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  1. In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to growth-affecting stress conditions such as nutrient deficiency, is ...

    Authors: Nabil Hanna, Safia Ouahrani-Bettache, Kenneth L Drake, L Garry Adams, Stephan Köhler and Alessandra Occhialini
    Citation: BMC Genomics 2013 14:459
    Content type: Research article Published on:

  2. Meat quality is an important economic trait in chickens. To identify loci and genes associated with meat quality traits, we conducted a genome-wide association study (GWAS) of F2 populations derived from a loc...

    Authors: Yanfa Sun, Guiping Zhao, Ranran Liu, Maiqing Zheng, Yaodong Hu, Dan Wu, Lei Zhang, Peng Li and Jie Wen
    Citation: BMC Genomics 2013 14:458
    Content type: Research article Published on:

  3. Elevated temperatures induce activation of the heat shock transcription factor 1 (HSF1) which in somatic cells leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (sperma...

    Authors: Małgorzata Kus-Liśkiewicz, Joanna Polańska, Joanna Korfanty, Magdalena Olbryt, Natalia Vydra, Agnieszka Toma and Wiesława Widłak
    Citation: BMC Genomics 2013 14:456
    Content type: Research article Published on:

  4. Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), ...

    Authors: Juzoh Umemori, Akihiro Mori, Kenji Ichiyanagi, Takeaki Uno and Tsuyoshi Koide
    Citation: BMC Genomics 2013 14:455
    Content type: Research article Published on:

  5. Alpha tubulin is a fundamental component of the cytoskeleton which is responsible for cell shape and is involved in cell division, ciliary and flagellar motility and intracellular transport. Alpha tubulin gene...

    Authors: César A Ramírez, José M Requena and Concepción J Puerta
    Citation: BMC Genomics 2013 14:454
    Content type: Research article Published on:

  6. Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growi...

    Authors: Ruth M Hamill, Ozlem Aslan, Anne M Mullen, John V O’Doherty, Jean McBryan, Dermot G Morris and Torres Sweeney
    Citation: BMC Genomics 2013 14:453
    Content type: Research article Published on:

  7. The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a ...

    Authors: Eric B Rondeau, Amber M Messmer, Dan S Sanderson, Stuart G Jantzen, Kristian R von Schalburg, David R Minkley, Jong S Leong, Graham M Macdonald, Amanda E Davidsen, William A Parker, Rosetta SA Mazzola, Briony Campbell and Ben F Koop
    Citation: BMC Genomics 2013 14:452
    Content type: Research article Published on:

  8. The microsporidia parasite Nosema contributes to the steep global decline of honey bees that are critical pollinators of food crops. There are two species of Nosema that have been found to infect honey bees, Nose...

    Authors: Yan ping Chen, Jeffery S Pettis, Yan Zhao, Xinyue Liu, Luke J Tallon, Lisa D Sadzewicz, Renhua Li, Huoqing Zheng, Shaokang Huang, Xuan Zhang, Michele C Hamilton, Stephen F Pernal, Andony P Melathopoulos, Xianghe Yan and Jay D Evans
    Citation: BMC Genomics 2013 14:451
    Content type: Research article Published on:

  9. The genetic network involved in the bacterial cell cycle is poorly understood even though it underpins the remarkable ability of bacteria to proliferate. How such network evolves is even less clear. The major ...

    Authors: Gang Fang, Karla D Passalacqua, Jason Hocking, Paula Montero Llopis, Mark Gerstein, Nicholas H Bergman and Christine Jacobs-Wagner
    Citation: BMC Genomics 2013 14:450
    Content type: Research article Published on:

  10. Copy number variable regions (CNVRs) can result in drastic phenotypic differences and may therefore be subject to selection during domestication. Studying copy number variation in relation to domestication is ...

