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  1. Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provi...

    Authors: Jesse D Riordan, Luke J Drury, Ryan P Smith, Benjamin T Brett, Laura M Rogers, Todd E Scheetz and Adam J Dupuy
    Citation: BMC Genomics 2014 15:1150
    Content type: Methodology article Published on:

  2. Enteromyxosis caused by the intestinal myxozoan parasite Enteromyxum scophthalmi is a serious threat for turbot (Scophthalmus maximus, L.) aquaculture, causing severe catarrhal enteritis leading to a cachectic sy...

    Authors: Diego Robledo, Paolo Ronza, Peter W Harrison, Ana Paula Losada, Roberto Bermúdez, Belén G Pardo, María José Redondo, Ariadna Sitjà-Bobadilla, María Isabel Quiroga and Paulino Martínez
    Citation: BMC Genomics 2014 15:1149
    Content type: Research article Published on:

  4. Tall fescue (Festuca arundinacea Schreb.) is major cool-season forage and turf grass species worldwide, but high-temperature is a major environmental stress that dramatically threaten forage production and turf m...

    Authors: Tao Hu, Xiaoyan Sun, Xunzhong Zhang, Eviatar Nevo and Jinmin Fu
    Citation: BMC Genomics 2014 15:1147
    Content type: Research article Published on:

  5. Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexibl...

    Authors: Adrián Cazares, Guillermo Mendoza-Hernández and Gabriel Guarneros
    Citation: BMC Genomics 2014 15:1146
    Content type: Research article Published on:

  6. Staphylococcus aureus is a human pathogen responsible for substantial morbidity and mortality through its ability to cause a number of human infections including bacteremia, pneumonia and soft tissue infections. ...

    Authors: Marcus B Jones, Christopher P Montgomery, Susan Boyle-Vavra, Kenneth Shatzkes, Rosslyn Maybank, Bryan C Frank, Scott N Peterson and Robert S Daum
    Citation: BMC Genomics 2014 15:1145
    Content type: Research article Published on:

  7. Identification of differentially expressed genes from transcriptomic studies is one of the most common mechanisms to identify tumor biomarkers. This approach however is not well suited to identify interaction ...

    Authors: Paul O’Reilly, Csaba Ortutay, Grainne Gernon, Enda O’Connell, Cathal Seoighe, Susan Boyce, Luis Serrano and Eva Szegezdi
    Citation: BMC Genomics 2014 15:1144
    Content type: Research article Published on:

  8. The 3′ splice site (SS) at the end of pre-mRNA introns has a consensus sequence (Y)nNYAG for constitutive splicing of mammalian genes. Deviation from this consensus could change or interrupt the usage of the spli...

    Authors: Muhammad Sohail, Wenguang Cao, Niaz Mahmood, Mike Myschyshyn, Say Pham Hong and Jiuyong Xie
    Citation: BMC Genomics 2014 15:1143
    Content type: Research article Published on:

  9. Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental ques...

    Authors: Alexey S Rozanov, Alla V Bryanskaya, Tatiana K Malup, Irina A Meshcheryakova, Elena V Lazareva, Oksana P Taran, Timofey V Ivanisenko, Vladimir A Ivanisenko, Sergey M Zhmodik, Nikolay A Kolchanov and Sergey E Peltek
    Citation: BMC Genomics 2014 15(Suppl 12):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  10. We perform the theoretical analysis of a gene network sub-system, composed of a feed-forward loop, in which the upstream transcription factor regulates the target gene via two parallel pathways: directly, and ...

    Authors: Maria A Duk, Maria G Samsonova and Alexander M Samsonov
    Citation: BMC Genomics 2014 15(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  11. Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is ...

    Authors: Victoria V Mironova, Nadezda A Omelyanchuk, Daniil S Wiebe and Victor G Levitsky
    Citation: BMC Genomics 2014 15(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  12. Etiology of complex disorders, such as cataract and neurodegenerative diseases including age-related macular degeneration (AMD), remains poorly understood due to the paucity of animal models, fully replicating...

    Authors: Elena E Korbolina, Nikita I Ershov, Leonid O Bryzgalov and Natalia G Kolosova
    Citation: BMC Genomics 2014 15(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  13. Long-term space travel simulation experiments enabled to discover different aspects of human metabolism such as the complexity of NaCl salt balance. Detailed proteomics data were collected during the Mars105 i...

