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  1. Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belon...

    Authors: Han Ming Gan, André O Hudson, Ahmad Yamin Abdul Rahman, Kok Gan Chan and Michael A Savka
    Citation: BMC Genomics 2013 14:431
    Content type: Research article Published on:

  2. How cells decipher the duration of an external signal into different transcriptional outcomes is poorly understood. The hormone gastrin can promote a variety of cellular responses including proliferation, diff...

    Authors: Linn-Karina M Selvik, Christina S Fjeldbo, Arnar Flatberg, Tonje S Steigedal, Kristine Misund, Endre Anderssen, Berit Doseth, Mette Langaas, Sushil Tripathi, Vidar Beisvag, Astrid Lægreid, Liv Thommesen and Torunn Bruland
    Citation: BMC Genomics 2013 14:429
    Content type: Research article Published on:

  3. Plasmodium parasites, the causative agents of malaria, express many variant antigens on cell surfaces. Variant surface antigens (VSAs) are typically organized into large subtelomeric gene families that play criti...

    Authors: Christian Frech and Nansheng Chen
    Citation: BMC Genomics 2013 14:427
    Content type: Research article Published on:

  4. Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and ...

    Authors: Seung Bin Cha, Won Jung Lee, Min Kyoung Shin, Myung Hwan Jung, Seung Won Shin, An Na Yoo, Jong Wan Kim and Han Sang Yoo
    Citation: BMC Genomics 2013 14:426
    Content type: Research article Published on:

  5. Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being ...

    Authors: Shanrong Zhao, Kurt Prenger, Lance Smith, Thomas Messina, Hongtao Fan, Edward Jaeger and Susan Stephens
    Citation: BMC Genomics 2013 14:425
    Content type: Software Published on:

  6. Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effec...

    Authors: Andrea Visioni, Alessandro Tondelli, Enrico Francia, Alexander Pswarayi, Marcos Malosetti, Joanne Russell, William Thomas, Robbie Waugh, Nicola Pecchioni, Ignacio Romagosa and Jordi Comadran
    Citation: BMC Genomics 2013 14:424
    Content type: Research article Published on:

  7. Wheat – Hessian fly interaction follows a typical gene-for-gene model. Hessian fly larvae die in wheat plants carrying an effective resistance gene, or thrive in susceptible plants that carry no effective resi...

    Authors: Chitvan Khajuria, Haiyan Wang, Xuming Liu, Shanda Wheeler, John C Reese, Mustapha El Bouhssini, R Jeff Whitworth and Ming-Shun Chen
    Citation: BMC Genomics 2013 14:423
    Content type: Research article Published on:

  8. Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characte...

    Authors: Henar Alonso, Sofía Samper, Carlos Martín and Isabel Otal
    Citation: BMC Genomics 2013 14:422
    Content type: Research article Published on:

  9. Lawsonia intracellularis is an obligate intracellular bacterium and the etiologic agent of proliferative enteropathy. The disease is endemic in pigs, emerging in horses and has been described in various other spe...

    Authors: Fabio A Vannucci, Douglas N Foster and Connie J Gebhart
    Citation: BMC Genomics 2013 14:421
    Content type: Research article Published on:

  12. In this paper, we address the evidence for the Ambush Hypothesis. Proposed by Seligmann and Pollock, this hypothesis posits that there exists a selection for off-frame stop codons (OSCs) to counteract the poss...

    Authors: David W Morgens, Charlotte H Chang and Andre RO Cavalcanti
    Citation: BMC Genomics 2013 14:418
    Content type: Research article Published on:

  13. Nilaparvata lugens (the brown planthopper, BPH) and Laodelphax striatellus (the small brown planthopper, SBPH) are two of the most important pests of rice. Up to now, there was only one mitochondrial genome of ri...

    Authors: Kai-Jun Zhang, Wen-Chao Zhu, Xia Rong, Yan-Kai Zhang, Xiu-Lei Ding, Jing Liu, Da-Song Chen, Yu Du and Xiao-Yue Hong
    Citation: BMC Genomics 2013 14:417
    Content type: Research article Published on:

  14. Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of col...

