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  1. In bacterial pathogens, both cell surface-exposed outer membrane proteins and proteins secreted into the extracellular environment play crucial roles in host-pathogen interaction and pathogenesis. Considerable...

    Authors: Wasna Viratyosin, Supawadee Ingsriswang, Eakasit Pacharawongsakda and Prasit Palittapongarnpim
    Citation: BMC Genomics 2008 9:181
    Content type: Research article Published on:

  2. Plant circadian systems regulate various biological processes in harmony with daily environmental changes. In Arabidopsis thaliana, the underlying clock mechanism is comprised of multiple integrated transcription...

    Authors: Shigeru Hanano, Ralf Stracke, Marc Jakoby, Thomas Merkle, Malgorzata A Domagalska, Bernd Weisshaar and Seth J Davis
    Citation: BMC Genomics 2008 9:182
    Content type: Research article Published on:

  3. Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently...

    Authors: Matthieu G Conte, Sylvain Gaillard, Gaetan Droc and Christophe Perin
    Citation: BMC Genomics 2008 9:183
    Content type: Methodology article Published on:

  4. The use of new, deep sequencing technologies has greatly accelerated microRNA discovery. We have applied this approach to the identification of chicken microRNAs and to the comparison of microRNAs in chicken e...

    Authors: Joan Burnside, Ming Ouyang, Amy Anderson, Erin Bernberg, Cheng Lu, Blake C Meyers, Pamela J Green, Milos Markis, Grace Isaacs, Emily Huang and Robin W Morgan
    Citation: BMC Genomics 2008 9:185
    Content type: Research article Published on:

  6. The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in catt...

    Authors: Mehar S Khatkar, Frank W Nicholas, Andrew R Collins, Kyall R Zenger, Julie AL Cavanagh, Wes Barris, Robert D Schnabel, Jeremy F Taylor and Herman W Raadsma
    Citation: BMC Genomics 2008 9:187
    Content type: Research article Published on:

  8. UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs hav...

    Authors: Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason TL Wang and Bin Tian
    Citation: BMC Genomics 2008 9:189
    Content type: Research article Published on:

  9. Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulenc...

    Authors: Sarinna Tumapa, Matthew TG Holden, Mongkol Vesaratchavest, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Wirongrong Chierakul, Edward J Feil, Bart J Currie, Nicholas PJ Day, William C Nierman and Sharon J Peacock
    Citation: BMC Genomics 2008 9:190
    Content type: Research article Published on:

  10. Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments ind...

    Authors: Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang and Yanda Li
    Citation: BMC Genomics 2008 9:191
    Content type: Research article Published on:

  11. Although microbiota play a critical role in the normal development and function of host immune systems, the underlying mechanisms, especially those involved in the large intestine (LI), remain unknown. In the ...

    Authors: Kaori Munakata, Masahiro Yamamoto, Naoko Anjiki, Mitsue Nishiyama, Sachiko Imamura, Seiichi Iizuka, Kiyoe Takashima, Atsushi Ishige, Kyoji Hioki, Yasuyuki Ohnishi and Kenji Watanabe
    Citation: BMC Genomics 2008 9:192
    Content type: Research article Published on:

  12. In teleosts, the Major Histocompatibility Complex (MHC) class I and class II molecules reside on different linkage groups as opposed to tetrapods and shark, where the class I and class II genes reside in one g...

    Authors: HÃ¥vard Harstad, Morten F Lukacs, Hege G Bakke and Unni Grimholt
    Citation: BMC Genomics 2008 9:193
    Content type: Research article Published on:

  13. WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three differe...

    Authors: Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Ãœner H Kolukisaoglu, Klaus Harter, Christer Jansson and Dierk Wanke
    Citation: BMC Genomics 2008 9:194
    Content type: Research article Published on:

  14. Spiroplama citri, the causal agent of citrus stubborn disease, is a bacterium of the class Mollicutes and is transmitted by phloem-feeding leafhopper vectors. In order to characterize candidate genes potentially ...

    Authors: Colette Saillard, Patricia Carle, Sybille Duret-Nurbel, Raphaël Henri, Nabil Killiny, Sébastien Carrère, Jérome Gouzy, Joseph-Marie Bové, Joël Renaudin and Xavier Foissac
    Citation: BMC Genomics 2008 9:195
    Content type: Research article Published on:

  15. The MAPK signaling proteins are involved in many eukaryotic cellular processes and signaling networks. However, specific functions of most of these proteins in vertebrate development remain elusive because of ...

    Authors: SF Gabby Krens, Maximiliano Corredor-Adámez, Shuning He, B Ewa Snaar-Jagalska and Herman P Spaink
    Citation: BMC Genomics 2008 9:196
    Content type: Research article Published on:

  16. Highly fecund mouse strains provide an ideal model to understand the factors affecting maternal performance. The QSi5 inbred strain of mice was selected for high fecundity and low inter-litter interval, and is...

