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  1. Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a singl...

    Authors: Junping Peng, Xiaobing Zhang, Jian Yang, Jing Wang, E Yang, Wen Bin, Candong Wei, Meisheng Sun and Qi Jin

    Citation: BMC Genomics 2006 7:218

    Content type: Research article

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  2. Aroclor 1254 is a well-known hepatotoxin and consists of a complex mixture of polychlorinated biphenyls (PCBs), some of which have the ability to activate the aryl hydrocarbon receptor (AhR) and other transcri...

    Authors: Susanne Reymann and Jürgen Borlak

    Citation: BMC Genomics 2006 7:217

    Content type: Research article

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  3. Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification...

    Authors: Robert Pinard, Alex de Winter, Gary J Sarkis, Mark B Gerstein, Karrie R Tartaro, Ramona N Plant, Michael Egholm, Jonathan M Rothberg and John H Leamon

    Citation: BMC Genomics 2006 7:216

    Content type: Research article

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  4. Effects on gene expression due to environmental or genetic changes can be easily measured using microarrays. However, indirect effects on expression can be substantial. The indirect effects of a perturbation n...

    Authors: Lin Tang, Xiao Liu and Neil D Clarke

    Citation: BMC Genomics 2006 7:215

    Content type: Research article

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  5. Complementary single-nucleotide polymorphisms (SNPs) may not be distributed equally between two DNA strands if the strands are functionally distinct, such as in transcribed genes. In introns, an excess of A↔G ...

    Authors: Hui-Qi Qu, Steve G Lawrence, Fan Guo, Jacek Majewski and Constantin Polychronakos

    Citation: BMC Genomics 2006 7:213

    Content type: Research article

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  6. The rodent specific reproductive homeobox (Rhox) gene cluster on the X chromosome has been reported to contain twelve homeobox-containing genes, Rhox1-12.

    Authors: Melany Jackson, Alistair J Watt, Philippe Gautier, Derek Gilchrist, Johanna Driehaus, Gerard J Graham, Jon Keebler, Franck Prugnolle, Philip Awadalla and Lesley M Forrester

    Citation: BMC Genomics 2006 7:212

    Content type: Research article

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  7. At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause tick-borne Lyme disease. Previous work including the genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a highly variable pla...

    Authors: Gernot Glöckner, Ulrike Schulte-Spechtel, Markus Schilhabel, Marius Felder, Jürgen Sühnel, Bettina Wilske and Matthias Platzer

    Citation: BMC Genomics 2006 7:211

    Content type: Research article

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  8. Mast cells are well established effectors of IgE-triggered allergic reactions and immune responses to parasitic infections. Recent studies indicate that mast cells may play roles in adaptive and innate immunit...

    Authors: Manikandan Jayapal, Hwee Kee Tay, Renji Reghunathan, Liang Zhi, Kah Kiong Chow, Mary Rauff and Alirio J Melendez

    Citation: BMC Genomics 2006 7:210

    Content type: Research article

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  9. Killer Immunoglobulin-like Receptors (KIR) are essential immuno-surveillance molecules. They are expressed on natural killer and T cells, and interact with human leukocyte antigens. KIR genes are highly polymo...

    Authors: Jennifer G Sambrook, Arman Bashirova, Hanne Andersen, Mike Piatak, George S Vernikos, Penny Coggill, Jeff D Lifson, Mary Carrington and Stephan Beck

    Citation: BMC Genomics 2006 7:209

    Content type: Research article

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  10. Mycelium-to-yeast transition in the human host is essential for pathogenicity by the fungus Paracoccidioides brasiliensis and both cell types are therefore critical to the establishment of paracoccidioidomycosis ...

    Authors: Rosângela V Andrade, Hugo C Paes, André M Nicola, Maria José A de Carvalho, Ana Lúcia Fachin, Renato S Cardoso, Simoneide S Silva, Larissa Fernandes, Silvana P Silva, Eduardo A Donadi, Elza T Sakamoto-Hojo, Geraldo AS Passos, Célia MA Soares, Marcelo M Brígido and Maria Sueli S Felipe

    Citation: BMC Genomics 2006 7:208

    Content type: Research article

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  11. Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this inform...

    Authors: Jakob Fredslund, Lene H Madsen, Birgit K Hougaard, Anna Marie Nielsen, David Bertioli, Niels Sandal, Jens Stougaard and Leif Schauser

    Citation: BMC Genomics 2006 7:207

    Content type: Research article

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  12. Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology ...