    Authors: Yogesh Paudel, Ole Madsen, Hendrik-Jan Megens, Laurent AF Frantz, Mirte Bosse, John WM Bastiaansen, Richard PMA Crooijmans and Martien AM Groenen
    Citation: BMC Genomics 2013 14:449
    Content type: Research article Published on:

  11. Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genoty...

    Authors: Daryl T Morishige, Patricia E Klein, Josie L Hilley, Sayed Mohammad Ebrahim Sahraeian, Arun Sharma and John E Mullet
    Citation: BMC Genomics 2013 14:448
    Content type: Methodology article Published on:

  12. In contrast to most animal genomes, mitochondrial genomes in species belonging to the phylum Cnidaria show distinct variations in genome structure, including the mtDNA structure (linear or circular) and the pr...

    Authors: Shen Song, Feng Jiang, Jianbo Yuan, Wei Guo and Yongwang Miao
    Citation: BMC Genomics 2013 14:447
    Content type: Research article Published on:

  13. Genome- and population-wide re-sequencing would allow for most efficient detection of causal trait variants. However, despite a strong decrease of costs for next-generation sequencing in the last few years, re...

    Authors: Sandra Jansen, Bernhard Aigner, Hubert Pausch, Michal Wysocki, Sebastian Eck, Anna Benet-Pagès, Elisabeth Graf, Thomas Wieland, Tim M Strom, Thomas Meitinger and Ruedi Fries
    Citation: BMC Genomics 2013 14:446
    Content type: Research article Published on:

  14. Pattern-oriented chemical profiling is increasingly being used to characterize the phytochemical composition of herbal medicines for quality control purposes. Ideally, a fingerprint of the biological effects s...

    Authors: Rebekah Cook, James R Hennell, Samiuela Lee, Cheang S Khoo, Maria C Carles, Vincent J Higgins, Suresh Govindaraghavan and Nikolaus J Sucher
    Citation: BMC Genomics 2013 14:445
    Content type: Research article Published on:

  15. With the advent of Next Generation Sequencing (NGS) technologies, the ability to generate large amounts of sequence data has revolutionized the genomics field. Most RNA viruses have relatively small genomes in...

    Authors: Denise A Marston, Lorraine M McElhinney, Richard J Ellis, Daniel L Horton, Emma L Wise, Stacey L Leech, Dan David, Xavier de Lamballerie and Anthony R Fooks
    Citation: BMC Genomics 2013 14:444
    Content type: Methodology article Published on:

  16. The heterogeneous progression of atherosclerotic disease in the peripheral arteries is currently not well understood. In humans, artery specific disease progression is partly attributed to the local hemodynami...

    Authors: Martin Bahls, Christopher A Bidwell, Juan Hu, Armando Tellez, Greg L Kaluza, Juan F Granada, Christian G Krueger, Jess D Reed, M Harold Laughlin, William G Van Alstine and Sean C Newcomer
    Citation: BMC Genomics 2013 14:443
    Content type: Research article Published on:

  17. Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is curren...

    Authors: Urte Schlüter, Christian Colmsee, Uwe Scholz, Andrea Bräutigam, Andreas PM Weber, Nina Zellerhoff, Marcel Bucher, Holger Fahnenstich and Uwe Sonnewald
    Citation: BMC Genomics 2013 14:442
    Content type: Research article Published on:

  18. DNA duplications constitute important precursors for genome variation. Here we analyzed an unequal duplication harboring a beneficial mutation that may provide alternative evolutionary outcomes.

    Authors: Ram P Maharjan, Joël Gaffé, Jessica Plucain, Martin Schliep, Lei Wang, Lu Feng, Olivier Tenaillon, Thomas Ferenci and Dominique Schneider
    Citation: BMC Genomics 2013 14:441
    Content type: Research article Published on:

  19. Many large-scale studies analyzed high-throughput genomic data to identify altered pathways essential to the development and progression of specific types of cancer. However, no previous study has been extende...

