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  1. Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism are largely unknown. Most mosaic alterations remain undetectable with current analyt...

    Authors: Joseph D Baugher, Benjamin D Baugher, Matthew D Shirley and Jonathan Pevsner
    Citation: BMC Genomics 2013 14:367
    Content type: Methodology article Published on:

  2. Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the spec...

    Authors: Christopher J Grim, Michael L Kotewicz, Karen A Power, Gopal Gopinath, Augusto A Franco, Karen G Jarvis, Qiong Q Yan, Scott A Jackson, Venugopal Sathyamoorthy, Lan Hu, Franco Pagotto, Carol Iversen, Angelika Lehner, Roger Stephan, Séamus Fanning and Ben D Tall
    Citation: BMC Genomics 2013 14:366
    Content type: Research article Published on:

  3. Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statis...

    Authors: Matthew R Hayward, Vincent AA Jansen and Martin J Woodward
    Citation: BMC Genomics 2013 14:365
    Content type: Research article Published on:

  4. Actinobacillus pleuropneumoniae is the Gram-negative bacterium responsible for porcine pleuropneumonia. This respiratory infection is highly contagious and characterized by high morbidity and mortality. The objec...

    Authors: Yannick DN Tremblay, Vincent Deslandes and Mario Jacques
    Citation: BMC Genomics 2013 14:364
    Content type: Research article Published on:

  5. Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared...

    Authors: Ron C Anafi, Renata Pellegrino, Keith R Shockley, Micah Romer, Sergio Tufik and Allan I Pack
    Citation: BMC Genomics 2013 14:362
    Content type: Research article Published on:

  6. Receptor tyrosine kinases (RTK) form a family of transmembrane proteins widely conserved in Metazoa, with key functions in cell-to-cell communication and control of multiple cellular processes. A new family of...

    Authors: Mathieu Vanderstraete, Nadège Gouignard, Arnaud Ahier, Marion Morel, Jérôme Vicogne and Colette Dissous
    Citation: BMC Genomics 2013 14:361
    Content type: Research article Published on:

  7. Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have...

    Authors: Erin L McAdam, Jules S Freeman, Simon P Whittock, Emily J Buck, Jernej Jakse, Andreja Cerenak, Branka Javornik, Andrzej Kilian, Cai-Hong Wang, Dave Andersen, René E Vaillancourt, Jason Carling, Ron Beatson, Lawrence Graham, Donna Graham, Peter Darby…
    Citation: BMC Genomics 2013 14:360
    Content type: Research article Published on:

  8. Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-w...

    Authors: Hua Bao, Eryang Li, Shawn D Mansfield, Quentin CB Cronk, Yousry A El-Kassaby and Carl J Douglas
    Citation: BMC Genomics 2013 14:359
    Content type: Research article Published on:

  9. Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little...

    Authors: Jianjun Qi, Na Zheng, Bing Zhang, Peng Sun, Songnian Hu, Wenjuan Xu, Qin Ma, Tingzhou Zhao, Lili Zhou, Mingjian Qin and Xianen Li
    Citation: BMC Genomics 2013 14:358
    Content type: Research article Published on:

  10. Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of exper...

    Authors: Eva Seifertova, Lyle B Zimmerman, Michael J Gilchrist, Jaroslav Macha, Svatava Kubickova, Halina Cernohorska, Vojtech Zarsky, Nick DL Owens, Abdul K Sesay, Tereza Tlapakova and Vladimir Krylov
    Citation: BMC Genomics 2013 14:357
    Content type: Research article Published on:

  11. Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been r...

    Authors: Nunzio D’Agostino, Tomek Golas, Henri van de Geest, Aureliano Bombarely, Thikra Dawood, Jan Zethof, Nicky Driedonks, Erik Wijnker, Joachim Bargsten, Jan-Peter Nap, Celestina Mariani and Ivo Rieu
    Citation: BMC Genomics 2013 14:356
    Content type: Research article Published on:

  12. The human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA...

    Authors: Kazuyoshi Hosomichi, Timothy A Jinam, Shigeki Mitsunaga, Hirofumi Nakaoka and Ituro Inoue
    Citation: BMC Genomics 2013 14:355
    Content type: Methodology article Published on:

  13. Many genome-wide association studies focus on associating single loci with target phenotypes. However, in the setting of rare variation, accumulating sufficient samples to assess these associations can be diff...

    Authors: Roxana Daneshjou, Nicholas P Tatonetti, Konrad J Karczewski, Hersh Sagreiya, Stephane Bourgeois, Katarzyna Drozda, James K Burmester, Tatsuhiko Tsunoda, Yusuke Nakamura, Michiaki Kubo, Matthew Tector, Nita A Limdi, Larisa H Cavallari, Minoli Perera, Julie A Johnson, Teri E Klein…
    Citation: BMC Genomics 2013 14(Suppl 3):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  14. It has been hypothesized that multivariate analysis and systematic detection of epistatic interactions between explanatory genotyping variables may help resolve the problem of "missing heritability" currently ...

