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  2. Adjacent gene pairs in the yeast genome have a tendency to express concurrently. Sharing of regulatory elements within the intergenic region of those adjacent gene pairs was often considered the major mechanis...

    Authors: Huai-Kuang Tsai, Cindy PC Su, Mei-Yeh J Lu, Ching-Hua Shih and Daryi Wang
    Citation: BMC Genomics 2007 8:352
    Content type: Research article Published on:

  3. Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of n...

    Authors: Vijayaraj Nagarajan and Mohamed O Elasri
    Citation: BMC Genomics 2007 8:351
    Content type: Database Published on:

  4. Cadmium is a persistent pollutant that threatens most biological organisms, including cyanobacteria that support a large part of the biosphere. Using a multifaceted approach, we have investigated the global re...

    Authors: Laetitia Houot, Martin Floutier, Benoit Marteyn, Magali Michaut, Antoine Picciocchi, Pierre Legrain, Jean-Christophe Aude, Corinne Cassier-Chauvat and Franck Chauvat
    Citation: BMC Genomics 2007 8:350
    Content type: Research article Published on:

  5. The aim of this study was to analyze the genomic diversity of several Tropheryma whipplei strains by microarray-based comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples r...

    Authors: My-Van La, Nicolas Crapoulet, Pascal Barbry, Didier Raoult and Patricia Renesto
    Citation: BMC Genomics 2007 8:349
    Content type: Research article Published on:

  9. Chromosomal instability (CIN) is the most prevalent type of genomic instability in gastric tumours, but its role in malignant transformation of the gastric mucosa is still obscure. In the present study, we set...

    Authors: Tineke E Buffart, Beatriz Carvalho, Thomas Mons, Rui M Reis, Cátia Moutinho, Paula Silva, Nicole CT van Grieken, Michael Vieth, Manfred Stolte, Cornelis JH van de Velde, Evelin Schrock, Anja Matthaei, Bauke Ylstra, Fátima Carneiro and Gerrit A Meijer
    Citation: BMC Genomics 2007 8:345
    Content type: Research article Published on:

  10. Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal inte...

    Authors: Neil S Graham, Martin R Broadley, John P Hammond, Philip J White and Sean T May
    Citation: BMC Genomics 2007 8:344
    Content type: Research article Published on:

  11. The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomic...

    Authors: Shin-Ju Park, Yong-Seok Lee and Ui Wook Hwang
    Citation: BMC Genomics 2007 8:343
    Content type: Research article Published on:

  12. The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequenc...

    Authors: Paulo Navarro-Costa, Luísa Pereira, Cíntia Alves, Leonor Gusmão, Carmen Proença, Pedro Marques-Vidal, Tiago Rocha, Sónia C Correia, Sónia Jorge, António Neves, Ana P Soares, Joaquim Nunes, Carlos Calhaz-Jorge, António Amorim, Carlos E Plancha and João Gonçalves
    Citation: BMC Genomics 2007 8:342
    Content type: Research article Published on:

  13. Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail Folsomia candida (Collembola) is an accepted standard t...

    Authors: Martijn JTN Timmermans, Muriel E de Boer, Benjamin Nota, Tjalf E de Boer, Janine Mariën, Rene M Klein-Lankhorst, Nico M van Straalen and Dick Roelofs
    Citation: BMC Genomics 2007 8:341
    Content type: Database Published on:

  14. In the most general sense, studies involving global analysis of gene expression aim to provide a comprehensive catalog of the components involved in the production of recognizable cellular phenotypes. These st...

    Authors: Roger A Barthelson, Georgina M Lambert, Cheryl Vanier, Ronald M Lynch and David W Galbraith
    Citation: BMC Genomics 2007 8:340
    Content type: Research article Published on:

  15. Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mit...

    Authors: Sarah MC Flynn and Steven M Carr
    Citation: BMC Genomics 2007 8:339
    Content type: Research article Published on:

  16. The superfamily of G protein-coupled receptors (GPCRs) is one of the largest within most mammals. GPCRs are important targets for pharmaceuticals and the rat is one of the most widely used model organisms in b...

    Authors: David E Gloriam, Robert Fredriksson and Helgi B Schiöth
    Citation: BMC Genomics 2007 8:338
    Content type: Research article Published on:

  17. Since its discovery around deep sea hydrothermal vents of the Galapagos Rift about 30 years ago, the chemoautotrophic symbiosis between the vestimentiferan tubeworm Riftia pachyptila and its symbiotic sulfide-oxi...

    Authors: Sophie Sanchez, Stéphane Hourdez and François H Lallier
    Citation: BMC Genomics 2007 8:337
    Content type: Research article Published on:

  18. Gene expression patterns in the brain are strongly influenced by the severity and duration of physiological stress at the time of death. This agonal effect, if not well controlled, can lead to spurious finding...

