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  1. Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with ex...

    Authors: Ju-Hoon Lee, VN Karamychev, SA Kozyavkin, D Mills, AR Pavlov, NV Pavlova, NN Polouchine, PM Richardson, VV Shakhova, AI Slesarev, B Weimer and DJ O'Sullivan
    Citation: BMC Genomics 2008 9:247
    Content type: Research article Published on:

  2. Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD) genes determine...

    Authors: Laura E Pascal, Lawrence D True, David S Campbell, Eric W Deutsch, Michael Risk, Ilsa M Coleman, Lillian J Eichner, Peter S Nelson and Alvin Y Liu
    Citation: BMC Genomics 2008 9:246
    Content type: Research article Published on:

  3. Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome seque...

    Authors: Wanwipa Vongsangnak, Peter Olsen, Kim Hansen, Steen Krogsgaard and Jens Nielsen
    Citation: BMC Genomics 2008 9:245
    Content type: Research article Published on:

  5. The medfly, Ceratitis capitata, is a highly invasive agricultural pest that has become a model insect for the development of biological control programs. Despite research into the behavior and classical and popul...

    Authors: Ludvik M Gomulski, George Dimopoulos, Zhiyong Xi, Marcelo B Soares, Maria F Bonaldo, Anna R Malacrida and Giuliano Gasperi
    Citation: BMC Genomics 2008 9:243
    Content type: Research article Published on:

  8. Endothelial differentiation occurs during normal vascular development in the developing embryo. This process is recapitulated in the adult when endothelial progenitor cells are generated in the bone marrow and...

    Authors: Vesna Nikolova-Krstevski, Manoj Bhasin, Hasan H Otu, Towia Libermann and Peter Oettgen
    Citation: BMC Genomics 2008 9:240
    Content type: Research article Published on:

  9. Estrogen receptor positive (ER+) breast cancers (BC) are heterogeneous with regard to their clinical behavior and response to therapies. The ER is currently the best predictor of response to the anti-estrogen ...

    Authors: Sherene Loi, Benjamin Haibe-Kains, Christine Desmedt, Pratyaksha Wirapati, Françoise Lallemand, Andrew M Tutt, Cheryl Gillet, Paul Ellis, Kenneth Ryder, James F Reid, Maria G Daidone, Marco A Pierotti, Els MJJ Berns, Maurice PHM Jansen, John A Foekens, Mauro Delorenzi…
    Citation: BMC Genomics 2008 9:239
    Content type: Research article Published on:

  10. Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex inter...

    Authors: Fatma Z Guerfali, Dhafer Laouini, Lamia Guizani-Tabbane, Florence Ottones, Khadija Ben-Aissa, Alia Benkahla, Laurent Manchon, David Piquemal, Sondos Smandi, Ons Mghirbi, Thérèse Commes, Jacques Marti and Koussay Dellagi
    Citation: BMC Genomics 2008 9:238
    Content type: Research article Published on:

  11. Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorti...

    Authors: Hana Šimková, Jan Šafář, Pavla Suchánková, Pavlína Kovářová, Jan Bartoš, Marie Kubaláková, Jaroslav Janda, Jarmila Číhalíková, Rohit Mago, Tamas Lelley and Jaroslav Doležel
    Citation: BMC Genomics 2008 9:237
    Content type: Research article Published on:

  12. Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unra...

    Authors: Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao and Runsheng Chen
    Citation: BMC Genomics 2008 9:236
    Content type: Research article Published on:

  15. In recent years, there have been several sialome projects revealing transcripts expressed in the salivary glands of ticks, which are important vectors of several human diseases. Here, we focused on the sialome...

    Authors: Jindřich Chmelař, Jennifer M Anderson, Jianbing Mu, Ryan C Jochim, Jesus G Valenzuela and Jan Kopecký
    Citation: BMC Genomics 2008 9:233
    Content type: Research article Published on:

  17. 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:

  18. Microarray comparative genomic hybridization (aCGH) evaluates the distribution of genes of sequenced bacterial strains among unsequenced strains of the same or related species. As genomic sequences from multip...

    Authors: Francisco R Pinto, Sandra I Aguiar, J Melo-Cristino and Mário Ramirez
    Citation: BMC Genomics 2008 9:230
    Content type: Methodology article Published on:

  19. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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