    Authors: Benjamin Goudey, David Rawlinson, Qiao Wang, Fan Shi, Herman Ferra, Richard M Campbell, Linda Stern, Michael T Inouye, Cheng Soon Ong and Adam Kowalczyk
    Citation: BMC Genomics 2013 14(Suppl 3):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  15. It is a great challenge of modern biology to determine the functional roles of non-synonymous Single Nucleotide Polymorphisms (nsSNPs) on complex phenotypes. Statistical and machine learning techniques establi...

    Authors: Li Xie, Clara Ng, Thahmina Ali, Raoul Valencia, Barbara L Ferreira, Vincent Xue, Maliha Tanweer, Dan Zhou, Gabriel G Haddad, Philip E Bourne and Lei Xie
    Citation: BMC Genomics 2013 14(Suppl 3):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  16. Every malignant tumor has a unique spectrum of genomic alterations including numerous protein mutations. There are also hundreds of personal germline variants to be taken into account. The combinatorial divers...

    Authors: B Reva
    Citation: BMC Genomics 2013 14(Suppl 3):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  17. Recent advances in sequencing technologies have greatly increased the identification of mutations in cancer genomes. However, it remains a significant challenge to identify cancer-driving mutations, since most...

    Authors: Florian Gnad, Albion Baucom, Kiran Mukhyala, Gerard Manning and Zemin Zhang
    Citation: BMC Genomics 2013 14(Suppl 3):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  18. SNPs&GO is a method for the prediction of deleterious Single Amino acid Polymorphisms (SAPs) using protein functional annotation. In this work, we present the web server implementation of SNPs&GO (WS-SNPs&GO)....

    Authors: Emidio Capriotti, Remo Calabrese, Piero Fariselli, Pier Luigi Martelli, Russ B Altman and Rita Casadio
    Citation: BMC Genomics 2013 14(Suppl 3):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  19. The body of disease mutations with known phenotypic relevance continues to increase and is expected to do so even faster with the advent of new experimental techniques such as whole-genome sequencing coupled w...

    Authors: Thomas A Peterson, DoHwan Park and Maricel G Kann
    Citation: BMC Genomics 2013 14(Suppl 3):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  20. Understanding and predicting the effects of mutations on protein structure and phenotype is an increasingly important area. Genes for many genetically linked diseases are now routinely sequenced in the clinic....

    Authors: Nouf S Al-Numair and Andrew CR Martin
    Citation: BMC Genomics 2013 14(Suppl 3):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  21. Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of spec...

    Authors: Hannah Carter, Christopher Douville, Peter D Stenson, David N Cooper and Rachel Karchin
    Citation: BMC Genomics 2013 14(Suppl 3):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  22. In recent years the number of human genetic variants deposited into the publicly available databases has been increasing exponentially. The latest version of dbSNP, for example, contains ~50 million validated ...

    Authors: Emidio Capriotti, Russ B Altman and Yana Bromberg
    Citation: BMC Genomics 2013 14(Suppl 3):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  24. The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and h...

    Authors: Marcela Víquez-Zamora, Ben Vosman, Henri van de Geest, Arnaud Bovy, Richard GF Visser, Richard Finkers and Adriaan W van Heusden
    Citation: BMC Genomics 2013 14:354
    Content type: Research article Published on:

  25. Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate imm...

    Authors: Wentao Li, Shuqing Liu, Yang Wang, Feng Deng, Weidong Yan, Kun Yang, Huanchun Chen, Qigai He, Catherine Charreyre and Jean-Christophe Audoneet
    Citation: BMC Genomics 2013 14:353
    Content type: Research article Published on:

  26. MicroRNAs have been suggested to play important roles in the regulation of gene expression in various biological processes. To investigate the function of miRNAs in chicken ovarian development and folliculogen...

    Authors: Li Kang, Xinxing Cui, Yujie Zhang, Chunhong Yang and Yunliang Jiang
    Citation: BMC Genomics 2013 14:352
    Content type: Research article Published on:

  27. Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response...

    Authors: Wen-Chang Chi, Yun-An Chen, Yu-Chywan Hsiung, Shih-Feng Fu, Chang-Hung Chou, Ngoc Nam Trinh, Ying-Chih Chen and Hao-Jen Huang
    Citation: BMC Genomics 2013 14:351
    Content type: Research article Published on:

  28. Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to ...

    Authors: James L Chitwood, Gonzalo Rincon, German G Kaiser, Juan F Medrano and Pablo J Ross
    Citation: BMC Genomics 2013 14:350
    Content type: Research article Published on:

  31. Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordan...

    Authors: Neda Zamani, Pamela Russell, Henrik Lantz, Marc P Hoeppner, Jennifer RS Meadows, Nagarjun Vijay, Evan Mauceli, Federica di Palma, Kerstin Lindblad-Toh, Patric Jern and Manfred G Grabherr
    Citation: BMC Genomics 2013 14:347
    Content type: Software Published on:

  32. The presence of homoeologous sequences and absence of a reference genome sequence make discovery and genotyping of single nucleotide polymorphisms (SNPs) more challenging in polyploid crops.

