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  1. Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase t...

    Authors: Anneleen Van Geystelen, Ronny Decorte and Maarten HD Larmuseau
    Citation: BMC Genomics 2013 14:101
    Content type: Methodology article Published on:

  2. White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white c...

    Authors: Istvan Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T Abberton and Dan Milbourne
    Citation: BMC Genomics 2013 14:100
    Content type: Research article Published on:

  3. The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipi...

    Authors: Milos Pjanic, Christoph D Schmid, Armelle Gaussin, Giovanna Ambrosini, Jozef Adamcik, Petar Pjanic, Genta Plasari, Jan Kerschgens, Giovani Dietler, Philipp Bucher and Nicolas Mermod
    Citation: BMC Genomics 2013 14:99
    Content type: Research article Published on:

  4. Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scal...

    Authors: Zhi-Qiang Du, Cai-Xia Yang, Max F Rothschild and Jason W Ross
    Citation: BMC Genomics 2013 14:98
    Content type: Research article Published on:

  5. Cotton (Gossypium hirsutum) anther development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. However, only a small number of genes are known to be specifically involv...

    Authors: Mingming Wei, Meizhen Song, Shuli Fan and Shuxun Yu
    Citation: BMC Genomics 2013 14:97
    Content type: Research article Published on:

  6. High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution,...

    Authors: Haiyin Chen-Harris, Monica K Borucki, Clinton Torres, Tom R Slezak and Jonathan E Allen
    Citation: BMC Genomics 2013 14:96
    Content type: Methodology article Published on:

  7. A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive rad...

    Authors: Chris M Rands, Aaron Darling, Matthew Fujita, Lesheng Kong, Matthew T Webster, Céline Clabaut, Richard D Emes, Andreas Heger, Stephen Meader, Michael Brent Hawkins, Michael B Eisen, Clotilde Teiling, Jason Affourtit, Benjamin Boese, Peter R Grant, Barbara Rosemary Grant…
    Citation: BMC Genomics 2013 14:95
    Content type: Research article Published on:

  8. Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms h...

    Authors: Dmitry A Ravcheev, Aaron A Best, Natalia V Sernova, Marat D Kazanov, Pavel S Novichkov and Dmitry A Rodionov
    Citation: BMC Genomics 2013 14:94
    Content type: Research article Published on:

  9. Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infectio...

    Authors: Reena Narsai, Chuang Wang, Jie Chen, Jianli Wu, Huixia Shou and James Whelan
    Citation: BMC Genomics 2013 14:93
    Content type: Research article Published on:

  10. The oxidative burst is one of the major antimicrobial mechanisms adopted by macrophages. The WKY rat strain is uniquely susceptible to experimentally induced macrophage-dependent crescentic glomerulonephritis ...

    Authors: Richard P Hull, Prashant K Srivastava, Zelpha D’Souza, Santosh S Atanur, Fatima Mechta-Grigoriou, Laurence Game, Enrico Petretto, H Terence Cook, Timothy J Aitman and Jacques Behmoaras
    Citation: BMC Genomics 2013 14:92
    Content type: Research article Published on:

  11. The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the C...

    Authors: Alinne Batista Ambrosio, Leandro Costa do Nascimento, Bruno V Oliveira, Paulo José P L Teixeira, Ricardo A Tiburcio, Daniela P Toledo Thomazella, Adriana F P Leme, Marcelo F Carazzolle, Ramon O Vidal, Piotr Mieczkowski, Lyndel W Meinhardt, Gonçalo A G Pereira and Odalys G Cabrera
    Citation: BMC Genomics 2013 14:91
    Content type: Research article Published on:

  12. The throughput of next-generation sequencing machines has increased dramatically over the last few years; yet the cost and time for library preparation have not changed proportionally, thus representing the ma...

    Authors: Stefan Wilkening, Manu M Tekkedil, Gen Lin, Emilie S Fritsch, Wu Wei, Julien Gagneur, David W Lazinski, Andrew Camilli and Lars M Steinmetz
    Citation: BMC Genomics 2013 14:90
    Content type: Methodology article Published on:

  13. The human KIR genes are arranged in at least six major gene-content haplotypes, all of which are combinations of four centromeric and two telomeric motifs. Several less frequent or minor haplotypes also exist, in...

