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  1. G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disea...

    Authors: Dharmendra B Goswami, Lisa M Ogawa, Joshua M Ward, Gregory M Miller and Eric J Vallender
    Citation: BMC Genomics 2013 14:703
  2. EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breedi...

    Authors: Ishminder K Mann, Jill L Wegrzyn and Om P Rajora
    Citation: BMC Genomics 2013 14:702
  3. Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are pa...

    Authors: Elena A Vidal, Tomás C Moyano, Gabriel Krouk, Manpreet S Katari, Milos Tanurdzic, W Richard McCombie, Gloria M Coruzzi and Rodrigo A Gutiérrez
    Citation: BMC Genomics 2013 14:701
  4. Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and ...

    Authors: Choumouss Kamoun, Thibaut Payen, Aurélie Hua-Van and Jonathan Filée
    Citation: BMC Genomics 2013 14:700
  5. Accurate bacterial genome annotations provide a framework to understanding cellular functions, behavior and pathogenicity and are essential for metabolic engineering. Annotations based only on in silico predictio...

    Authors: Esteban Marcellin, Cuauhtemoc Licona-Cassani, Tim R Mercer, Robin W Palfreyman and Lars K Nielsen
    Citation: BMC Genomics 2013 14:699
  6. Mercury is a ubiquitous environmental toxicant that exists in multiple chemical forms. A paucity of information exists regarding the differences or similarities by which different mercurials act at the molecul...

    Authors: Matthew K McElwee, Lindsey A Ho, Jeff W Chou, Marjolein V Smith and Jonathan H Freedman
    Citation: BMC Genomics 2013 14:698
  7. The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to inter...

    Authors: Vincent P Richards, Haruo Suzuki, Michael J Stanhope and Mahmood S Shivji
    Citation: BMC Genomics 2013 14:697
  8. MicroRNAs (miRNAs) have recently been shown to play important roles in development of the immune system and in fine-tuning of immune responses. Human miR-146 family members are known as inflammation-inducible ...

    Authors: Anita Ordas, Zakia Kanwal, Valesca Lindenberg, Julien Rougeot, Matyas Mink, Herman P Spaink and Annemarie H Meijer
    Citation: BMC Genomics 2013 14:696
  9. The dimorphic fungus Histoplasma capsulatum causes respiratory and systemic disease in mammalian hosts by expression of factors that enable survival within phagocytic cells of the immune system. Histoplasma’s dim...

    Authors: Jessica A Edwards, Chenxi Chen, Megan M Kemski, Jinnan Hu, Thomas K Mitchell and Chad A Rappleye
    Citation: BMC Genomics 2013 14:695
  10. The initial interaction between host cell and pathogen sets the stage for the ensuing infection and ultimately determine the course of disease. However, there is limited knowledge of the transcripts utilized b...

    Authors: Elise A Lamont, Wayne W Xu and Srinand Sreevatsan
    Citation: BMC Genomics 2013 14:694
  11. Lyme disease is caused by spirochete bacteria from the Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) species complex. To reconstruct the evolution of B. burgdorferi s.l. and identify the genomic basis of ...

    Authors: Emmanuel F Mongodin, Sherwood R Casjens, John F Bruno, Yun Xu, Elliott Franco Drabek, David R Riley, Brandi L Cantarel, Pedro E Pagan, Yozen A Hernandez, Levy C Vargas, John J Dunn, Steven E Schutzer, Claire M Fraser, Wei-Gang Qiu and Benjamin J Luft
    Citation: BMC Genomics 2013 14:693
  12. CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylate...

    Authors: Sergio Cocozza, Giovanni Scala, Gennaro Miele, Imma Castaldo and Antonella Monticelli
    Citation: BMC Genomics 2013 14:692
  13. Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary mod...

    Authors: You-Jun Huang, Li-Li Liu, Jian-Qin Huang, Zheng-Jia Wang, Fang-Fang Chen, Qi-Xiang Zhang, Bing-Song Zheng and Ming Chen
    Citation: BMC Genomics 2013 14:691
  14. The Oncotype DX® Prostate Cancer Assay is a multi-gene RT-PCR expression assay that was developed for use with fixed paraffin-embedded (FPE) diagnostic prostate needle biopsies containing as little as 1 mm of pro...

    Authors: Dejan Knezevic, Audrey D Goddard, Nisha Natraj, Diana B Cherbavaz, Kim M Clark-Langone, Jay Snable, Drew Watson, Sara M Falzarano, Cristina Magi-Galluzzi, Eric A Klein and Christopher Quale
    Citation: BMC Genomics 2013 14:690
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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

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

  37. 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

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

  38. 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

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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

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