    Authors: Oliver KI Bezuidt, Jens Klockgether, Sylvie Elsen, Ina Attree, Colin F Davenport and Burkhard Tümmler
    Citation: BMC Genomics 2013 14:416
    Content type: Research article Published on:

  15. Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Change...

    Authors: Xin-Chao Wang, Qiong-Yi Zhao, Chun-Lei Ma, Zong-Hong Zhang, Hong-Li Cao, Yi-Meng Kong, Chuan Yue, Xin-Yuan Hao, Liang Chen, Jian-Qiang Ma, Ji-Qiang Jin, Xuan Li and Ya-Jun Yang
    Citation: BMC Genomics 2013 14:415
    Content type: Research article Published on:

  16. Analyses of mitochondrial (mt) genome sequences in recent years challenge the current working hypothesis of Nematoda phylogeny proposed from morphology, ecology and nuclear small subunit rRNA gene sequences, a...

    Authors: Guo-Hua Liu, Renfu Shao, Jia-Yuan Li, Dong-Hui Zhou, Hu Li and Xing-Quan Zhu
    Citation: BMC Genomics 2013 14:414
    Content type: Research article Published on:

  18. Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive exp...

    Authors: Sara J Hanson, Claus-Peter Stelzer, David B Mark Welch and John M Logsdon Jr
    Citation: BMC Genomics 2013 14:412
    Content type: Research article Published on:

  19. Nomuraea rileyi is used as an environmental-friendly biopesticide. However, mass production and commercialization of this organism are limited due to its fastidious growth and sporulation requirements. When cultu...

    Authors: Zhangyong Song, Youping Yin, Shasha Jiang, Juanjuan Liu, Huan Chen and Zhongkang Wang
    Citation: BMC Genomics 2013 14:411
    Content type: Research article Published on:

  20. Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group,...

    Authors: Kyle C Smith, Eduardo Castro-Nallar, Joshua NB Fisher, Donald P Breakwell, Julianne H Grose and Sandra H Burnett
    Citation: BMC Genomics 2013 14:410
    Content type: Research article Published on:

  22. Caligid copepods, also called sea lice, are fish ectoparasites, some species of which cause significant problems in the mariculture of salmon, where the annual cost of infection is in excess of €300 million gl...

    Authors: Stephen N Carmichael, James E Bron, John B Taggart, Jacqueline H Ireland, Michaël Bekaert, Stewart TG Burgess, Philip J Skuce, Alasdair J Nisbet, Karim Gharbi and Armin Sturm
    Citation: BMC Genomics 2013 14:408
    Content type: Research article Published on:

  23. Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The i...

    Authors: Michele Vidotto, Alessandro Grapputo, Elisa Boscari, Federica Barbisan, Alessandro Coppe, Gilberto Grandi, Abhishek Kumar and Leonardo Congiu
    Citation: BMC Genomics 2013 14:407
    Content type: Research article Published on:

  24. It was recently established that changes in methylation during development are dynamic and involve both methylation and demethylation processes. Yet, which genomic sites are changing and what are the contribut...

    Authors: Béatrice de Montera, Eric Fournier, Habib Allah Shojaei Saadi, Dominic Gagné, Isabelle Laflamme, Patrick Blondin, Marc-André Sirard and Claude Robert
    Citation: BMC Genomics 2013 14:406
    Content type: Research article Published on:

  25. Cubilin is an endocytic receptor that is necessary for renal and intestinal absorption of a range of ligands. Endocytosis mediated by cubilin and its co-receptor megalin is the principal mechanism for proximal...

    Authors: Obaidullah Aseem, Jeremy L Barth, Sandra C Klatt, Brian T Smith and W Scott Argraves
    Citation: BMC Genomics 2013 14:405
    Content type: Research article Published on:

  26. Tuberculosis remains a major public health problem. Clinical tuberculosis manifests often as pulmonary and occasionally as extra-pulmonary tuberculosis. The emergence of drug resistant tubercle bacilli and its as...

    Authors: Sarbashis Das, Tanmoy Roychowdhury, Parameet Kumar, Anil Kumar, Priya Kalra, Jitendra Singh, Sarman Singh, HK Prasad and Alok Bhattacharya
    Citation: BMC Genomics 2013 14:404
    Content type: Research article Published on:

  27. Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or ot...