    Authors: Chul-Woo Pyo, Ruihan Wang, Quyen Vu, Nezih Cereb, Soo Young Yang, Fuh-Mei Duh, Steven Wolinsky, Maureen P Martin, Mary Carrington and Daniel E Geraghty
    Citation: BMC Genomics 2013 14:89
    Content type: Research article Published on:

  14. The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemen...

    Authors: Minghui Wang, Lin Wang, Ning Jiang, Tianye Jia and Zewei Luo
    Citation: BMC Genomics 2013 14:88
    Content type: Methodology article Published on:

  15. Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was ...

    Authors: Emanuel Heitlinger, Stephen Bridgett, Anna Montazam, Horst Taraschewski and Mark Blaxter
    Citation: BMC Genomics 2013 14:87
    Content type: Research article Published on:

  16. Polymorphism is key to the evolutionary potential of populations. Understanding which factors shape levels of genetic diversity within genomes forms a central question in evolutionary genomics and is of import...

    Authors: Carina F Mugal, Benoit Nabholz and Hans Ellegren
    Citation: BMC Genomics 2013 14:86
    Content type: Research article Published on:

  18. The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is depe...

    Authors: Li-Wei Chang, Andreu Viader, Nobish Varghese, Jacqueline E Payton, Jeffrey Milbrandt and Rakesh Nagarajan
    Citation: BMC Genomics 2013 14:84
    Content type: Research article Published on:

  19. Whereas temporal gene expression in mammalian herpesviruses has been studied extensively, little is known about gene expression in fish herpesviruses. Here we report a genome-wide transcription analysis of a f...

    Authors: Steven J van Beurden, Ben PH Peeters, Peter JM Rottier, Andrew J Davison and Marc Y Engelsma
    Citation: BMC Genomics 2013 14:83
    Content type: Research article Published on:

  20. Tissues and their component cells have unique DNA methylation profiles comprising DNA methylation patterns of tissue-dependent and differentially methylated regions (T-DMRs). Previous studies reported that DNA...

    Authors: Keiji Hirabayashi, Kunio Shiota and Shintaro Yagi
    Citation: BMC Genomics 2013 14:82
    Content type: Research article Published on:

  21. Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete unde...

    Authors: Eric J de Muinck, Karin Lagesen, Jan Egil Afset, Xavier Didelot, Kjersti S Rønningen, Knut Rudi, Nils Chr Stenseth and Pål Trosvik
    Citation: BMC Genomics 2013 14:81
    Content type: Research article Published on:

  22. Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low direct mortality, EP is responsible for major economic losses in...

    Authors: Wei Liu, Shaobo Xiao, Mao Li, Shaohua Guo, Sha Li, Rui Luo, Zhixin Feng, Bin Li, Zhemin Zhou, Guoqing Shao, Huanchun Chen and Liurong Fang
    Citation: BMC Genomics 2013 14:80
    Content type: Research article Published on:

  23. The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. ang...

    Authors: Michał Książkiewicz, Katarzyna Wyrwa, Anna Szczepaniak, Sandra Rychel, Karolina Majcherkiewicz, Łucja Przysiecka, Wojciech Karlowski, Bogdan Wolko and Barbara Naganowska
    Citation: BMC Genomics 2013 14:79
    Content type: Research article Published on:

  24. Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in ...

    Authors: Marco A N Passos, Viviane Oliveira de Cruz, Flavia L Emediato, Cristiane Camargo de Teixeira, Vânia C Rennó Azevedo, Ana C M Brasileiro, Edson P Amorim, Claudia F Ferreira, Natalia F Martins, Roberto C Togawa, Georgios J Pappas Júnior, Orzenil Bonfim da Silva Jr and Robert NG Miller
    Citation: BMC Genomics 2013 14:78
    Content type: Research article Published on:

  25. Phosphorus (P) is an essential macronutrient for plant growth and development. To modulate their P homeostasis, plants must balance P uptake, mobilisation, and partitioning to various organs. Despite the world...

    Authors: Youko Oono, Fuminori Kobayashi, Yoshihiro Kawahara, Takayuki Yazawa, Hirokazu Handa, Takeshi Itoh and Takashi Matsumoto
    Citation: BMC Genomics 2013 14:77
    Content type: Research article Published on:

  26. Among repetitive genomic sequence, the class of tri-nucleotide repeats has received much attention due to their association with human diseases. Tri-nucleotide repeat diseases are caused by excessive sequence ...

