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  1. Blood–brain barrier (BBB) disruption is an integral feature of numerous neurological disorders. However, there is a relative lack of knowledge regarding the underlying molecular mechanisms of immune-mediated B...

    Authors: Holly L Johnson, Lisa M Hanson, Yi Chen, Allan J Bieber, Russell J Buono, Thomas N Ferraro, Istvan Pirko and Aaron J Johnson
    Citation: BMC Genomics 2013 14:678
    Content type: Research article Published on:

  2. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is one the most important citrus diseases, and affects all varieties of sweet orange (Citrus sinensis L. Osb). On the other hand, among the Citrus ...

    Authors: Carolina M Rodrigues, Alessandra A de Souza, Marco A Takita, Luciano T Kishi and Marcos A Machado
    Citation: BMC Genomics 2013 14:676
    Content type: Research article Published on:

  3. Massively parallel sequencing offers the possibility of revolutionizing the study of viral populations by providing ultra deep sequencing (tens to hundreds of thousand fold coverage) of complete viral genomes....

    Authors: Xiao Yang, Patrick Charlebois, Alex Macalalad, Matthew R Henn and Michael C Zody
    Citation: BMC Genomics 2013 14:674
    Content type: Methodology article Published on:

  4. Release of domesticated strains of fish into nature may pose a threat to wild populations with respect to their evolved genetic structure and fitness. Understanding alterations that have occurred in both physi...

    Authors: Samantha L White, Dionne Sakhrani, Roy G Danzmann and Robert H Devlin
    Citation: BMC Genomics 2013 14:673
    Content type: Research article Published on:

  5. Multiple myeloma (MM) is a malignant proliferation of plasma B cells. Based on recurrent aneuploidy such as copy number alterations (CNAs), myeloma is divided into two subtypes with different CNA patterns and ...

    Authors: Mehmet K Samur, Parantu K Shah, Xujun Wang, Stéphane Minvielle, Florence Magrangeas, Hervé Avet-Loiseau, Nikhil C Munshi and Cheng Li
    Citation: BMC Genomics 2013 14:672
    Content type: Research article Published on:

  6. Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased geno...

    Authors: Marco Ferrarini, Marco Moretto, Judson A Ward, Nada Šurbanovski, Vladimir Stevanović, Lara Giongo, Roberto Viola, Duccio Cavalieri, Riccardo Velasco, Alessandro Cestaro and Daniel J Sargent
    Citation: BMC Genomics 2013 14:670
    Content type: Research article Published on:

  7. Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To thi...

    Authors: Tao Wu, Zhigang Zhang, Bin Liu, Dezhi Hou, Yun Liang, Jie Zhang and Peng Shi
    Citation: BMC Genomics 2013 14:669
    Content type: Research article Published on:

  8. Crown gall (CG) (Agrobacterium tumefaciens) and the root lesion nematodes (RLNs) (Pratylenchus vulnus) are major challenges faced by the California walnut industry, reducing productivity and increasing the cost o...

    Authors: Sriema L Walawage, Monica T Britton, Charles A Leslie, Sandra L Uratsu, YingYue Li and Abhaya M Dandekar
    Citation: BMC Genomics 2013 14:668
    Content type: Research article Published on:

  9. The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change...

    Authors: Sandra Wiegand, Sascha Dietrich, Robert Hertel, Johannes Bongaerts, Stefan Evers, Sonja Volland, Rolf Daniel and Heiko Liesegang
    Citation: BMC Genomics 2013 14:667
    Content type: Research article Published on:

  10. Essential proteins are indispensable for cell survive. Identifying essential proteins is very important for improving our understanding the way of a cell working. There are various types of features related to...

    Authors: Jiancheng Zhong, Jianxin Wang, Wei Peng, Zhen Zhang and Yi Pan
    Citation: BMC Genomics 2013 14(Suppl 4):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  11. In this paper, we propose an Advanced Bayesian-based Personalized Laboratory Tests recommendation (BPLT+) model. Given a patient, we estimate whether a new laboratory test should belong to a "taken" or "not-taken...

    Authors: Jiashu Zhao, Jimmy Xiangji Huang and Xiaohua Hu
    Citation: BMC Genomics 2013 14(Suppl 4):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  12. The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first orde...