    Authors: Peter Wenzl, Haobing Li, Jason Carling, Meixue Zhou, Harsh Raman, Edie Paul, Phillippa Hearnden, Christina Maier, Ling Xia, Vanessa Caig, Jaroslava Ovesná, Mehmet Cakir, David Poulsen, Junping Wang, Rosy Raman, Kevin P Smith…

    Citation: BMC Genomics 2006 7:206

    Content type: Research article

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  13. Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and r...

    Authors: Sascha Mormann, Alexander Lömker, Christian Rückert, Lars Gaigalat, Andreas Tauch, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2006 7:205

    Content type: Research article

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  14. Uncoupling protein 2 (UCP2) belongs to the superfamily of mitochondrial anion carriers that dissociate the respiratory chain from ATP synthesis. It has been determined that UCP2 plays a role in several physiol...

    Authors: Issa Coulibaly, Scott A Gahr, Yniv Palti, Jianbo Yao and Caird E Rexroad III

    Citation: BMC Genomics 2006 7:203

    Content type: Research article

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  15. The Aβ-binding alcohol dehydrogenase/17β-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's dise...

    Authors: Alexandra T Marques, Agostinho Antunes, Pedro A Fernandes and Maria J Ramos

    Citation: BMC Genomics 2006 7:202

    Content type: Research article

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  16. For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, ...

    Authors: Elke Clynen, Jurgen Huybrechts, Peter Verleyen, Arnold De Loof and Liliane Schoofs

    Citation: BMC Genomics 2006 7:201

    Content type: Research article

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  17. With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding...

    Authors: Barbara L Hass-Jacobus, Montona Futrell-Griggs, Brian Abernathy, Rick Westerman, Jose-Luis Goicoechea, Joshua Stein, Patricia Klein, Bonnie Hurwitz, Bin Zhou, Fariborz Rakhshan, Abhijit Sanyal, Navdeep Gill, Jer-Young Lin, Jason G Walling, Mei Zhong Luo, Jetty Siva S Ammiraju…

    Citation: BMC Genomics 2006 7:199

    Content type: Research article

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  18. Mucins are large glycoproteins that cover epithelial surfaces of the body. All mucins contain at least one PTS domain, a region rich in proline, threonine and serine. Mucins are also characterized by von Wille...

    Authors: Tiange Lang, Gunnar C Hansson and Tore Samuelsson

    Citation: BMC Genomics 2006 7:197

    Content type: Research article

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  19. The major royal jelly proteins/yellow (MRJP/YELLOW) family possesses several physiological and chemical functions in the development of Apis mellifera and Drosophila melanogaster. Each protein of the family has a...

    Authors: Ai-Hua Xia, Qing-Xiang Zhou, Lin-Lin Yu, Wei-Guo Li, Yong-Zhu Yi, Yao-Zhou Zhang and Zhi-Fang Zhang

    Citation: BMC Genomics 2006 7:195

    Content type: Research article

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  20. Comparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species...

    Authors: Laurent Schibler, Anne Roig, Marie-Françoise Mahe, Pascal Laurent, Hélène Hayes, François Rodolphe and Edmond P Cribiu

    Citation: BMC Genomics 2006 7:194

    Content type: Research article

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  21. The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" wa...

    Authors: Juan Antonio Vizcaíno, Francisco Javier González, M Belén Suárez, José Redondo, Julian Heinrich, Jesús Delgado-Jarana, Rosa Hermosa, Santiago Gutiérrez, Enrique Monte, Antonio Llobell and Manuel Rey

    Citation: BMC Genomics 2006 7:193

    Content type: Research article

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  22. Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conserv...

    Authors: Heikki J Ryynänen and Craig R Primmer

    Citation: BMC Genomics 2006 7:192

    Content type: Methodology article

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  23. Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear ...

    Authors: S Manjulata Devi, Irshad Ahmed, Aleem A Khan, Syed Asad Rahman, Ayesha Alvi, Leonardo A Sechi and Niyaz Ahmed

    Citation: BMC Genomics 2006 7:191

    Content type: Research article

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  24. Although microscopic diagnosis has been playing the decisive role in cancer diagnostics, there have been cases in which it does not satisfy the clinical need. Differential diagnosis of malignant and benign thy...

    Authors: Naoto Yukinawa, Shigeyuki Oba, Kikuya Kato, Kazuya Taniguchi, Kyoko Iwao-Koizumi, Yasuhiro Tamaki, Shinzaburo Noguchi and Shin Ishii

    Citation: BMC Genomics 2006 7:190

    Content type: Methodology article

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  25. Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolut...