    Authors: Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S Tiys, Vladimir A Ivanisenko, Nikolay A Kolchanov, Alexey Kononikhin, Igor Popov, Evgeny N Nikolaev, Lyudmila Kh Pastushkova and Irina M Larina
    Citation: BMC Genomics 2014 15(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  14. The life cycle of human immunodeficiency virus type-1 (HIV-1) makes possible the realization of regulatory strategies that can lead to complex dynamical behavior of the system. We analyze the strategy which is...

    Authors: Vitaly A Likhoshvai, Tamara M Khlebodarova, Sergei I Bazhan, Irina A Gainova, Valery A Chereshnev and Gennady A Bocharov
    Citation: BMC Genomics 2014 15(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  15. The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptio...

    Authors: Ricardo Martí-Arbona, Fangping Mu, Kristy L Nowak-Lovato, Melinda S Wren, Clifford J Unkefer and Pat J Unkefer
    Citation: BMC Genomics 2014 15:1142
    Content type: Research article Published on:

  16. Chemoreception is based on the senses of smell and taste that are crucial for animals to find new food sources, shelter, and mates. The initial step in olfaction involves the translocation of odorants from the...

    Authors: Stefan Dippel, Georg Oberhofer, Jörg Kahnt, Lizzy Gerischer, Lennart Opitz, Joachim Schachtner, Mario Stanke, Stefan Schütz, Ernst A Wimmer and Sergio Angeli
    Citation: BMC Genomics 2014 15:1141
    Content type: Research article Published on:

  17. Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isot...

    Authors: Qiang Kou, Si Wu and Xiaowen Liu
    Citation: BMC Genomics 2014 15:1140
    Content type: Research article Published on:

  18. Acetogenic bacteria are able to use CO2 as terminal electron acceptor of an anaerobic respiration, thereby producing acetate with electrons coming from H2. Due to this feature, acetogens came into focus as platfo...

    Authors: Verena Hess, Anja Poehlein, Marie Charlotte Weghoff, Rolf Daniel and Volker Müller
    Citation: BMC Genomics 2014 15:1139
    Content type: Research article Published on:

  19. Highly parallel, ‘second generation’ sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population g...

    Authors: Holly B Bratcher, Craig Corton, Keith A Jolley, Julian Parkhill and Martin CJ Maiden
    Citation: BMC Genomics 2014 15:1138
    Content type: Methodology article Published on:

  20. Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the prote...

    Authors: Tatiana Q Aguiar, Orquídea Ribeiro, Mikko Arvas, Marilyn G Wiebe, Merja Penttilä and Lucília Domingues
    Citation: BMC Genomics 2014 15:1137
    Content type: Research article Published on:

  21. The adult skeletal muscle is a plastic tissue with a remarkable ability to adapt to different levels of activity by altering its excitability, its contractile and metabolic phenotype and its mass. We previousl...

    Authors: Arjan P Palstra, Mireia Rovira, David Rizo-Roca, Joan Ramon Torrella, Herman P Spaink and Josep V Planas
    Citation: BMC Genomics 2014 15:1136
    Content type: Research article Published on:

  22. Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinica...

    Authors: Lei Li, Hin-chung Wong, Wenyan Nong, Man Kit Cheung, Patrick Tik Wan Law, Kai Man Kam and Hoi Shan Kwan
    Citation: BMC Genomics 2014 15:1135
    Content type: Research article Published on:

  23. Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not ...

    Authors: Marty Kwok-Shing Wong, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki and Yoshio Takei
    Citation: BMC Genomics 2014 15:1134
    Content type: Research article Published on:

  25. In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. Identification of repeats is important not only because it improves ge...

    Authors: Braham Dhillon, Navdeep Gill, Richard C Hamelin and Stephen B Goodwin
    Citation: BMC Genomics 2014 15:1132
    Content type: Research article Published on:

  26. Plant NBS-LRR -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability. In melon, half of the 81 predicted NBS-LRR genes group in nine clusters, and a 1 Mb re...

    Authors: Víctor M González, Núria Aventín, Emilio Centeno and Pere Puigdomènech
    Citation: BMC Genomics 2014 15:1131
    Content type: Research article Published on:

  27. MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20–24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes s...

