun-Feng Lou and Jin-Feng Chen
    Citation: BMC Genomics 2017 18:896
    Content type: Research article Published on:

  15. Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying ...

    Authors: Hana Hall, Patrick Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, Rebecca Doerge and Vikki M. Weake
    Citation: BMC Genomics 2017 18:894
    Content type: Research article Published on:

  16. The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can ...

    Authors: Xinglin Zhang, Vincent de Maat, Ana M. Guzmán Prieto, Tomasz K. Prajsnar, Jumamurat R. Bayjanov, Mark de Been, Malbert R. C. Rogers, Marc J. M. Bonten, Stéphane Mesnage, Rob J. L. Willems and Willem van Schaik
    Citation: BMC Genomics 2017 18:893
    Content type: Research article Published on:

  17. In addition to additive genetic effects, epistatic interactions can play key roles in the control of phenotypic variation of traits of interest. In the current study, 475 male birds from lean and fat chicken l...

    Authors: Hui Zhang, Jia-Qiang Yu, Li-Li Yang, Luke M. Kramer, Xin-Yang Zhang, Wei Na, James M. Reecy and Hui Li
    Citation: BMC Genomics 2017 18:892
    Content type: Research article Published on:

  18. Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of...

    Authors: Márcia Carvalho, María Muñoz-Amatriaín, Isaura Castro, Teresa Lino-Neto, Manuela Matos, Marcos Egea-Cortines, Eduardo Rosa, Timothy Close and Valdemar Carnide
    Citation: BMC Genomics 2017 18:891
    Content type: Research Published on:

  20. Many genes important for reproductive performance are shared by both sexes. However, fecundity indices are primarily based on female parameters such as litter size. We examined a fertility mouse line (FL2), wh...

    Authors: Marten Michaelis, Alexander Sobczak, Dirk Koczan, Martina Langhammer, Norbert Reinsch, Jennifer Schoen and Joachim M. Weitzel
    Citation: BMC Genomics 2017 18:889
    Content type: Research article Published on:

  21. Trichophyton mentagrophytes is an important zoonotic dermatophytic (ringworm) pathogen; causing severe skin infection in humans and other animals worldwide. Fortunately, commonly used ...

    Authors: Xinke Zhang, Pengxiu Dai, Yongping Gao, Xiaowen Gong, Hao Cui, Yipeng Jin and Yihua Zhang
    Citation: BMC Genomics 2017 18:888
    Content type: Research article Published on:

  22. The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of severa...

    Authors: Aaron W. Kolb, Andrew C. Lewin, Ralph Moeller Trane, Gillian J. McLellan and Curtis R. Brandt
    Citation: BMC Genomics 2017 18:887
    Content type: Research article Published on:

  23. To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutri...

    Authors: L. M. Vera, C. Metochis, J. F. Taylor, M. Clarkson, K. H. Skjærven, H. Migaud and D. R. Tocher
    Citation: BMC Genomics 2017 18:886
    Content type: Research article Published on:

  24. Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. TEs are believed to promote speciation and their activities play a significant role in human d...

    Authors: Lingling Jin, Ian McQuillan and Longhai Li
    Citation: BMC Genomics 2017 18(Suppl 9):862
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 9

  25. Gene expression is a key intermediate level that genotypes lead to a particular trait. Gene expression is affected by various factors including genotypes of genetic variants. With an aim of delineating the gen...

    Authors: Rui Xie, Jia Wen, Andrew Quitadamo, Jianlin Cheng and Xinghua Shi
    Citation: BMC Genomics 2017 18(Suppl 9):845
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 9

  26. The reconstruction of gene regulatory network (GRN) from gene expression data can discover regulatory relationships among genes and gain deep insights into the complicated regulation mechanism of life. However...

    Authors: Linlin Xing, Maozu Guo, Xiaoyan Liu, Chunyu Wang, Lei Wang and Yin Zhang
    Citation: BMC Genomics 2017 18(Suppl 9):844
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 9

  27. The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA...

    Authors: Hong Zhou, Michael Zhou, Daisy Li, Joseph Manthey, Ekaterina Lioutikova, Hong Wang and Xiao Zeng
    Citation: BMC Genomics 2017 18(Suppl 9):826
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 9

  28. Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein...

