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  1. The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not ...

    Authors: Ming-Cheng Luo, Yaqin Ma, Frank M You, Olin D Anderson, David Kopecký, Hana Šimková, Jan Šafář, Jaroslav Doležel, Bikram Gill, Patrick E McGuire and Jan Dvorak
    Citation: BMC Genomics 2010 11:122
    Content type: Research article Published on:

  3. A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isola...

    Authors: Matthew W Gilmour, Morag Graham, Gary Van Domselaar, Shaun Tyler, Heather Kent, Keri M Trout-Yakel, Oscar Larios, Vanessa Allen, Barbara Lee and Celine Nadon
    Citation: BMC Genomics 2010 11:120
    Content type: Research article Published on:

  4. MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression in a variety of organisms, including insects, vertebrates, and plants. miRNAs play important roles in cell deve...

    Authors: Rebecca L Skalsky, Dana L Vanlandingham, Frank Scholle, Stephen Higgs and Bryan R Cullen
    Citation: BMC Genomics 2010 11:119
    Content type: Research article Published on:

  6. Downy mildew is a destructive grapevine disease caused by Plasmopara viticola (Berk. and Curt.) Berl. and de Toni, which can only be controlled by intensive fungicide treatments. Natural sources of resistance fro...

    Authors: Marianna Polesani, Luisa Bortesi, Alberto Ferrarini, Anita Zamboni, Marianna Fasoli, Claudia Zadra, Arianna Lovato, Mario Pezzotti, Massimo Delledonne and Annalisa Polverari
    Citation: BMC Genomics 2010 11:117
    Content type: Research article Published on:

  7. Outbreaks of the casuarina moth, Lymantria xylina Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of h...

    Authors: Yu-Shin Nai, Chih-Yu Wu, Tai-Chuan Wang, Yun-Ru Chen, Wei-Hong Lau, Chu-Fang Lo, Meng-Feng Tsai and Chung-Hsiung Wang
    Citation: BMC Genomics 2010 11:116
    Content type: Research article Published on:

  8. Physarum polycephalum is a free-living amoebozoan protist displaying a complex life cycle, including alternation between single- and multinucleate stages through sporulation, a simple form of cell differentiation...

    Authors: Israel Barrantes, Gernot Glockner, Sonja Meyer and Wolfgang Marwan
    Citation: BMC Genomics 2010 11:115
    Content type: Research article Published on:

  9. Genome-wide computational analysis of alternative splicing (AS) in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part ...

    Authors: Adam Labadorf, Alicia Link, Mark F Rogers, Julie Thomas, Anireddy SN Reddy and Asa Ben-Hur
    Citation: BMC Genomics 2010 11:114
    Content type: Research article Published on:

  10. Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their ho...

    Authors: Jianchang Du, David Grant, Zhixi Tian, Rex T Nelson, Liucun Zhu, Randy C Shoemaker and Jianxin Ma
    Citation: BMC Genomics 2010 11:113
    Content type: Database Published on:

  11. Ratio-based analysis is the current standard for the analysis of dual-color microarray data. Indeed, this method provides a powerful means to account for potential technical variations such as differences in b...

    Authors: Koen Bossers, Bauke Ylstra, Ruud H Brakenhoff, Serge J Smeets, Joost Verhaagen and Mark A van de Wiel
    Citation: BMC Genomics 2010 11:112
    Content type: Methodology article Published on:

  12. Cyclotides are a family of circular peptides that exhibit a range of biological activities, including anti-bacterial, cytotoxic, anti-HIV activities, and are proposed to function in plant defence. Their high s...

    Authors: Qiaoping Qin, Emily J McCallum, Quentin Kaas, Jan Suda, Ivana Saska, David J Craik and Joshua S Mylne
    Citation: BMC Genomics 2010 11:111
    Content type: Research article Published on:

  13. The bumblebee, Bombus terrestris (Order Hymenoptera), is of widespread importance. This species is extensively used for commercial pollination in Europe, and along with other Bombus spp. is a key member of natura...