    Authors: Matthew K Gilbert, Rickie B Turley, Hee Jin Kim, Ping Li, Gregory Thyssen, Yuhong Tang, Christopher D Delhom, Marina Naoumkina and David D Fang
    Citation: BMC Genomics 2013 14:403
    Content type: Research article Published on:

  29. The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitocho...

    Authors: Hua-Ling Wang, Jiao Yang, Laura M Boykin, Qiong-Yi Zhao, Qian Li, Xiao-Wei Wang and Shu-Sheng Liu
    Citation: BMC Genomics 2013 14:401
    Content type: Research article Published on:

  30. As a step towards understanding coral immunity we present the first whole transcriptome analysis of the acute responses of Acropora millepora to challenge with the bacterial cell wall derivative MDP and the viral...

    Authors: Yvonne Weiss, Sylvain Forêt, David C Hayward, Tracy Ainsworth, Rob King, Eldon E Ball and David J Miller
    Citation: BMC Genomics 2013 14:400
    Content type: Research article Published on:

  31. In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form...

    Authors: Claudine Bleykasten-Grosshans, Anne Friedrich and Joseph Schacherer
    Citation: BMC Genomics 2013 14:399
    Content type: Research article Published on:

  32. Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNP...

    Authors: Richard PMA Crooijmans, Mark S Fife, Tomas W Fitzgerald, Shurnevia Strickland, Hans H Cheng, Pete Kaiser, Richard Redon and Martien AM Groenen
    Citation: BMC Genomics 2013 14:398
    Content type: Research article Published on:

  33. Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines ...

    Authors: Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko and James Taylor
    Citation: BMC Genomics 2013 14:397
    Content type: Software Published on:

  34. Arachidonic acid (ArA) is important for human health because it is one of the major components of mammalian brain membrane phospholipids. The interest in ArA inspired the search for a new sustainable source, a...

    Authors: Long-Ling Ouyang, Si-Hong Chen, Yan Li and Zhi-Gang Zhou
    Citation: BMC Genomics 2013 14:396
    Content type: Research article Published on:

  35. Recent studies have illuminated the diversity of roles for microRNAs in cellular, developmental, and pathophysiological processes. The study of microRNAs in human liver tissue promises to clarify the therapeut...

    Authors: Eric R Gamazon, Federico Innocenti, Rongrong Wei, Libo Wang, Min Zhang, Snezana Mirkov, Jacqueline Ramírez, R Stephanie Huang, Nancy J Cox, Mark J Ratain and Wanqing Liu
    Citation: BMC Genomics 2013 14:395
    Content type: Research article Published on:

  36. Snake venoms generally show sequence and quantitative variation within and between species, but some rattlesnakes have undergone exceptionally rapid, dramatic shifts in the composition, lethality, and pharmaco...

    Authors: Darin R Rokyta, Kenneth P Wray and Mark J Margres
    Citation: BMC Genomics 2013 14:394
    Content type: Research article Published on:

  37. Understanding the genetic architecture of quantitative traits is important for developing genome-based crop improvement methods. Genome-wide association study (GWAS) is a powerful technique for mining novel fu...

    Authors: Satish Kumar, Dorian J Garrick, Marco CAM Bink, Claire Whitworth, David Chagné and Richard K Volz
    Citation: BMC Genomics 2013 14:393
    Content type: Research article Published on:

  38. Eukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. C...

    Authors: Wanwan Liang, Bo Yang, Bao-Jun Yu, Zili Zhou, Cui Li, Ming Jia, Yun Sun, Yue Zhang, Feifei Wu, Hanfeng Zhang, Boya Wang, Michael K Deyholos and Yuan-Qing Jiang
    Citation: BMC Genomics 2013 14:392
    Content type: Research article Published on:

  39. Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is direct...

    Authors: Narasimharao Nalabothula, Liqun Xi, Sucharita Bhattacharyya, Jonathan Widom, Ji-Ping Wang, John N Reeve, Thomas J Santangelo and Yvonne N Fondufe-Mittendorf
    Citation: BMC Genomics 2013 14:391
    Content type: Research article Published on:

  40. Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with disease; however, little is known about t...