    Authors: Kai Willadsen, Minh Duc Cao, Janet Wiles, Sureshkumar Balasubramanian and Mikael Bodén
    Citation: BMC Genomics 2013 14:76
    Content type: Research article Published on:

  27. Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical ...

    Authors: Ahmad Yamin Abdul Rahman, Abhilash O Usharraj, Biswapriya B Misra, Gincy P Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz…
    Citation: BMC Genomics 2013 14:75
    Content type: Research article Published on:

  28. Tuberculosis (TB) continues to cause a high toll of disease and death among children worldwide. The diagnosis of childhood TB is challenged by the paucibacillary nature of the disease and the difficulties in o...

    Authors: Lilly M Verhagen, Aldert Zomer, Mailis Maes, Julian A Villalba, Berenice del Nogal, Marc Eleveld, Sacha AFT van Hijum, Jacobus H de Waard and Peter WM Hermans
    Citation: BMC Genomics 2013 14:74
    Content type: Research article Published on:

  29. Buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in Buchnera has been a matter of ...

    Authors: Lilia Brinza, Federica Calevro and Hubert Charles
    Citation: BMC Genomics 2013 14:73
    Content type: Research article Published on:

  30. Polyploidy is an important evolutionary mechanism in flowering plants that often induces immediate extensive changes in gene expression through genomic merging and doubling. Brassica napus L. is one of the most e...

    Authors: Jinjin Jiang, Yanlin Shao, Kun Du, Liping Ran, Xiaoping Fang and Youping Wang
    Citation: BMC Genomics 2013 14:72
    Content type: Research article Published on:

  31. Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a n...

    Authors: Yujun Han, Shanshan Qin and Susan R Wessler
    Citation: BMC Genomics 2013 14:71
    Content type: Research article Published on:

  32. An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organi...

    Authors: Junbai Wang, Xun Lan, Pei-Yin Hsu, Hang-Kai Hsu, Kun Huang, Jeffrey Parvin, Tim H-M Huang and Victor X Jin
    Citation: BMC Genomics 2013 14:70
    Content type: Research article Published on:

  33. Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species hav...

    Authors: Gianni Liti, Alex N Nguyen Ba, Martin Blythe, Carolin A Müller, Anders Bergström, Francisco A Cubillos, Felix Dafhnis-Calas, Shima Khoshraftar, Sunir Malla, Neel Mehta, Cheuk C Siow, Jonas Warringer, Alan M Moses, Edward J Louis and Conrad A Nieduszynski
    Citation: BMC Genomics 2013 14:69
    Content type: Research article Published on:

  34. Alzheimer’s disease (AD) is intimately tied to amyloid-β (Aβ) peptide. Extraneuronal brain plaques consisting primarily of Aβ aggregates are a hallmark of AD. Intraneuronal Aβ subunits are strongly implicated ...

    Authors: Debomoy K Lahiri, Bryan Maloney, Jack T Rogers and Yuan-Wen Ge
    Citation: BMC Genomics 2013 14:68
    Content type: Research article Published on:

  35. Meiotic recombination events are not randomly located, but rather cluster at hotspot regions. Recently, the fine-scale mapping of genome-wide human recombination hotspots was performed. Here, we systematically...

    Authors: Tao Zhou, Zhibin Hu, Zuomin Zhou, Xuejiang Guo and Jiahao Sha
    Citation: BMC Genomics 2013 14:67
    Content type: Research article Published on:

  36. Phosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean lea...

    Authors: Feng Xu, Qian Liu, Luying Chen, Jiebin Kuang, Thomas Walk, Jinxiang Wang and Hong Liao
    Citation: BMC Genomics 2013 14:66
    Content type: Research article Published on:

  37. The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explana...

    Authors: Liandong Yang, Ming Zou, Beide Fu and Shunping He
    Citation: BMC Genomics 2013 14:65
    Content type: Research article Published on:

  38. Marek’s disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek’s disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is d...

    Authors: Sudeep Perumbakkam, William M Muir, Alexis Black-Pyrkosz, Ron Okimoto and Hans H Cheng
    Citation: BMC Genomics 2013 14:64
    Content type: Research article Published on:

  39. Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered i...

    Authors: Megumi Kasai, Hideo Matsumura, Kentaro Yoshida, Ryohei Terauchi, Akito Taneda and Akira Kanazawa
    Citation: BMC Genomics 2013 14:63
    Content type: Research article Published on:

  40. The molecular bases of mammalian pancreatic α cells higher resistance than β to proinflammatory cytokines are very poorly defined. MicroRNAs are master regulators of cell networks, but only scanty data are ava...