    Authors: Ben M Sadd, Michael Kube, Sven Klages, Richard Reinhardt and Paul Schmid-Hempel
    Citation: BMC Genomics 2010 11:110
    Content type: Research article Published on:

  14. The version of this article published in BMC Genomics 2009, 10: 558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted b...

    Authors: Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè and David S Horner
    Citation: BMC Genomics 2010 11:109
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2009 10:558

  15. The use of functional genomics has largely increased our understanding of cell biology and promises to help the development of systems biology needed to understand the complex order of events that regulates ce...

    Authors: Jenny Zetterblad, Hong Qian, Sasan Zandi, Robert MÃ¥nsson, Anna Lagergren, Frida Hansson, David Bryder, Nils Paulsson and Mikael Sigvardsson
    Citation: BMC Genomics 2010 11:108
    Content type: Research article Published on:

  16. Delineating the genetic basis of body composition is important to agriculture and medicine. In addition, the incorporation of gene-gene interactions in the statistical model provides further insight into the g...

    Authors: Georgina A Ankra-Badu, Daniel Shriner, Elisabeth Le Bihan-Duval, Sandrine Mignon-Grasteau, Frédérique Pitel, Catherine Beaumont, Michel J Duclos, Jean Simon, Tom E Porter, Alain Vignal, Larry A Cogburn, David B Allison, Nengjun Yi and Samuel E Aggrey
    Citation: BMC Genomics 2010 11:107
    Content type: Research article Published on:

  18. Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (...

    Authors: Jaeyoung Choi, Jongsun Park, Donghan Kim, Kyongyong Jung, Seogchan Kang and Yong-Hwan Lee
    Citation: BMC Genomics 2010 11:105
    Content type: Database Published on:

  19. Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these inter...

    Authors: Soonok Kim, Jongsun Park, Sook-Young Park, Thomas K Mitchell and Yong-Hwan Lee
    Citation: BMC Genomics 2010 11:104
    Content type: Research article Published on:

  20. The marine cyanobacterium Prochlorococcus marinus, having multiple ecotypes of distinct genotypic/phenotypic traits and being the first documented example of genome shrinkage in free-living organisms, offers an i...

    Authors: Sandip Paul, Anirban Dutta, Sumit K Bag, Sabyasachi Das and Chitra Dutta
    Citation: BMC Genomics 2010 11:103
    Content type: Research article Published on:

  21. Algorithms designed to predict protein disorder play an important role in structural and functional genomics, as disordered regions have been reported to participate in important cellular processes. Consequent...

    Authors: Fernanda L Sirota, Hong-Sain Ooi, Tobias Gattermayer, Georg Schneider, Frank Eisenhaber and Sebastian Maurer-Stroh
    Citation: BMC Genomics 2010 11(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  22. A bioinformatic search was carried for plant homologues of human serine-threonine protein kinases involved in regulation of cell division and microtubule protein phosphorylation (SLK, PAK6, PAK7, MARK1, MAST2,...

    Authors: Pavel A Karpov, Elena S Nadezhdina, Alla I Yemets, Vadym G Matusov, Alexey Yu Nyporko, Nadezhda Yu Shashina and Yaroslav B Blume
    Citation: BMC Genomics 2010 11(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  23. Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift an...

    Authors: Nedim Mujezinovic, Georg Schneider, Michael Wildpaner, Karl Mechtler and Frank Eisenhaber
    Citation: BMC Genomics 2010 11(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  24. Transcription factor (TF)-DNA binding loci are explored by analyzing massive datasets generated with application of Chromatin Immuno-Precipitation (ChIP)-based high-throughput sequencing technologies. These da...

    Authors: Vladimir A Kuznetsov, Onkar Singh and Piroon Jenjaroenpun
    Citation: BMC Genomics 2010 11(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  25. Alu elements occupy about eleven percent of the human genome and are still growing in copy numbers. Since Alu elements substantially impact the shape of our genome, there is a need for modeling the amplificati...