    Authors: Xue Cao, Zhen Wu, Fangling Jiang, Rong Zhou and Zeen Yang
    Citation: BMC Genomics 2014 15:1130
    Content type: Research article Published on:

  28. Although profiling of RNA in single cells has broadened our understanding of development, cancer biology and mechanisms of disease dissemination, it requires the development of reliable and flexible methods. H...

    Authors: Dominic G Rothwell, Yaoyong Li, Mahmood Ayub, Catriona Tate, Gillian Newton, Yvonne Hey, Louise Carter, Suzanne Faulkner, Massimo Moro, Stuart Pepper, Crispin Miller, Fiona Blackhall, Giulia Bertolini, Luca Roz, Caroline Dive and Ged Brady
    Citation: BMC Genomics 2014 15:1129
    Content type: Research article Published on:

  29. The mosquito species Aedes aegypti is the primary vector of many arboviral diseases, including dengue and yellow fevers, that are responsible for a large worldwide health burden. The biological rhythms of mosquit...

    Authors: Matthew T Leming, Samuel SC Rund, Susanta K Behura, Giles E Duffield and Joseph E O’Tousa
    Citation: BMC Genomics 2014 15:1128
    Content type: Database Published on:

  30. Congenital heart defects (CHD), as the most common congenital anomaly, have been reported to be frequently associated with pathogenic copy number variants (CNVs). Currently, patients with CHD are routinely off...

    Authors: Juan Geng, Jonathan Picker, Zhaojing Zheng, Xiaoqing Zhang, Jian Wang, Fuki Hisama, David W Brown, Mary P Mullen, David Harris, Joan Stoler, Ann Seman, David T Miller, Qihua Fu, Amy E Roberts and Yiping Shen
    Citation: BMC Genomics 2014 15:1127
    Content type: Research article Published on:

  31. Sheepgrass (Leymus chinensis) is an important perennial forage grass across the Eurasian Steppe and is adaptable to various environmental conditions, but little is known about its molecular mechanism responding t...

    Authors: Xin Huang, Xianjun Peng, Lexin Zhang, Shuangyan Chen, Liqin Cheng and Gongshe Liu
    Citation: BMC Genomics 2014 15:1126
    Content type: Research article Published on:

  32. A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs...

    Authors: Libo Xing, Dong Zhang, Youmei Li, Caiping Zhao, Songwen Zhang, Yawen Shen, Na An and Mingyu Han
    Citation: BMC Genomics 2014 15:1125
    Content type: Research article Published on:

  33. Follicle mites of the genus Demodex are found on a wide diversity of mammals, including humans; surprisingly little is known, however, about the evolution of this association. Additional sequence information prom...

    Authors: Michael F Palopoli, Samuel Minot, Dorothy Pei, Alicia Satterly and Julie Endrizzi
    Citation: BMC Genomics 2014 15:1124
    Content type: Research article Published on:

  34. Myxococcus xanthus is a bacterium that undergoes multicellular development when starved. Cells move to aggregation centers and form fruiting bodies in which cells differentiate into dormant spores. MrpC appears t...

    Authors: Mark Robinson, Bongjun Son, David Kroos and Lee Kroos
    Citation: BMC Genomics 2014 15:1123
    Content type: Research article Published on:

  35. The two-spotted spider mite, Tetranychus urticae, is infected with Wolbachia, which have the ability to manipulate host reproduction and fitness. MicroRNAs (miRNAs) are small non-coding RNAs that are involved in ...

    Authors: Xia Rong, Yan-Kai Zhang, Kai-Jun Zhang and Xiao-Yue Hong
    Citation: BMC Genomics 2014 15:1122
    Content type: Research article Published on:

  36. Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 reques...

    Authors: Stephen J Forsythe, Benjamin Dickins and Keith A Jolley
    Citation: BMC Genomics 2014 15:1121
    Content type: Research article Published on:

  38. Studies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly moll...

    Authors: Xiaotong Wang, Qiye Li, Jinmin Lian, Li Li, Lijun Jin, Huimin Cai, Fei Xu, Haigang Qi, Linlin Zhang, Fucun Wu, Jie Meng, Huayong Que, Xiaodong Fang, Ximing Guo and Guofan Zhang
    Citation: BMC Genomics 2014 15:1119
    Content type: Research article Published on:

  39. Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturat...

    Authors: Pablo F Cavagnaro, Massimo Iorizzo, Mehtap Yildiz, Douglas Senalik, Joshua Parsons, Shelby Ellison and Philipp W Simon
    Citation: BMC Genomics 2014 15:1118
    Content type: Research article Published on:

  40. Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of devel...