    Authors: Takeshi Ara, Fabrice Lopez, William Ritchie, Philippe Benech and Daniel Gautheret

    Citation: BMC Genomics 2006 7:189

    Content type: Research article

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  26. Doublecortin (DCX) domains serve as protein-interaction platforms. Mutations in members of this protein superfamily are linked to several genetic diseases. Mutations in the human DCX gene result in abnormal neuro...

    Authors: Orly Reiner, Frédéric M Coquelle, Bastian Peter, Talia Levy, Anna Kaplan, Tamar Sapir, Irit Orr, Naama Barkai, Gregor Eichele and Sven Bergmann

    Citation: BMC Genomics 2006 7:188

    Content type: Research article

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  27. Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. Ther...

    Authors: Chad L Myers, Daniel R Barrett, Matthew A Hibbs, Curtis Huttenhower and Olga G Troyanskaya

    Citation: BMC Genomics 2006 7:187

    Content type: Research article

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  28. Nanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the Archaea and provided a model of choice to study the genom...

    Authors: Sabyasachi Das, Sandip Paul, Sumit K Bag and Chitra Dutta

    Citation: BMC Genomics 2006 7:186

    Content type: Research article

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  29. Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation o...

    Authors: Ryan L Parr, Jennifer Maki, Brian Reguly, Gabriel D Dakubo, Andrea Aguirre, Roy Wittock, Kerry Robinson, John P Jakupciak and Robert E Thayer

    Citation: BMC Genomics 2006 7:185

    Content type: Research article

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  30. In the recent years a strong resemblance has been observed between the insect immune system and the mammalian innate immune mechanisms suggesting their common origin. Among the insects, only the dipterans (Drosop...

    Authors: Archana S Gandhe, K P Arunkumar, Serene H John and J Nagaraju

    Citation: BMC Genomics 2006 7:184

    Content type: Research article

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  31. DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DN...

    Authors: Luke O Dannenberg and Howard J Edenberg

    Citation: BMC Genomics 2006 7:181

    Content type: Research article

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  32. Currently most pastoral farmers rely on anthelmintic drenches to control gastrointestinal parasitic nematodes in sheep. Resistance to anthelmintics is rapidly increasing in nematode populations such that on so...

    Authors: Allan M Crawford, Korena A Paterson, Ken G Dodds, Cristina Diez Tascon, Penny A Williamson, Meredith Roberts Thomson, Stewart A Bisset, Anne E Beattie, Gordon J Greer, Richard S Green, Roger Wheeler, Richard J Shaw, Kevin Knowler and John C McEwan

    Citation: BMC Genomics 2006 7:178

    Content type: Research article

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  33. Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage sit...

    Authors: Dorota Retelska, Christian Iseli, Philipp Bucher, C Victor Jongeneel and Felix Naef

    Citation: BMC Genomics 2006 7:176

    Content type: Research article

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  34. Transcriptomic techniques are now being applied in ecotoxicology and toxicology to measure the impact of stressors and develop understanding of mechanisms of toxicity. Microarray technology in particular offer...

    Authors: Lars-Henrik Heckmann, Richard Connon, Thomas H Hutchinson, Steve J Maund, Richard M Sibly and Amanda Callaghan

    Citation: BMC Genomics 2006 7:175

    Content type: Research article

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  35. High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candid...

    Authors: Nathalie Pavy, Lee S Parsons, Charles Paule, John MacKay and Jean Bousquet

    Citation: BMC Genomics 2006 7:174

    Content type: Research article

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  36. Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been seq...

    Authors: Huan Nie, Fan Yang, Xiaobing Zhang, Jian Yang, Lihong Chen, Jing Wang, Zhaohui Xiong, Junping Peng, Lilian Sun, Jie Dong, Ying Xue, Xingye Xu, Shuxia Chen, Zhijian Yao, Yan Shen and Qi Jin

    Citation: BMC Genomics 2006 7:173

    Content type: Research article

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  37. The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relativ...

    Authors: Jochen Hecht, Heiner Kuhl, Stefan A Haas, Sebastian Bauer, Albert J Poustka, Jasmin Lienau, Hanna Schell, Asita C Stiege, Volkhard Seitz, Richard Reinhardt, Georg N Duda, Stefan Mundlos and Peter N Robinson

    Citation: BMC Genomics 2006 7:172

    Content type: Research article

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  38. Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing o...

    Authors: Boris A Legault, Arantxa Lopez-Lopez, Jose Carlos Alba-Casado, W Ford Doolittle, Henk Bolhuis, Francisco Rodriguez-Valera and R Thane Papke

    Citation: BMC Genomics 2006 7:171

    Content type: Research article

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