    Authors: Philipp Thomas, Hannes Matuschek and Ramon Grima
    Citation: BMC Genomics 2013 14(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  14. Successful management of chronic human immunodeficiency virus type 1 (HIV-1) infection with a cocktail of antiretroviral medications can be negatively affected by the presence of drug resistant mutations in th...

    Authors: Majid Masso and Iosif I Vaisman
    Citation: BMC Genomics 2013 14(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  15. Identifying modules from time series biological data helps us understand biological functionalities of a group of proteins/genes interacting together and how responses of these proteins/genes dynamically chang...

    Authors: Xutao Li, Yunming Ye, Michael Ng and Qingyao Wu
    Citation: BMC Genomics 2013 14(Suppl 4):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  16. Drug addiction is a complex and chronic mental disease, which places a large burden on the American healthcare system due to its negative effects on patients and their families. Recently, network pharmacology ...

    Authors: Ravi V Atreya, Jingchun Sun and Zhongming Zhao
    Citation: BMC Genomics 2013 14(Suppl 4):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  17. Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly...

    Authors: Pablo Cingolani, Xiaoyi Cao, Radhika S Khetani, Chieh-Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig-Fischer, Susan Land, Yun Huang, Matthew E Hudson, Mark D Garfinkel, Sheng Zhong, Gene E Robinson and Douglas M Ruden
    Citation: BMC Genomics 2013 14:666
    Content type: Research article Published on:

  18. Analyzing the RNA pool or transcription start sites requires effective means to convert RNA into cDNA libraries for digital expression counting. With current high-speed sequencers, it is necessary to flank the...

    Authors: Matthias Harbers, Sachi Kato, Michiel de Hoon, Yoshihide Hayashizaki, Piero Carninci and Charles Plessy
    Citation: BMC Genomics 2013 14:665
    Content type: Methodology article Published on:

  19. Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, B...

    Authors: Jingyin Yu, Meixia Zhao, Xiaowu Wang, Chaobo Tong, Shunmou Huang, Sadia Tehrim, Yumei Liu, Wei Hua and Shengyi Liu
    Citation: BMC Genomics 2013 14:664
    Content type: Database Published on:

  20. Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The m...

    Authors: Aleksandrina Patyshakuliyeva, Edita Jurak, Annegret Kohler, Adam Baker, Evy Battaglia, Wouter de Bruijn, Kerry S Burton, Michael P Challen, Pedro M Coutinho, Daniel C Eastwood, Birgit S Gruben, Miia R Mäkelä, Francis Martin, Marina Nadal, Joost van den Brink, Ad Wiebenga…
    Citation: BMC Genomics 2013 14:663
    Content type: Research article Published on:

  21. Chrysanthemum is one of the most important ornamental crops in the world and drought stress seriously limits its production and distribution. In order to generate a functional genomics resource and obtain a de...

    Authors: Yanjie Xu, Shan Gao, Yingjie Yang, Mingyun Huang, Lina Cheng, Qian Wei, Zhangjun Fei, Junping Gao and Bo Hong
    Citation: BMC Genomics 2013 14:662
    Content type: Research article Published on:

  22. Small non-coding RNAs (ncRNAs) are important regulators of gene expression in eukaryotes. Previously, only microRNAs (miRNAs) and piRNAs have been identified in the silkworm, Bombyx mori. Furthermore, only ncRNAs...

    Authors: Zuoming Nie, Fang Zhou, Dan Li, Zhengbing Lv, Jian Chen, Yue Liu, Jianhong Shu, Qing Sheng, Wei Yu, Wenping Zhang, Caiying Jiang, Yuhua Yao, Juming Yao, Yongfeng Jin and Yaozhou Zhang
    Citation: BMC Genomics 2013 14:661
    Content type: Research article Published on:

  23. The eastern mosquitofish (Gambusia holbrooki) has the potential to become a bioindicator organism of endocrine disrupting chemicals (EDCs) due to its androgen-driven secondary sexual characteristics. However, the...

    Authors: Erica K Brockmeier, Fahong Yu, David Moraga Amador, Timothy A Bargar and Nancy D Denslow
    Citation: BMC Genomics 2013 14:660
    Content type: Research article Published on:

  24. Drosophila melanogaster adult males perform an elaborate courtship ritual to entice females to mate. fruitless (fru), a gene that is one of the key regulators of male courtship behavior, encodes multiple male-spe...