    Authors: Arash Kianianmomeni, Cheng Soon Ong, Gunnar Rätsch and Armin Hallmann
    Citation: BMC Genomics 2014 15:1117
    Content type: Research article Published on:

  41. Vitis vinifera (grape) is one of the most economically significant fruit crops in the world. The availability of the recently released grape genome sequence offers an opportunity to identify and analyze some impo...

    Authors: Jun Cao, Xi Han, Ticao Zhang, Yongping Yang, Jinling Huang and Xiangyang Hu
    Citation: BMC Genomics 2014 15:1116
    Content type: Research article Published on:

  42. There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there ...

    Authors: Kenji Nakahigashi, Yuki Takai, Yuh Shiwa, Mei Wada, Masayuki Honma, Hirofumi Yoshikawa, Masaru Tomita, Akio Kanai and Hirotada Mori
    Citation: BMC Genomics 2014 15:1115
    Content type: Research article Published on:

  43. Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improve rice yields. However, the molecular mechanisms ...

    Authors: Yufang Pan, Qiaofeng Li, Zhizheng Wang, Yang Wang, Rui Ma, Lili Zhu, Guangcun He and Rongzhi Chen
    Citation: BMC Genomics 2014 15:1114
    Content type: Research article Published on:

  44. Interspecies somatic cell nuclear transfer (iSCNT) has been regarded as a potential alternative for rescuing highly endangered species and can be used as a model for studying nuclear–cytoplasmic interactions. ...

    Authors: Yongchun Zuo, Yu Gao, Guanghua Su, Chunling Bai, Zhuying Wei, Kun Liu, Qianzhong Li, Shorgan Bou and Guangpeng Li
    Citation: BMC Genomics 2014 15:1113
    Content type: Research article Published on:

  45. The importance of mutations in disease phenotype has been studied, with information available in databases such as OMIM. However, it remains a research challenge for the possibility of clustering amino acid re...

    Authors: Jose Guevara-Coto, Charles E Schwartz and Liangjiang Wang
    Citation: BMC Genomics 2014 15(Suppl 11):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  46. Epigallocatechin-3-gallate (EGCG) has been demonstrated to inhibit cancer in experimental studies through its antioxidant activity and modulations on cellular functions by binding specific proteins. We demonst...

    Authors: Hong Zhou, Jayson X Chen, Chung S Yang, Mary Qu Yang, Youping Deng and Hong Wang
    Citation: BMC Genomics 2014 15(Suppl 11):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  47. Protein structure data in Protein Data Bank (PDB) are widely used in studies of protein function and evolution and in protein structure prediction. However, there are two main barriers in large-scale usage of ...

    Authors: Zhiquan He, Chao Zhang, Yang Xu, Shuai Zeng, Jingfen Zhang and Dong Xu
    Citation: BMC Genomics 2014 15(Suppl 11):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  48. RDX is a well-known pollutant to induce neurotoxicity. MicroRNAs (miRNA) and messenger RNA (mRNA) profiles are useful tools for toxicogenomics studies. It is worthy to integrate MiRNA and mRNA expression data ...

    Authors: Youping Deng, Junmei Ai, Xin Guan, Zhaohui Wang, Bin Yan, Daqin Zhang, Chang Liu, Mitch S Wilbanks, Barbara Lynn Escalon, Sharon A Meyers, Mary Qu Yang and Edward J Perkins
    Citation: BMC Genomics 2014 15(Suppl 11):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  49. Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathwa...

    Authors: Mary Qu Yang, Kenji Yoshigoe, William Yang, Weida Tong, Xiang Qin, A Keith Dunker, Zhongxue Chen, Hamid R Arbania, Jun S Liu, Andrzej Niemierko and Jack Y Yang
    Citation: BMC Genomics 2014 15(Suppl 11):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  50. Genome wide association study (GWAS) has been proven to be a powerful tool for detecting genomic variants associated with complex traits. However, the specific genes and causal variants underlying these traits...

    Authors: Li Jiang, Xuan Liu, Jie Yang, Haifei Wang, Jicai Jiang, Lili Liu, Sang He, Xiangdong Ding, Jianfeng Liu and Qin Zhang
    Citation: BMC Genomics 2014 15:1105
    Content type: Research article Published on:

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