    Authors: Zongxin Ling, Xia Liu, Yueqiu Luo, Li Yuan, Karen E Nelson, Yuezhu Wang, Charlie Xiang and Lanjuan Li
    Citation: BMC Genomics 2013 14:390
    Content type: Research article Published on:

  41. Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in c...

    Authors: Ruiwen Fan, Jianshan Xie, Junming Bai, Haidong Wang, Xue Tian, Rui Bai, Xiaoyun Jia, Lei Yang, Yunfei Song, Muren Herrid, Wenjun Gao, Xiaoyan He, Jianbo Yao, George W Smith and Changsheng Dong
    Citation: BMC Genomics 2013 14:389
    Content type: Research article Published on:

  42. White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available,...

    Authors: Andrew G Griffiths, Brent A Barrett, Deborah Simon, Anar K Khan, Paul Bickerstaff, Craig B Anderson, Benjamin K Franzmayr, Kerry R Hancock and Chris S Jones
    Citation: BMC Genomics 2013 14:388
    Content type: Research article Published on:

  43. Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United Stat...

    Authors: Yu Zhang, Shikai Liu, Jianguo Lu, Yanliang Jiang, Xiaoyu Gao, Parichart Ninwichian, Chao Li, Geoff Waldbieser and Zhanjiang Liu
    Citation: BMC Genomics 2013 14:387
    Content type: Research article Published on:

  44. Obesity-associated organ-specific pathological states can be ensued from the dysregulation of the functions of the adipose tissues, liver and muscle. However, the influence of genetic differences underlying gr...

    Authors: Ayca Dogan, Peter Lasch, Christina Neuschl, Marion K Millrose, Rudi Alberts, Klaus Schughart, Dieter Naumann and Gudrun A Brockmann
    Citation: BMC Genomics 2013 14:386
    Content type: Research article Published on:

  45. Repetitive extragenic palindromic elements (REPs) constitute a group of bacterial genomic repeats known for their high abundance and several roles in host cells´ physiology. We analyzed the phylogenetic distri...

    Authors: Jaroslav Nunvar, Irena Licha and Bohdan Schneider
    Citation: BMC Genomics 2013 14:385
    Content type: Research article Published on:

  46. There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecol...

    Authors: Hanno Schmidt, Bastian Greshake, Barbara Feldmeyer, Thomas Hankeln and Markus Pfenninger
    Citation: BMC Genomics 2013 14:384
    Content type: Research article Published on:

  47. Streptococcus pneumoniae is a leading cause of childhood morbidity and mortality worldwide, despite the availability of effective pneumococcal vaccines. Understanding the molecular interactions between the bacter...

    Authors: Sheila Z Kimaro Mlacha, Sandra Romero-Steiner, Julie C Dunning Hotopp, Nikhil Kumar, Nadeeza Ishmael, David R Riley, Umar Farooq, Todd H Creasy, Luke J Tallon, Xinyue Liu, Cynthia S Goldsmith, Jacquelyn Sampson, George M Carlone, Susan K Hollingshead, J Anthony G Scott and Hervé Tettelin
    Citation: BMC Genomics 2013 14:383
    Content type: Research article Published on:

  48. The Fra-1/AP-1 transcription factor regulates the expression of genes controlling various processes including migration, invasion, and survival as well as extracellular remodeling. We recently demonstrated tha...

    Authors: Subbiah Rajasekaran, Narsa M Reddy, Wei Zhang and Sekhar P Reddy
    Citation: BMC Genomics 2013 14:381
    Content type: Research article Published on:

  49. Anecdotal evidence of the involvement of alternative splicing (AS) in the regulation of protein-protein interactions has been reported by several studies. AS events have been shown to significantly occur in re...

    Authors: Alessio Colantoni, Valerio Bianchi, Pier Federico Gherardini, Gianpaolo Scalia Tomba, Gabriele Ausiello, Manuela Helmer-Citterich and Fabrizio Ferrè
    Citation: BMC Genomics 2013 14:379
    Content type: Research article Published on:

  50. Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have been transferred among bacteria thro...

    Authors: Zhe Ma, Jianing Geng, Li Yi, Bin Xu, Ruoyu Jia, Yue Li, Qingshu Meng, Hongjie Fan and Songnian Hu
    Citation: BMC Genomics 2013 14:377
    Content type: Research article Published on:

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BMC Genomics

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