    Authors: Justin E Dalton, Justin M Fear, Simon Knott, Bruce S Baker, Lauren M McIntyre and Michelle N Arbeitman
    Citation: BMC Genomics 2013 14:659
    Content type: Research article Published on:

  25. Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of t...

    Authors: Monique Royer, Ralf Koebnik, Mélanie Marguerettaz, Valérie Barbe, Guillaume P Robin, Chrystelle Brin, Sébastien Carrere, Camila Gomez, Manuela Hügelland, Ginka H Völler, Julie Noëll, Isabelle Pieretti, Saskia Rausch, Valérie Verdier, Stéphane Poussier, Philippe Rott…
    Citation: BMC Genomics 2013 14:658
    Content type: Research article Published on:

  26. The tropical ascomycete Trichoderma reesei (Hypocrea jecorina) represents one of the most efficient plant cell wall degraders. Regulation of the enzymes required for this process is affected by nutritional signal...

    Authors: Doris Tisch and Monika Schmoll
    Citation: BMC Genomics 2013 14:657
    Content type: Research article Published on:

  27. Adult human fibroblasts grown in low oxygen and with FGF2 supplementation have the capacity to tip the healing outcome of skeletal muscle injury – by favoring regeneration response in vivo over scar formation. He...

    Authors: Olga Kashpur, David LaPointe, Sakthikumar Ambady, Elizabeth F Ryder and Tanja Dominko
    Citation: BMC Genomics 2013 14:656
    Content type: Research article Published on:

  28. The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology,...

    Authors: Richard S Fletcher, Jack L Mullen, Seth Yoder, William L Bauerle, Gretchen Reuning, Saunak Sen, Eli Meyer, Thomas E Juenger and John K McKay
    Citation: BMC Genomics 2013 14:655
    Content type: Methodology article Published on:

  30. The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from w...

    Authors: Aziz Mithani, Eric J Belfield, Carly Brown, Caifu Jiang, Lindsey J Leach and Nicholas P Harberd
    Citation: BMC Genomics 2013 14:653
    Content type: Methodology article Published on:

  32. Though most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies the importance of identifyin...

    Authors: Qiongshi Lu, Sijin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang and Tingting Li
    Citation: BMC Genomics 2013 14:651
    Content type: Methodology article Published on:

  33. Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘n...

    Authors: Rajeswaran Jagadeesan, Amelia Fotheringham, Paul R Ebert and David I Schlipalius
    Citation: BMC Genomics 2013 14:650
    Content type: Research article Published on:

  34. Copy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organ...

    Authors: Ping Yu, Cai-Hong Wang, Qun Xu, Yue Feng, Xiao-Ping Yuan, Han-Yong Yu, Yi-Ping Wang, Sheng-Xiang Tang and Xing-Hua Wei
    Citation: BMC Genomics 2013 14:649
    Content type: Research article Published on:

  35. It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e.g. coded from small Open Reading Frames, sORFs) is very difficult as the shor...

    Authors: Jeroen Crappé, Wim Van Criekinge, Geert Trooskens, Eisuke Hayakawa, Walter Luyten, Geert Baggerman and Gerben Menschaert
    Citation: BMC Genomics 2013 14:648
    Content type: Research article Published on:

  36. Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such c...

    Authors: Jyoti Bhardwaj, Rohit Chauhan, Mohit Kumar Swarnkar, Rakesh Kumar Chahota, Anil Kumar Singh, Ravi Shankar and Sudesh Kumar Yadav
    Citation: BMC Genomics 2013 14:647
    Content type: Research article Published on:

  37. In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via ar...

    Authors: Hui Xiang, Xin Li, Fangyin Dai, Xun Xu, Anjiang Tan, Lei Chen, Guojie Zhang, Yun Ding, Qiye Li, Jinmin Lian, Andrew Willden, Qiuhong Guo, Qingyou Xia, Jun Wang and Wen Wang
    Citation: BMC Genomics 2013 14:646
    Content type: Research article Published on:

  38. Xor-genotype is a cost-effective alternative to the genotype sequence of an individual. Recent methods developed for haplotype inference have aimed at finding the solution based on xor-genotype data. Given the...

    Authors: Abdulkadir Elmas, Guido H Jajamovich and Xiaodong Wang
    Citation: BMC Genomics 2013 14:645
    Content type: Research article Published on:

  39. Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap ...