    Authors: Md. Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Gopal Saha, Manosh Kumar Biswas, Hoy-Taek Kim and Ill-Sup Nou
    Citation: BMC Genomics 2017 18:885
    Content type: Research Published on:

  29. Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 ...

    Authors: Chen Wu, Victoria G. Twort, Ross N. Crowhurst, Richard D. Newcomb and Thomas R. Buckley
    Citation: BMC Genomics 2017 18:884
    Content type: Research article Published on:

  30. Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of ...

    Authors: Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Antonio G. Pisabarro and Lucía Ramírez
    Citation: BMC Genomics 2017 18:883
    Content type: Research article Published on:

  31. Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with oth...

    Authors: Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin and Hélène Chiapello
    Citation: BMC Genomics 2017 18:882
    Content type: Research article Published on:

  32. Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negative...

    Authors: Chandran Nithin, Amal Thomas, Jolly Basak and Ranjit Prasad Bahadur
    Citation: BMC Genomics 2017 18:878
    Content type: Research article Published on:

  33. While the influence of nature (genes) and nurture (environment) on elite sporting performance remains difficult to precisely determine, the dismissal of either as a contributing factor to performance is unwarr...

    Authors: Evelina Georgiades, Vassilis Klissouras, Jamie Baulch, Guan Wang and Yannis Pitsiladis
    Citation: BMC Genomics 2017 18(Suppl 8):835
    Content type: Commentary Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  34. Cardiorespiratory fitness (VO2max) is an excellent predictor of chronic disease morbidity and mortality risk. Guidelines recommend individuals undertake exercise training to improve VO2max for chronic disease red...

    Authors: Camilla J. Williams, Mark G. Williams, Nir Eynon, Kevin J. Ashton, Jonathan P. Little, Ulrik Wisloff and Jeff S. Coombes
    Citation: BMC Genomics 2017 18(Suppl 8):831
    Content type: Review Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  35. This article provides a critical overview of the ethics and governance of genetic biobank research, using the Athlome Consortium as a large scale instance of collaborative sports genetic biobanking. We present...

    Authors: Rachel Thompson and Michael J. McNamee
    Citation: BMC Genomics 2017 18(Suppl 8):830
    Content type: Review Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  37. The gene SMART (genes and the Skeletal Muscle Adaptive Response to Training) Study aims to identify genetic variants that predict the response to both a single session of High-Intensity Interval Exercise (HIIE...

    Authors: Xu Yan, Nir Eynon, Ioannis D. Papadimitriou, Jujiao Kuang, Fiona Munson, Oren Tirosh, Lannie O’Keefe, Lyn R. Griffiths, Kevin J. Ashton, Nuala Byrne, Yannis P. Pitsiladis and David J. Bishop
    Citation: BMC Genomics 2017 18(Suppl 8):821
    Content type: Review Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  38. Two common single nucleotide polymorphisms within the COL5A1 gene (SNPs; rs12722 C/T and rs3196378 C/A) have previously been associated with tendon and ligament pathologies. Given the high incidence of tendon and...

    Authors: Shane M. Heffernan, Liam P. Kilduff, Robert M. Erskine, Stephen H. Day, Georgina K. Stebbings, Christian J. Cook, Stuart M. Raleigh, Mark A. Bennett, Guan Wang, Malcolm Collins, Yannis P. Pitsiladis and Alun G. Williams
    Citation: BMC Genomics 2017 18(Suppl 8):820
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  39. We recently described the genotype/phenotype features of all Spanish patients diagnosed with McArdle disease as of January 2011 (n = 239, prevalence of ~1/167,000) (J Neurol Neurosurg Psychiatry 2012;83:322–8). S...

    Authors: Alfredo Santalla, Gisela Nogales-Gadea, Alberto Blázquez Encinar, Irene Vieitez, Adrian González-Quintana, Pablo Serrano-Lorenzo, Inés García Consuegra, Sara Asensio, Alfonsina Ballester-Lopez, Guillem Pintos-Morell, Jaume Coll-Cantí, Helios Pareja-Galeano, Jorge Díez-Bermejo, Margarita Pérez, Antoni L. Andreu, Tomàs Pinós…
    Citation: BMC Genomics 2017 18(Suppl 8):819
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  40. There has been considerable growth in basic knowledge and understanding of how genes are influencing response to exercise training and predisposition to injuries and chronic diseases. On the basis of this know...