    Authors: Davide Barbagallo, Salvatore Piro, Angelo G Condorelli, Loriana G Mascali, Francesca Urbano, Nunziatina Parrinello, Adelina Monello, Luisa Statello, Marco Ragusa, Agata M Rabuazzo, Cinzia Di Pietro, Francesco Purrello and Michele Purrello
    Citation: BMC Genomics 2013 14:62
    Content type: Research article Published on:

  41. Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture...

    Authors: Giorgio Pea, Htay Htay Aung, Elisabetta Frascaroli, Pierangelo Landi and Mario Enrico Pè
    Citation: BMC Genomics 2013 14:61
    Content type: Research article Published on:

  42. Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. Th...

    Authors: John P Fellers, Bahram M Soltani, Myron Bruce, Rob Linning, Christina A Cuomo, Les J Szabo and Guus Bakkeren
    Citation: BMC Genomics 2013 14:60
    Content type: Research article Published on:

  43. High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high r...

    Authors: Andreas Kranis, Almas A Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser, Paul M Hocking, Mark Fife, Nigel Salmon, Janet Fulton, Tim M Strom, Georg Haberer…
    Citation: BMC Genomics 2013 14:59
    Content type: Research article Published on:

  44. Tilapia is the common name for a group of cichlid fishes and is one of the most important aquacultured freshwater food fish. Mozambique tilapia and its hybrids, including red tilapia are main representatives o...

    Authors: Feng Liu, Fei Sun, Jian Li, Jun Hong Xia, Grace Lin, Rong Jian Tu and Gen Hua Yue
    Citation: BMC Genomics 2013 14:58
    Content type: Research article Published on:

  45. Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lyc...

    Authors: Riccardo Aiese Cigliano, Walter Sanseverino, Gaetana Cremona, Maria R Ercolano, Clara Conicella and Federica M Consiglio
    Citation: BMC Genomics 2013 14:57
    Content type: Research article Published on:

  46. Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at pr...

    Authors: Zhen Qin, Zhengqiu Cai, Guangmin Xia and Mengcheng Wang
    Citation: BMC Genomics 2013 14:56
    Content type: Research article Published on:

  47. Colorectal cancer (CRC) is a disease of complex aetiology, with much of the expected inherited risk being due to several common low risk variants. Genome-Wide Association Studies (GWAS) have identified 20 CRC ...

    Authors: Ceres Fernandez-Rozadilla, Jean-Baptiste Cazier, Ian P Tomlinson, Luis G Carvajal-Carmona, Claire Palles, María J Lamas, Montserrat Baiget, Luis A López-Fernández, Alejandro Brea-Fernández, Anna Abulí, Luis Bujanda, Juan Clofent, Dolors Gonzalez, Rosa Xicola, Montserrat Andreu, Xavier Bessa…
    Citation: BMC Genomics 2013 14:55
    Content type: Research article Published on:

  48. Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of sec...

    Authors: Miguel Redondo-Nieto, Matthieu Barret, John Morrissey, Kieran Germaine, Francisco Martínez-Granero, Emma Barahona, Ana Navazo, María Sánchez-Contreras, Jennifer A Moynihan, Candela Muriel, David Dowling, Fergal O’Gara, Marta Martín and Rafael Rivilla
    Citation: BMC Genomics 2013 14:54
    Content type: Research article Published on:

  49. Small RNA mediated gene silencing is a well-conserved regulatory pathway. In the parasite Entamoeba histolytica an endogenous RNAi pathway exists, however, the depth and diversity of the small RNA population rema...

    Authors: Hanbang Zhang, Gretchen M Ehrenkaufer, Neil Hall and Upinder Singh
    Citation: BMC Genomics 2013 14:53
    Content type: Research article Published on:

  50. Genomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-si...

    Authors: Qiang Gong, Yong Tao, Jian-Rong Yang, Jun Cai, Yunfei Yuan, Jue Ruan, Jin Yang, Hailiang Liu, Wanghua Li, Xuemei Lu, Shi-Mei Zhuang, San Ming Wang and Chung-I Wu
    Citation: BMC Genomics 2013 14:51
    Content type: Methodology article Published on:

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BMC Genomics

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