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  1. The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation...

    Authors: Willem Albert Rensink, Yuandan Lee, Jia Liu, Stacy Iobst, Shu Ouyang and C Robin Buell

    Citation: BMC Genomics 2005 6:124

    Content type: Research article

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  2. Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly imp...

    Authors: Alexander Sczyrba, Michael Beckstette, Ali H Brivanlou, Robert Giegerich and Curtis R Altmann

    Citation: BMC Genomics 2005 6:123

    Content type: Database

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  3. Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressu...

    Authors: Stefano Campanaro, Alessandro Vezzi, Nicola Vitulo, Federico M Lauro, Michela D'Angelo, Francesca Simonato, Alessandro Cestaro, Giorgio Malacrida, Giulio Bertoloni, Giorgio Valle and Douglas H Bartlett

    Citation: BMC Genomics 2005 6:122

    Content type: Research article

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  4. Corynebacterium glutamicum is a high-GC Gram-positive soil bacterium of great biotechnological importance for the production of amino acids. To facilitate the rational design of sulphur amino acid-producing strai...

    Authors: Christian Rückert, Daniel J Koch, Daniel A Rey, Andreas Albersmeier, Sascha Mormann, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2005 6:121

    Content type: Research article

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  5. In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two- and three-factor mapping to measuring recombination across whole chromos...

    Authors: M Wayne Davis, Marc Hammarlund, Tracey Harrach, Patrick Hullett, Shawn Olsen and Erik M Jorgensen

    Citation: BMC Genomics 2005 6:118

    Content type: Methodology article

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  6. The human genome carries a high load of proviral-like sequences, called Human Endogenous Retroviruses (HERVs), which are the genomic traces of ancient infections by active retroviruses. These elements are in m...

    Authors: Nathalie de Parseval, Gora Diop, Sandra Blaise, François Helle, Alexandre Vasilescu, Fumihiko Matsuda and Thierry Heidmann

    Citation: BMC Genomics 2005 6:117

    Content type: Research article

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  7. Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal di...

    Authors: Soumyadeep Nandi, Nipun Mehra, Andrew M Lynn and Alok Bhattacharya

    Citation: BMC Genomics 2005 6:116

    Content type: Research article

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  8. Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds wi...

    Authors: Wook Chang, David A Small, Freshteh Toghrol and William E Bentley

    Citation: BMC Genomics 2005 6:115

    Content type: Research article

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  9. The fibrinogen-like (FBG) domain, which consists of approximately 200 amino acid residues, has high sequence similarity to the C-terminal halves of fibrinogen β and γ chains. Fibrinogen-related proteins (FREPs...

    Authors: Xinguo Wang, Qin Zhao and Bruce M Christensen

    Citation: BMC Genomics 2005 6:114

    Content type: Research article

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  10. As a first step to explore the possible relationships existing between the effects of low oxygen pressure in the first trimester placenta and placental pathologies developing from mid-gestation, two subtracted...

    Authors: Daniel Vaiman, Françoise Mondon, Alexandra Garcès-Duran, Thérèse-Marie Mignot, Brigitte Robert, Régis Rebourcet, Hélène Jammes, Sonia T Chelbi, Frédérique Quetin, Geoffrey Marceau, Vincent Sapin, François Piumi, Jean-Louis Danan, Virginie Rigourd, Bruno Carbonne and Françoise Ferré

    Citation: BMC Genomics 2005 6:111

    Content type: Research article

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  11. Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets o...

    Authors: Rebecca Petersen Brown and Martin E Feder

    Citation: BMC Genomics 2005 6:110

    Content type: Research article

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  12. We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes...

    Authors: Juan Jose Lozano, Marta Soler, Raquel Bermudo, David Abia, Pedro L Fernandez, Timothy M Thomson and Angel R Ortiz

    Citation: BMC Genomics 2005 6:109

    Content type: Research article

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  13. At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a tra...

    Authors: Hiromi Nishida, Takahiro Suzuki, Hiroki Ookawa, Yasuhiro Tomaru and Yoshihide Hayashizaki

    Citation: BMC Genomics 2005 6:108

    Content type: Research article

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  14. Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid...