    Authors: Andrew May, Scott Hazelhurst, Yali Li, Shane A Norris, Nimmisha Govind, Mohammed Tikly, Claudia Hon, Keith J Johnson, Nicole Hartmann, Frank Staedtler and Michèle Ramsay
    Citation: BMC Genomics 2013 14:644
    Content type: Research article Published on:

  40. This study focuses on the analysis of miRNAs expression data in a cohort of 181 well characterised breast cancer samples composed primarily of triple-negative (ER/PR/HER2-negative) tumours with associated geno...

    Authors: Emanuele de Rinaldis, Patrycja Gazinska, Anca Mera, Zora Modrusan, Grazyna M Fedorowicz, Brian Burford, Cheryl Gillett, Pierfrancesco Marra, Anita Grigoriadis, David Dornan, Lars Holmberg, Sarah Pinder and Andrew Tutt
    Citation: BMC Genomics 2013 14:643
    Content type: Research article Published on:

  41. Edwardsiella tarda is an enterobacterium which causes edwardsiellosis, a fatal disease of cultured fishes such as red sea bream, eel, and flounder. Preventing the occurrence of E. tarda infection has thus been an...

    Authors: Yoji Nakamura, Tomokazu Takano, Motoshige Yasuike, Takamitsu Sakai, Tomomasa Matsuyama and Motohiko Sano
    Citation: BMC Genomics 2013 14:642
    Content type: Research article Published on:

  43. Propionibacteria are part of the human microbiota. Many studies have addressed the predominant colonizer of sebaceous follicles of the skin, Propionibacterium acnes, and investigated its association with the skin...

    Authors: Tim N Mak, Monika Schmid, Elzbieta Brzuszkiewicz, Guanghong Zeng, Rikke Meyer, Karen S Sfanos, Volker Brinkmann, Thomas F Meyer and Holger Brüggemann
    Citation: BMC Genomics 2013 14:640
    Content type: Research article Published on:

  44. Lymphatic filariasis is a neglected tropical disease afflicting more than 120 million people, while another 1.3 billion people are at risk of infection. The nematode worm Brugia malayi is one of the causative age...

    Authors: Panagiotis Ioannidis, Kelly L Johnston, David R Riley, Nikhil Kumar, James R White, Karen T Olarte, Sandra Ott, Luke J Tallon, Jeremy M Foster, Mark J Taylor and Julie C Dunning Hotopp
    Citation: BMC Genomics 2013 14:639
    Content type: Research article Published on:

  46. Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, is the most severe disease in cotton (Gossypium spp.), causing great lint losses worldwide. Disease management could be achieved in the field...

    Authors: Yan Zhang, Xing Fen Wang, Ze Guo Ding, Qing Ma, Gui Rong Zhang, Shu Ling Zhang, Zhi Kun Li, Li Qiang Wu, Gui Yin Zhang and Zhi Ying Ma
    Citation: BMC Genomics 2013 14:637
    Content type: Research article Published on:

  47. One of the challenges in insect chemical ecology is to understand how insect pheromones are synthesised, detected and degraded. Genome wide survey by comparative sequencing and gene specific expression profili...

    Authors: Shao-Hua Gu, Kong-Ming Wu, Yu-Yuan Guo, John A Pickett, Linda M Field, Jing-Jiang Zhou and Yong-Jun Zhang
    Citation: BMC Genomics 2013 14:636
    Content type: Research article Published on:

  48. It has been demonstrated that the umbilical cord matrix, represented by the Wharton’s Jelly (WJ), contains a great number of mesenchymal stem cells (MSCs), characterized by the expression of specific MSCs mark...

    Authors: Valentina Gatta, Marco D’Aurora, Paola Lanuti, Laura Pierdomenico, Samantha Sperduti, Giandomenico Palka, Marco Gesi, Marco Marchisio, Sebastiano Miscia and Liborio Stuppia
    Citation: BMC Genomics 2013 14:635
    Content type: Research article Published on:

  49. Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of ...

    Authors: Kevin T Bilyk and C-H Christina Cheng
    Citation: BMC Genomics 2013 14:634
    Content type: Research article Published on:

  50. Mitochondrial genomic (mitogenomic) reorganizations are rarely found in closely-related animals, yet drastic reorganizations have been found in the Ranoides frogs. The phylogenetic relationships of the three m...

    Authors: Atsushi Kurabayashi and Masayuki Sumida
    Citation: BMC Genomics 2013 14:633
    Content type: Research article Published on:

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BMC Genomics

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