    Authors: Xun Chen, Xuemin Li, Bing Zhang, Jinsong Xu, Zhikun Wu, Bo Wang, Haitao Li, Muhammad Younas, Lei Huang, Yingfeng Luo, Jiangsheng Wu, Songnian Hu and Kede Liu
    Citation: BMC Genomics 2013 14:346
    Content type: Research article Published on:

  35. Ever since the recent completion of the peach genome, the focus of genetic research in this area has turned to the identification of genes related to important traits, such as fruit aroma volatiles. Of the ove...

    Authors: Gerardo Sánchez, Mónica Venegas-Calerón, Joaquín J Salas, Antonio Monforte, María L Badenes and Antonio Granell
    Citation: BMC Genomics 2013 14:343
    Content type: Research article Published on:

  36. Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Hel...

    Authors: Heather C Rowe and Loren H Rieseberg
    Citation: BMC Genomics 2013 14:342
    Content type: Research article Published on:

  38. The late blight pathogen Phytophthora infestans can attack both potato foliage and tubers. Although interaction transcriptome dynamics between potato foliage and various pathogens have been reported, no transcrip...

    Authors: Liangliang Gao, Zheng Jin Tu, Benjamin P Millett and James M Bradeen
    Citation: BMC Genomics 2013 14:340
    Content type: Research article Published on:

  39. The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for hu...

    Authors: Li Chen, Qun Yue, Xinyu Zhang, Meichun Xiang, Chengshu Wang, Shaojie Li, Yongsheng Che, Francisco Javier Ortiz-López, Gerald F Bills, Xingzhong Liu and Zhiqiang An
    Citation: BMC Genomics 2013 14:339
    Content type: Research article Published on:

  41. Metabolic homeostasis in mammals critically depends on the regulation of fasting-induced genes by CREB in the liver. Previous genome-wide analysis has shown that only a small percentage of CREB target genes ar...

    Authors: Logan J Everett, John Le Lay, Sabina Lukovac, Diana Bernstein, David J Steger, Mitchell A Lazar and Klaus H Kaestner
    Citation: BMC Genomics 2013 14:337
    Content type: Research article Published on:

  42. A small number of prognostic and predictive tests based on gene expression are currently offered as reference laboratory tests. In contrast to such success stories, a number of flaws and errors have recently b...

    Authors: Luigi Marchionni, Bahman Afsari, Donald Geman and Jeffrey T Leek
    Citation: BMC Genomics 2013 14:336
    Content type: Methodology article Published on:

  43. The sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R-genes in Cucurbitaceae genomes remains unk...

    Authors: Xiao Lin, Yu Zhang, Hanhui Kuang and Jiongjiong Chen
    Citation: BMC Genomics 2013 14:335
    Content type: Research article Published on:

  44. Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered much attention in the poultry industry because of the possible risk to the health of affected animals and the damage it causes to the ap...

    Authors: Chenglong Luo, Hao Qu, Jie Wang, Yan Wang, Jie Ma, Chunyu Li, Chunfen Yang, Xiaoxiang Hu, Ning Li and Dingming Shu
    Citation: BMC Genomics 2013 14:334
    Content type: Research article Published on:

  45. Clostridium botulinum is a group of four physiologically and phylogenetically distinct bacteria that produce botulinum neurotoxin. While studies have characterised variability between strains of Group I (proteoly...

    Authors: Sandra C Stringer, Andrew T Carter, Martin D Webb, Ewelina Wachnicka, Lisa C Crossman, Mohammed Sebaihia and Michael W Peck
    Citation: BMC Genomics 2013 14:333
    Content type: Research article Published on:

  46. The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the...

    Authors: Harry D Dawson, Jane E Loveland, Géraldine Pascal, James GR Gilbert, Hirohide Uenishi, Katherine M Mann, Yongming Sang, Jie Zhang, Denise Carvalho-Silva, Toby Hunt, Matthew Hardy, Zhiliang Hu, Shu-Hong Zhao, Anna Anselmo, Hiroki Shinkai, Celine Chen…
    Citation: BMC Genomics 2013 14:332
    Content type: Research article Published on:

  47. Zebrafish embryos are transcriptionally silent until activation of the zygotic genome during the 10th cell cycle. Onset of transcription is followed by cellular and morphological changes involving cell speciation...

    Authors: Håvard Aanes, Olga Østrup, Ingrid S Andersen, Lars F Moen, Sinnakaruppan Mathavan, Philippe Collas and Peter Alestrom
    Citation: BMC Genomics 2013 14:331
    Content type: Research article Published on:

  48. Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about...

    Authors: Max Lundberg, John Boss, Björn Canbäck, Miriam Liedvogel, Keith W Larson, Mats Grahn, Susanne Åkesson, Staffan Bensch and Anthony Wright
    Citation: BMC Genomics 2013 14:330
    Content type: Research article Published on:

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BMC Genomics

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