    Authors: Tae Hyun Hwang, Gowtham Atluri, Rui Kuang, Vipin Kumar, Timothy Starr, Kevin AT Silverstein, Peter M Haverty, Zemin Zhang and Jinfeng Liu
    Citation: BMC Genomics 2013 14:440
    Content type: Research article Published on:

  20. DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA o...

    Authors: Susan E Johnston, Meri Lindqvist, Eero Niemelä, Panu Orell, Jaakko Erkinaro, Matthew P Kent, Sigbjørn Lien, Juha-Pekka Vähä, Anti Vasemägi and Craig R Primmer
    Citation: BMC Genomics 2013 14:439
    Content type: Methodology article Published on:

  21. MicroRNAs are very small non-coding RNAs that interact with microRNA recognition elements (MREs) on their target messenger RNAs. Varying the concentration of a given microRNA may influence the expression of ma...

    Authors: Cheng-Tao Wu, Chien-Ying Chiou, Ho-Chen Chiu and Ueng-Cheng Yang
    Citation: BMC Genomics 2013 14:438
    Content type: Research article Published on:

  22. Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so a...

    Authors: Julie King, Ann Thomas, Caron James, Ian King and Ian Armstead
    Citation: BMC Genomics 2013 14:437
    Content type: Research article Published on:

  23. The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully character...

    Authors: Kerstin J Williams, William A Bryant, Victoria A Jenkins, Geraint R Barton, Adam A Witney, John W Pinney and Brian D Robertson
    Citation: BMC Genomics 2013 14:436
    Content type: Research article Published on:

  24. Legionella is a water and soil bacterium that can infect humans, causing a pneumonia known as Legionnaires’ disease. The pneumonia is almost exclusively caused by the species L. pneumophila, of which serogroup 1 ...

    Authors: Jeroen W Den Boer, Sjoerd M Euser, Nico J Nagelkerke, Frank Schuren, Sophie Jarraud and Jerome Etienne
    Citation: BMC Genomics 2013 14:435
    Content type: Research article Published on:

  25. Salamanders are unique among vertebrates in their ability to completely regenerate amputated limbs through the mediation of blastema cells located at the stump ends. This regeneration is nerve-dependent becaus...

    Authors: Cheng-Han Wu, Mong-Hsun Tsai, Chia-Chuan Ho, Chien-Yu Chen and Hsuan-Shu Lee
    Citation: BMC Genomics 2013 14:434
    Content type: Research article Published on:

  26. Calcium-dependent protein kinases (CDPKs) have been shown to play important roles in various physiological processes, including plant growth and development, abiotic and biotic stress responses and plant hormo...

    Authors: Xiangpei Kong, Wei Lv, Shanshan Jiang, Dan Zhang, Guohua Cai, Jiaowen Pan and Dequan Li
    Citation: BMC Genomics 2013 14:433
    Content type: Research article Published on:

  27. The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histo...

    Authors: Vandana Kumari, Lakshmi Rani Iyer, Riti Roy, Varsha Bhargava, Suchita Panda, Jaishree Paul, Jaco J Verweij, C Graham Clark, Alok Bhattacharya and Sudha Bhattacharya
    Citation: BMC Genomics 2013 14:432
    Content type: Research article Published on:

  28. 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:

  29. Mutans streptococci are a group of bacteria significantly contributing to tooth decay. Their genetic variability is however still not well understood.

    Authors: Lifu Song, Wei Wang, Georg Conrads, Anke Rheinberg, Helena Sztajer, Michael Reck, Irene Wagner-Döbler and An-Ping Zeng
    Citation: BMC Genomics 2013 14:430
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2013 14:811

  30. 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:

  31. Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially b...

    Authors: Ximiao He, Raghunath Chatterjee, Sam John, Hector Bravo, B K Sathyanarayana, Simon C Biddie, Peter C FitzGerald, John A Stamatoyannopoulos, Gordon L Hager and Charles Vinson
    Citation: BMC Genomics 2013 14:428
    Content type: Research article Published on:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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