    Authors: Aleksei Krasnov, Heikki Koskinen, Sergey Afanasyev and Hannu Mölsä

    Citation: BMC Genomics 2005 6:107

    Content type: Research article

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  15. The cell-membrane G-protein coupled receptors (GPCRs) are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. ...

    Authors: Raghu Prasad Rao Metpally and Ramanathan Sowdhamini

    Citation: BMC Genomics 2005 6:106

    Content type: Research article

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  16. Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belong to the genetically close-knit Bacillus cereus sensu lato group, a family of rod-shaped Gram-positive bacteria. pAW63 is the first conjugative ...

    Authors: Géraldine A Van der Auwera, Lars Andrup and Jacques Mahillon

    Citation: BMC Genomics 2005 6:103

    Content type: Research article

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  17. DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed ...

    Authors: Yvonne CM Staal, Marcel HM van Herwijnen, Frederik J van Schooten and Joost HM van Delft

    Citation: BMC Genomics 2005 6:101

    Content type: Methodology article

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  18. To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcript...

    Authors: Isabelle Callebaut, Karine Prat, Edwige Meurice, Jean-Paul Mornon and Stanislas Tomavo

    Citation: BMC Genomics 2005 6:100

    Content type: Research article

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  19. Microarray studies of the same phenomenon in different labs often appear at variance because the published lists of regulated transcripts have disproportionately small intersections. We demonstrate that compar...

    Authors: Mayte Suárez-Fariñas, Scott Noggle, Michael Heke, Ali Hemmati-Brivanlou and Marcelo O Magnasco

    Citation: BMC Genomics 2005 6:99

    Content type: Methodology article

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  20. Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characteriz...

    Authors: R Turk, E Sterrenburg, EJ de Meijer, G-JB van Ommen, JT den Dunnen and PAC 't Hoen

    Citation: BMC Genomics 2005 6:98

    Content type: Research article

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  21. Loss of chromosome 11q defines a subset of high-stage aggressive neuroblastomas. Deletions are typically large and mapping efforts have thus far not lead to a well defined consensus region, which hampers the i...

    Authors: Katleen De Preter, Jo Vandesompele, Björn Menten, Philippa Carr, Heike Fiegler, Anders Edsjö, Nigel P Carter, Nurten Yigit, Wim Waelput, Nadine Van Roy, Scott Bader, Sven Påhlman and Frank Speleman

    Citation: BMC Genomics 2005 6:97

    Content type: Research article

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  22. Insecticidal toxins from Bacillus thuringiensis bind to receptors on midgut epithelial cells of susceptible insect larvae. Aminopeptidases N (APNs) from several insect species have been shown to be putative recep...

    Authors: Salvador Herrero, Tsanko Gechev, Petra L Bakker, William J Moar and Ruud A de Maagd

    Citation: BMC Genomics 2005 6:96

    Content type: Research article

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  23. DNA microarray technology is widely used to determine the expression levels of thousands of genes in a single experiment, for a broad range of organisms. Optimal design of immobilized nucleic acids has a direc...

    Authors: Yvan Charbonnier, Brian Gettler, Patrice François, Manuela Bento, Adriana Renzoni, Pierre Vaudaux, Werner Schlegel and Jacques Schrenzel

    Citation: BMC Genomics 2005 6:95

    Content type: Research article

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  24. Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyce...

    Authors: Moshe Havilio, Erez Y Levanon, Galia Lerman, Martin Kupiec and Eli Eisenberg

    Citation: BMC Genomics 2005 6:93

    Content type: Research article

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  25. Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenas...

    Authors: Harshavardhan Doddapaneni, Ranajit Chakraborty and Jagjit S Yadav

    Citation: BMC Genomics 2005 6:92

    Content type: Research article

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  26. Serial Analysis of Gene Expression (SAGE) and microarrays have found awidespread application, but much ambiguity exists regarding the evaluation of these technologies. Cross-platform utilization of gene expres...

    Authors: Fred van Ruissen, Jan M Ruijter, Gerben J Schaaf, Lida Asgharnegad, Danny A Zwijnenburg, Marcel Kool and Frank Baas

    Citation: BMC Genomics 2005 6:91

    Content type: Methodology article

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  27. Since transcription factors are often regulated at the post-transcriptional level, their activities, rather than expression levels may provide valuable information for investigating functions and their interac...