    Authors: Palaniappan Ramanathan, Ian C Martin, Margaret Gardiner-Garden, Peter C Thomson, Rosanne M Taylor, Christopher J Ormandy, Christopher Moran and Peter Williamson
    Citation: BMC Genomics 2008 9:197
    Content type: Research article Published on:

  17. Recent genome-wide association studies searching for candidate susceptibility loci for common complex diseases such as type 2 diabetes mellitus (T2DM) and its common complications have uncovered novel disease-...

    Authors: Jeanette Feder, Ilana Blech, Ofer Ovadia, Shirly Amar, Julio Wainstein, Itamar Raz, Sarah Dadon, Dan E Arking, Benjamin Glaser and Dan Mishmar
    Citation: BMC Genomics 2008 9:198
    Content type: Research article Published on:

  19. Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from...

    Authors: Bryony AP Williams, Renny CH Lee, James J Becnel, Louis M Weiss, Naomi M Fast and Patrick J Keeling
    Citation: BMC Genomics 2008 9:200
    Content type: Research article Published on:

  20. Targeting tumor angiogenesis and vasculature is a promising strategy for the inhibition of tumor growth and dissemination. Evidence suggests that tumor vasculature expresses unique markers that distinguish it ...

    Authors: Carmen Ghilardi, Giovanna Chiorino, Romina Dossi, Zsuzsanna Nagy, Raffaella Giavazzi and MariaRosa Bani
    Citation: BMC Genomics 2008 9:201
    Content type: Research article Published on:

  21. The splicing of pre-mRNAs is conspicuously often variable and produces multiple alternatively spliced (AS) isoforms that encode different messages from one gene locus. Computational studies uncovered a class o...

    Authors: Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster and Dirk Holste
    Citation: BMC Genomics 2008 9:202
    Content type: Research article Published on:

  22. Puccinia striiformis f. sp. tritici is an obligate biotrophic pathogen that causes leaf stripe rust on wheat. Although it is critical to understand molecular mechanisms of pathogenesis in the wheat stripe rust fu...

    Authors: Yonghong Zhang, Zhipeng Qu, Wenming Zheng, Bo Liu, Xiaojie Wang, Xiaodan Xue, Liangsheng Xu, Lili Huang, Qingmei Han, Jie Zhao and Zhensheng Kang
    Citation: BMC Genomics 2008 9:203
    Content type: Research article Published on:

  23. Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome se...

    Authors: Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna…
    Citation: BMC Genomics 2008 9:204
    Content type: Research article Published on:

  24. Parent-specific methylation of specific CpG residues is critical to imprinting in eutherian mammals, but its importance to imprinting in marsupials and, thus, the evolutionary origins of the imprinting mechani...

    Authors: Betty R Lawton, Benjamin R Carone, Craig J Obergfell, Gianni C Ferreri, Christina M Gondolphi, John L VandeBerg, Ikhide Imumorin, Rachel J O'Neill and Michael J O'Neill
    Citation: BMC Genomics 2008 9:205
    Content type: Research article Published on:

  25. Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. These p...

    Authors: Stephen P Karaganis, Vinod Kumar, Phillip D Beremand, Michael J Bailey, Terry L Thomas and Vincent M Cassone
    Citation: BMC Genomics 2008 9:206
    Content type: Research article Published on:

  26. The substitution of rare codons with more frequent codons is a commonly applied method in heterologous gene expression to increase protein yields. However, in some cases these substitutions lead to a decrease ...

    Authors: Michael Widmann, Marie Clairo, Jürgen Dippon and Jürgen Pleiss
    Citation: BMC Genomics 2008 9:207
    Content type: Research article Published on:

  27. The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electri...

    Authors: Ravi Kiran Reddy Kalathur, Nicolas Gagniere, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard and Olivier Poch
    Citation: BMC Genomics 2008 9:208
    Content type: Database Published on:

  28. The small intestinal epithelium mediates vital functions of nutrient absorption and host defense. The spatial organization of the epithelial cells along the crypt-villus axis segregates them into regions of sp...

    Authors: Michael D George, Jan Wehkamp, Robert J Kays, Christian M Leutenegger, Sadiah Sabir, Irina Grishina, Satya Dandekar and Charles L Bevins
    Citation: BMC Genomics 2008 9:209
    Content type: Research article Published on:

  29. The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low tempe...

    Authors: Monica Riley, James T Staley, Antoine Danchin, Ting Zhang Wang, Thomas S Brettin, Loren J Hauser, Miriam L Land and Linda S Thompson
    Citation: BMC Genomics 2008 9:210
    Content type: Research article Published on:

  30. Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surpr...

    Authors: Rose Ann Cattolico, Michael A Jacobs, Yang Zhou, Jean Chang, Melinda Duplessis, Terry Lybrand, John McKay, Han Chuan Ong, Elizabeth Sims and Gabrielle Rocap
    Citation: BMC Genomics 2008 9:211
    Content type: Research article Published on:

  32. Human adenovirus type 37 (HAdV-37) is a major etiologic agent of epidemic keratoconjunctivitis, a common and severe eye infection associated with long-term visual morbidity due to persistent corneal inflammati...