    Authors: Nicole Vlahovich, David C. Hughes, Lyn R. Griffiths, Guan Wang, Yannis P. Pitsiladis, Fabio Pigozzi, Nobert Bachl and Nir Eynon
    Citation: BMC Genomics 2017 18(Suppl 8):818
    Content type: Review Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  41. Recombinant human erythropoietin (rHuEpo) can improve human performance and is therefore frequently abused by athletes. As a result, the World Anti-Doping Agency (WADA) introduced the Athlete Biological Passpo...

    Authors: Guan Wang, Jérôme Durussel, Jonathan Shurlock, Martin Mooses, Noriyuki Fuku, Georgie Bruinvels, Charles Pedlar, Richard Burden, Andrew Murray, Brendan Yee, Anne Keenan, John D. McClure, Pierre-Edouard Sottas and Yannis P. Pitsiladis
    Citation: BMC Genomics 2017 18(Suppl 8):817
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  42. Forkhead box O3A (FOXOA3) and apolipoprotein E (APOE) are arguably the strongest gene candidates to influence human exceptional longevity (EL, i.e., being a centenarian), but inconsistency exists among cohorts. E...

    Authors: Noriyuki Fuku, Roberto Díaz-Peña, Yasumichi Arai, Yukiko Abe, Hirofumi Zempo, Hisashi Naito, Haruka Murakami, Motohiko Miyachi, Carlos Spuch, José A. Serra-Rexach, Enzo Emanuele, Nobuyoshi Hirose and Alejandro Lucia
    Citation: BMC Genomics 2017 18(Suppl 8):803
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  43. Epigenetic modification refers to heritable changes in gene function that cannot be explained by alterations in the DNA sequence. The current literature clearly demonstrates that the epigenetic response is hig...

    Authors: Elisa Grazioli, Ivan Dimauro, Neri Mercatelli, Guan Wang, Yannis Pitsiladis, Luigi Di Luigi and Daniela Caporossi
    Citation: BMC Genomics 2017 18(Suppl 8):802
    Content type: Review Published on:

    This article is part of a Supplement: Volume 18 Supplement 8

  44. Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and...

    Authors: Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang and Jinping Hua
    Citation: BMC Genomics 2017 18:876
    Content type: Research article Published on:

  45. Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5′-monophosphate (IMP) contributes to umami taste in beef. Thus, t...

    Authors: Yoshinobu Uemoto, Tsuyoshi Ohtake, Nanae Sasago, Masayuki Takeda, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima and Shinji Sasaki
    Citation: BMC Genomics 2017 18:874
    Content type: Research Published on:

  46. The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and...

    Authors: Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li and Dongfeng Zhang
    Citation: BMC Genomics 2017 18:872
    Content type: Research article Published on:

  47. Soybean is one of most important oilseed crop worldwide, however, its production is often limited by many insect pests. Bean pyralid is one of the major soybean leaf-feeding insects in China. To explore the de...

    Authors: Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang and Xiangmin Tang
    Citation: BMC Genomics 2017 18:871
    Content type: Research article Published on:

  48. Auxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo whi...

    Authors: Wenjia Wang, Lianfeng Gu, Shanwen Ye, Hangxiao Zhang, Changyang Cai, Mengqi Xiang, Yubang Gao, Qin Wang, Chentao Lin and Qiang Zhu
    Citation: BMC Genomics 2017 18:870
    Content type: Research article Published on:

  49. Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis pro...

    Authors: Anita Lerch, Cristian Koepfli, Natalie E. Hofmann, Camilla Messerli, Stephen Wilcox, Johanna H. Kattenberg, Inoni Betuela, Liam O’Connor, Ivo Mueller and Ingrid Felger
    Citation: BMC Genomics 2017 18:864
    Content type: Methdology article Published on:

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