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  1. The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of whole genome ...

    Authors: Chaobo Tong, Xiaowu Wang, Jingyin Yu, Jian Wu, Wanshun Li, Junyan Huang, Caihua Dong, Wei Hua and Shengyi Liu
    Citation: BMC Genomics 2013 14:689
    Content type: Research article Published on:

  2. Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacte...

    Authors: Li M Chen, Xin A Zhou, Wen B Li, Wei Chang, Rong Zhou, Cheng Wang, Ai H Sha, Zhi H Shan, Chan J Zhang, De Z Qiu, Zhong L Yang and Shui L Chen
    Citation: BMC Genomics 2013 14:687
    Content type: Research article Published on:

  3. Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational appr...

    Authors: Lucia Natali, Rosa Maria Cossu, Elena Barghini, Tommaso Giordani, Matteo Buti, Flavia Mascagni, Michele Morgante, Navdeep Gill, Nolan C Kane, Loren Rieseberg and Andrea Cavallini
    Citation: BMC Genomics 2013 14:686
    Content type: Research article Published on:

  4. Genomic imprinting is an epigenetically regulated process wherein genes are expressed in a parent-of-origin specific manner. Many imprinted genes were initially identified in mice; some of these were subsequen...

    Authors: Radhika Das, Yew Kok Lee, Ruslan Strogantsev, Shengnan Jin, Yen Ching Lim, Poh Yong Ng, Xueqin Michelle Lin, Keefe Chng, George SH Yeo, Anne C Ferguson-Smith and Chunming Ding
    Citation: BMC Genomics 2013 14:685
    Content type: Research article Published on:

  5. Serum alkaline phosphatase (ALP) is a complex phenotype influenced by both genetic and environmental factors. Recent Genome-Wide Association Studies (GWAS) have identified several loci affecting ALP levels; ho...

    Authors: Jun Li, Lixuan Gui, Chen Wu, Yunfeng He, Li Zhou, Huan Guo, Jing Yuan, Binyao Yang, Xiayun Dai, Qifei Deng, Suli Huang, Lei Guan, Die Hu, Siyun Deng, Tian Wang, Jiang Zhu…
    Citation: BMC Genomics 2013 14:684
    Content type: Research article Published on:

  6. Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been assoc...

    Authors: Mark W Davey, Ranganath Gudimella, Jennifer Ann Harikrishna, Lee Wan Sin, Norzulaani Khalid and Johan Keulemans
    Citation: BMC Genomics 2013 14:683
    Content type: Research article Published on:

  7. Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, pro...

    Authors: Jian Xu, Qiang Li, Liming Xu, Shaolin Wang, Yanliang Jiang, Zixia Zhao, Yan Zhang, Jiongtang Li, Chuanju Dong, Peng Xu and Xiaowen Sun
    Citation: BMC Genomics 2013 14:682
    Content type: Research article Published on:

  8. Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this ...

    Authors: Christian Brion, Chloé Ambroset, Isabelle Sanchez, Jean-Luc Legras and Bruno Blondin
    Citation: BMC Genomics 2013 14:681
    Content type: Research article Published on:

  9. The epithelial-to-mesenchymal transition is an important mechanism in cancer metastasis. Although transcription factors including SNAIL, SLUG, and TWIST1 regulate the epithelial-to-mesenchymal transition, othe...

    Authors: Haiyun Wang, Clifford A Meyer, Teng Fei, Gang Wang, Fan Zhang and X Shirley Liu
    Citation: BMC Genomics 2013 14:680
    Content type: Research article Published on:

  10. The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of...

    Authors: Wenwei Xiong, Limei He, Yubin Li, Hugo K Dooner and Chunguang Du
    Citation: BMC Genomics 2013 14:679
    Content type: Software Published on:

  11. 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:

  12. Shigella flexneri is the major cause of shigellosis in the developing countries. The O-antigen component of the lipopolysaccharide is one of the key virulence determinants required for the pathogenesis of S. flex...

    Authors: Richa Jakhetia, Kaisar A Talukder and Naresh K Verma
    Citation: BMC Genomics 2013 14:677
    Content type: Research article Published on:

  13. 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:

  14. With the price of next generation sequencing steadily decreasing, bacterial genome assembly is now accessible to a wide range of researchers. It is therefore necessary to understand the best methods for genera...

    Authors: Jason G Powers, Victor J Weigman, Jenny Shu, John M Pufky, Donald Cox and Patrick Hurban
    Citation: BMC Genomics 2013 14:675
    Content type: Methodology article Published on:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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

  23. 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

  24. 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

  26. 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

  27. 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

  28. 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

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  42. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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