    Authors: Christopher M Robinson, Fatemeh Shariati, Allison F Gillaspy, David W Dyer and James Chodosh
    Citation: BMC Genomics 2008 9:213
    Content type: Research article Published on:

  33. The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identificati...

    Authors: Isabelle Meusnier, Gregory AC Singer, Jean-François Landry, Donal A Hickey, Paul DN Hebert and Mehrdad Hajibabaei
    Citation: BMC Genomics 2008 9:214
    Content type: Research article Published on:

  34. Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cel...

    Authors: Eunsoo Kim, Christopher E Lane, Bruce A Curtis, Catherine Kozera, Sharen Bowman and John M Archibald
    Citation: BMC Genomics 2008 9:215
    Content type: Research article Published on:

  35. Tumor-predominant splice isoforms were identified during comparative in silico sequence analysis of EST clones, suggesting that global aberrant alternative pre-mRNA splicing may be an epigenetic phenomenon in can...

    Authors: Hannah C Cheung, Keith A Baggerly, Spiridon Tsavachidis, Linda L Bachinski, Valerie L Neubauer, Tamara J Nixon, Kenneth D Aldape, Gilbert J Cote and Ralf Krahe
    Citation: BMC Genomics 2008 9:216
    Content type: Research article Published on:

  36. The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, ...

    Authors: Josef Pánek, Jan Bobek, Karel Mikulík, Marek Basler and Jiří Vohradský
    Citation: BMC Genomics 2008 9:217
    Content type: Research article Published on:

  38. Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: ...

    Authors: Antonio Marco and Ignacio Marín
    Citation: BMC Genomics 2008 9:219
    Content type: Research article Published on:

  39. The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other...

    Authors: Arthur G Hunt, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P Forbes, Lisa R Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken and Qingshun Quinn Li
    Citation: BMC Genomics 2008 9:220
    Content type: Research article Published on:

  40. Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA...

    Authors: Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A Setterquist, Peter JM Rottier and Cornelis AM de Haan
    Citation: BMC Genomics 2008 9:221
    Content type: Methodology article Published on:

  41. The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now class...

    Authors: Hisayuki Nomiyama, Kunio Hieshima, Naoki Osada, Yoko Kato-Unoki, Kaori Otsuka-Ono, Sumio Takegawa, Toshiaki Izawa, Akio Yoshizawa, Yutaka Kikuchi, Sumio Tanase, Retsu Miura, Jun Kusuda, Miki Nakao and Osamu Yoshie
    Citation: BMC Genomics 2008 9:222
    Content type: Research article Published on:

  42. The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage map...

    Authors: Thomas Moen, Ben Hayes, Matthew Baranski, Paul R Berg, Sissel Kjøglum, Ben F Koop, Willie S Davidson, Stig W Omholt and Sigbjørn Lien
    Citation: BMC Genomics 2008 9:223
    Content type: Research article Published on:

  43. Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful...

    Authors: Ming-Wei Li, Rui-Qing Lin, Hui-Qun Song, Xiang-Yun Wu and Xing-Quan Zhu
    Citation: BMC Genomics 2008 9:224
    Content type: Research article Published on:

  44. T-cell activation is an essential step of the immune response and relies on the tightly controlled orchestration of hundreds of genes/proteins, yet the cellular and molecular events underlying this complex pro...

    Authors: Min Wang, Dirk Windgassen and Eleftherios T Papoutsakis
    Citation: BMC Genomics 2008 9:225
    Content type: Research article Published on:

  45. The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements enc...

    Authors: Nalini Polavarapu, Leonardo Mariño-Ramírez, David Landsman, John F McDonald and I King Jordan
    Citation: BMC Genomics 2008 9:226
    Content type: Research article Published on:

  46. Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide ins...

    Authors: Anna Cohuet, Sujatha Krishnakumar, Frédéric Simard, Isabelle Morlais, Anastasios Koutsos, Didier Fontenille, Michael Mindrinos and Fotis C Kafatos
    Citation: BMC Genomics 2008 9:227
    Content type: Research article Published on:

  48. Photorhabdus luminescens is a Gram-negative luminescent enterobacterium and a symbiote to soil nematodes belonging to the species Heterorhabditis bacteriophora. P.luminescens is simultaneously highly pathogenic t...

    Authors: Anna Münch, Lavinia Stingl, Kirsten Jung and Ralf Heermann
    Citation: BMC Genomics 2008 9:229
    Content type: Research article Published on:

  49. The selective absorption of nutrients and other food constituents in the small intestine is mediated by a group of transport proteins and metabolic enzymes, often collectively called 'intestinal barrier protei...

    Authors: Heleen M de Vogel-van den Bosch, Meike Bünger, Philip J de Groot, Hanneke Bosch-Vermeulen, Guido JEJ Hooiveld and Michael Müller
    Citation: BMC Genomics 2008 9:231
    Content type: Research article Published on:

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BMC Genomics

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