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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more...

    Authors: Warren M Snelling, Eduardo Casas, Roger T Stone, John W Keele, Gregory P Harhay, Gary L Bennett and Timothy PL Smith
    Citation: BMC Genomics 2005 6:74
  38. Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cD...

    Authors: Jerilyn A Timlin, David M Haaland, Michael B Sinclair, Anthony D Aragon, M Juanita Martinez and Margaret Werner-Washburne
    Citation: BMC Genomics 2005 6:72
  39. Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the ...

    Authors: Rasmus Wernersson, Mikkel H Schierup, Frank G Jørgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Stærfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshøj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane KS Wong…
    Citation: BMC Genomics 2005 6:70
  40. The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing ...

    Authors: Pascale Anderle, Thierry Sengstag, David M Mutch, Martin Rumbo, Viviane Praz, Robert Mansourian, Mauro Delorenzi, Gary Williamson and Matthew-Alan Roberts
    Citation: BMC Genomics 2005 6:69

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