    Authors: Marek Kimmel and Matthias Mathaes
    Citation: BMC Genomics 2010 11(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  26. Transposons are "jumping genes" that account for large quantities of repetitive content in genomes. They are known to affect transcriptional regulation in several different ways, and are implicated in many hum...

    Authors: Paul T Edlefsen and Jun S Liu
    Citation: BMC Genomics 2010 11(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  27. A sense-antisense gene pair (SAGP) is a gene pair where two oppositely transcribed genes share a common nucleotide sequence region. In eukaryotic genomes, SAGPs can be organized in complex sense-antisense arch...

    Authors: Oleg V Grinchuk, Efthimios Motakis and Vladimir A Kuznetsov
    Citation: BMC Genomics 2010 11(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  28. We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were found on multiple micro...

    Authors: Marina Bessarabova, Eugene Kirillov, Weiwei Shi, Andrej Bugrim, Yuri Nikolsky and Tatiana Nikolskaya
    Citation: BMC Genomics 2010 11(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  29. Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable ...

    Authors: Bernhard Mlecnik, Fatima Sanchez-Cabo, Pornpimol Charoentong, Gabriela Bindea, Franck Pagès, Anne Berger, Jerome Galon and Zlatko Trajanoski
    Citation: BMC Genomics 2010 11(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  30. Recent literature has revealed that genetic exchange of microRNA between cells can be essential for cell-cell communication, tissue-specificity and developmental processes. In stem cells, as in other cells, th...

    Authors: Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir Kuznetsov, Lim Sai Kiang and Vivek Tanavde
    Citation: BMC Genomics 2010 11(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  31. The N terminal transactivation domain of p53 is regulated by ligases and coactivator proteins. The functional conformation of this region appears to be an alpha helix which is necessary for its appropriate int...

    Authors: Jagadeesh N Mavinahalli, Arumugam Madhumalar, Roger W Beuerman, David P Lane and Chandra Verma
    Citation: BMC Genomics 2010 11(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  32. We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions com...

    Authors: Alexander A Kanapin, Nicola Mulder and Vladimir A Kuznetsov
    Citation: BMC Genomics 2010 11(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  33. Most proteins form macromolecular complexes to perform their biological functions. However, experimentally determined protein complex data, especially of those involving more than two protein partners, are rel...

    Authors: Xiaoli Li, Min Wu, Chee-Keong Kwoh and See-Kiong Ng
    Citation: BMC Genomics 2010 11(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  34. The interaction of a multiplicity of scales in both time and space is a fundamental feature of biological systems. The complementation of macroscopic (entire organism) and microscopic (molecular biology) views...

    Authors: Alessandro Giuliani
    Citation: BMC Genomics 2010 11(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  37. In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent st...

    Authors: Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita and Akio Kanai
    Citation: BMC Genomics 2010 11:101
    Content type: Research article Published on:

  38. γδ T cells differ from αβ T cells with regard to the types of antigen with which their T cell receptors interact; γδ T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are consi...

    Authors: Carolyn TA Herzig, Marie-Paule Lefranc and Cynthia L Baldwin
    Citation: BMC Genomics 2010 11:100
    Content type: Research article Published on:

  39. Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted prote...

    Authors: Christophe J Noël, Nicia Diaz, Thomas Sicheritz-Ponten, Lucie Safarikova, Jan Tachezy, Petrus Tang, Pier-Luigi Fiori and Robert P Hirt
    Citation: BMC Genomics 2010 11:99
    Content type: Research article Published on:

  40. Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, na...

    Authors: Vincent Deslandes, Martine Denicourt, Christiane Girard, Josée Harel, John HE Nash and Mario Jacques
    Citation: BMC Genomics 2010 11:98
    Content type: Research article Published on:

  41. Although polyploidy has long been recognized as a major force in the evolution of plants, most of what we know about the genetic consequences of polyploidy comes from the study of crops and model systems. Furt...