    Authors: Young-Lyeol Yang, Jason Suen, Mark P Brynildsen, Simon J Galbraith and James C Liao

    Citation: BMC Genomics 2005 6:90

    Content type: Research article

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  28. Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical ...

    Authors: Takayuki Katagiri, Celeste Kidd, Elizabeth Tomasino, Jesse T Davis, Cassandra Wishon, Justin E Stern, Karen L Carleton, Aimee E Howe and Thomas D Kocher

    Citation: BMC Genomics 2005 6:89

    Content type: Research article

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  29. The Japanese quail (Coturnix japonica) is both an animal model in biology and a commercial bird for egg and meat production. Modern research developments with this bird, however, have been slowed down by the limi...

    Authors: Francis Minvielle, Boniface B Kayang, Miho Inoue-Murayama, Mitsuru Miwa, Alain Vignal, David Gourichon, André Neau, Jean-Louis Monvoisin and Shin'ichi Ito

    Citation: BMC Genomics 2005 6:87

    Content type: Research article

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  30. The genus Corynebacterium includes Gram-positive microorganisms of great biotechnologically importance, such as Corynebacterium glutamicum and Corynebacterium efficiens, as well as serious human pathogens, such a...

    Authors: Iris Brune, Karina Brinkrolf, Jörn Kalinowski, Alfred Pühler and Andreas Tauch

    Citation: BMC Genomics 2005 6:86

    Content type: Research article

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  31. The lycophyte Selaginella moellendorffii is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150–200 million years earl...

    Authors: Jing-Ke Weng, Milos Tanurdzic and Clint Chapple

    Citation: BMC Genomics 2005 6:85

    Content type: Research article

    Published on:

  32. Although the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe dir...

    Authors: Anne-Sophie Carpentier, Bruno Torrésani, Alex Grossmann and Alain Hénaut

    Citation: BMC Genomics 2005 6:84

    Content type: Research article

    Published on:

  33. Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CA)n repeats exhibit length variability, display genome-wide distribution, and are abundant in the hu...

    Authors: Vineet K Sharma, Samir K Brahmachari and Srinivasan Ramachandran

    Citation: BMC Genomics 2005 6:83

    Content type: Research article

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  34. The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial i...

    Authors: Betsy M Martinez-Vaz, Yang Xie, Wei Pan and Arkady B Khodursky

    Citation: BMC Genomics 2005 6:81

    Content type: Methodology article

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  35. Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and pho...

    Authors: Jeremiah D Hackett, Todd E Scheetz, Hwan Su Yoon, Marcelo B Soares, Maria F Bonaldo, Thomas L Casavant and Debashish Bhattacharya

    Citation: BMC Genomics 2005 6:80

    Content type: Research article

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  36. Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases.

    Authors: Sudipto Saha, Manoj Bhasin and Gajendra PS Raghava

    Citation: BMC Genomics 2005 6:79

    Content type: Database

    Published on:

  37. Microarray-based Comparative Genomic Hybridization (M-CGH) has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the whole-genome level. Although conventional microarr...

    Authors: Eduardo N Taboada, Rey R Acedillo, Christian C Luebbert, Wendy A Findlay and John HE Nash

    Citation: BMC Genomics 2005 6:78

    Content type: Research article

    Published on:

  38. In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data qual...

    Authors: Sacha AFT van Hijum, Anne de Jong, Richard JS Baerends, Harma A Karsens, Naomi E Kramer, Rasmus Larsen, Chris D den Hengst, Casper J Albers, Jan Kok and Oscar P Kuipers

    Citation: BMC Genomics 2005 6:77

    Content type: Methodology article

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  39. Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the ...

    Authors: Amélie Paillisson, Sébastien Dadé, Isabelle Callebaut, Martine Bontoux, Rozenn Dalbiès-Tran, Daniel Vaiman and Philippe Monget

    Citation: BMC Genomics 2005 6:76

    Content type: Research article

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  40. Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The effective correlation of observed changes in gene expression with shared transcription r...

    Authors: Chris Cheadle, Jinshui Fan, Yoon S Cho-Chung, Thomas Werner, Jill Ray, Lana Do, Myriam Gorospe and Kevin G Becker

    Citation: BMC Genomics 2005 6:75

    Content type: Research article

    Published on:

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