    Authors: Jin Koh, Pamela S Soltis and Douglas E Soltis
    Citation: BMC Genomics 2010 11:97
    Content type: Research article Published on:

  42. Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However,...

    Authors: Josine L Min, Amy Barrett, Tim Watts, Fredrik H Pettersson, Helen E Lockstone, Cecilia M Lindgren, Jennifer M Taylor, Maxine Allen, Krina T Zondervan and Mark I McCarthy
    Citation: BMC Genomics 2010 11:96
    Content type: Research article Published on:

  43. ClpB-cyt/HSP100 protein acts as chaperone, mediating disaggregation of denatured proteins. Previous studies have shown that ClpB-cyt/HSP100 gene belongs to the group class I Clp ATPase proteins and ClpB-cyt/HS...

    Authors: Amanjot Singh, Upasana Singh, Dheeraj Mittal and Anil Grover
    Citation: BMC Genomics 2010 11:95
    Content type: Research article Published on:

  44. Epimedium sagittatum (Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain Epimedium species are endangered due to commercial ove...

    Authors: Shaohua Zeng, Gong Xiao, Juan Guo, Zhangjun Fei, Yanqin Xu, Bruce A Roe and Ying Wang
    Citation: BMC Genomics 2010 11:94
    Content type: Research article Published on:

  45. Even though the process of potato tuber starch biosynthesis is well understood, mechanisms regulating biosynthesis are still unclear. Transcriptome analysis provides valuable information as to how genes are re...

    Authors: Stephanus J Ferreira, Melanie Senning, Sophia Sonnewald, Petra-Maria Keßling, Ralf Goldstein and Uwe Sonnewald
    Citation: BMC Genomics 2010 11:93
    Content type: Research article Published on:

  46. The methylation of eukaryotic proteins has been proposed to be widespread, but this has not been conclusively shown to date. In this study, we examined 36,854 previously generated peptide mass spectra from 2,607

    Authors: Chi Nam Ignatius Pang, Elisabeth Gasteiger and Marc R Wilkins
    Citation: BMC Genomics 2010 11:92
    Content type: Research article Published on:

  47. Corynebacterium aurimucosum is a slightly yellowish, non-lipophilic, facultative anaerobic member of the genus Corynebacterium and predominantly isolated from human clinical specimens. Unusual black-pigmented var...

    Authors: Eva Trost, Susanne Götker, Jessica Schneider, Susanne Schneiker-Bekel, Rafael Szczepanowski, Alexandra Tilker, Prisca Viehoever, Walter Arnold, Thomas Bekel, Jochen Blom, Karl-Heinz Gartemann, Burkhard Linke, Alexander Goesmann, Alfred Pühler, Sanjay K Shukla and Andreas Tauch
    Citation: BMC Genomics 2010 11:91
    Content type: Research article Published on:

  48. Burkholderia cepacia complex bacteria are opportunistic pathogens, which can cause severe respiratory tract infections in patients with cystic fibrosis (CF). As treatment of infected CF patients is problematic, m...

    Authors: Elke Peeters, Andrea Sass, Eshwar Mahenthiralingam, Hans Nelis and Tom Coenye
    Citation: BMC Genomics 2010 11:90
    Content type: Research article Published on:

  49. Retrotransposons are key players in the evolution of eukaryotic genomes. Moreover, it is now known that some retrotransposon classes, like the abundant and plant-specific Sireviruses, have intriguingly distinc...

    Authors: Alexandros Bousios, Nikos Darzentas, Athanasios Tsaftaris and Stephen R Pearce
    Citation: BMC Genomics 2010 11:89
    Content type: Research article Published on:

  50. Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to id...

    Authors: Carlos L Araya, Celia Payen, Maitreya J Dunham and Stanley Fields
    Citation: BMC Genomics 2010 11:88
    Content type: Methodology article Published on:

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