    Authors: Jun Z Li, Fan Meng, Larisa Tsavaler, Simon J Evans, Prabhakara V Choudary, Hiroaki Tomita, Marquis P Vawter, David Walsh, Vida Shokoohi, Tisha Chung, William E Bunney, Edward G Jones, Huda Akil, Stanley J Watson and Richard M Myers
    Citation: BMC Genomics 2007 8:336
    Content type: Research article Published on:

  19. The silver homologue(SILV) gene plays a major role in melanosome development. SILV is a target for studies concerning melanoma diagnostics and therapy in humans as well as on skin and coat color pigmentation in m...

    Authors: Christa Kuehn and Rosemarie Weikard
    Citation: BMC Genomics 2007 8:335
    Content type: Research article Published on:

  20. Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism,...

    Authors: Eric CH Ho, Matt J Cahill and Barry J Saville
    Citation: BMC Genomics 2007 8:334
    Content type: Research article Published on:

  21. Deep transcriptome analysis will underpin a large fraction of post-genomic biology. 'Closed' technologies, such as microarray analysis, only detect the set of transcripts chosen for analysis, whereas 'open' e.g. ...

    Authors: Lawrence Hene, Vattipally B Sreenu, Mai T Vuong, S Hussain I Abidi, Julian K Sutton, Sarah L Rowland-Jones, Simon J Davis and Edward J Evans
    Citation: BMC Genomics 2007 8:333
    Content type: Methodology article Published on:

  22. It becomes increasingly clear that our current taxonomy of clinical phenotypes is mixed with molecular heterogeneity. Of vital importance for refined clinical practice and improved intervention strategies is t...

    Authors: Wei Zhang, Li Li, Xia Li, Wei Jiang, Jianmin Huo, Yadong Wang, Meihua Lin and Shaoqi Rao
    Citation: BMC Genomics 2007 8:332
    Content type: Research article Published on:

  23. Gene expression profiles based on microarray data have been suggested by many studies as potential molecular prognostic indexes of breast cancer. However, due to the confounding effect of clinical background, ...

    Authors: Zhe Zhang, Dechang Chen and David A Fenstermacher
    Citation: BMC Genomics 2007 8:331
    Content type: Research article Published on:

  24. Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Dep...

    Authors: Jessica A Schlueter, Jer-Young Lin, Shannon D Schlueter, Iryna F Vasylenko-Sanders, Shweta Deshpande, Jing Yi, Majesta O'Bleness, Bruce A Roe, Rex T Nelson, Brian E Scheffler, Scott A Jackson and Randy C Shoemaker
    Citation: BMC Genomics 2007 8:330
    Content type: Research article Published on:

  25. Providing quantitative microarray data that is sensitive to very small differences in target sequence would be a useful tool in any number of venues where a sample can consist of a multiple related sequences p...

    Authors: Xujing Wang, Shuang Jia, Lisa Meyer, Maryam B Yassai, Yuri N Naumov, Jack Gorski and Martin J Hessner
    Citation: BMC Genomics 2007 8:329
    Content type: Methodology article Published on:

  26. Fast, efficiently growing animals have increased protein synthesis and/or reduced protein degradation relative to slow, inefficiently growing animals. Consequently, minimizing the energetic cost of protein tur...

    Authors: Mohamed Salem, Jeff Silverstein, Caird E Rexroad III and Jianbo Yao
    Citation: BMC Genomics 2007 8:328
    Content type: Research article Published on:

  28. The saprophagous and coprophagous maggots of the drone fly Eristalis tenax (Insecta, Diptera) have evolved the unique ability to survive in aquatic habitats with extreme microbial stress such as drains, sewage po...

    Authors: Boran Altincicek and Andreas Vilcinskas
    Citation: BMC Genomics 2007 8:326
    Content type: Research article Published on:

  29. Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail...

    Authors: Mikko Arvas, Teemu Kivioja, Alex Mitchell, Markku Saloheimo, David Ussery, Merja Penttila and Stephen Oliver
    Citation: BMC Genomics 2007 8:325
    Content type: Research article Published on:

  31. DNA polymerase γ(Pol-γ) has been shown to be essential for maintenance of the mitochondrial genome (mtDNA) in the petite-positive budding yeast Saccharomyces cerevisiae. Budding yeast cells lacking mitochondria e...

    Authors: Zhaoqing Chu, Juntao Li, Majid Eshaghi, R Krishna Murthy Karuturi, Kui Lin and Jianhua Liu
    Citation: BMC Genomics 2007 8:323
    Content type: Research article Published on:

  32. SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.

    Authors: Jennifer A McCann, Enrique M Muro, Claire Palmer, Gareth Palidwor, Christopher J Porter, Miguel A Andrade-Navarro and Michael A Rudnicki
    Citation: BMC Genomics 2007 8:322
    Content type: Methodology article Published on:

  33. In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 9...

    Authors: Phil Latreille, Stacie Norton, Barry S Goldman, John Henkhaus, Nancy Miller, Brad Barbazuk, Helge B Bode, Creg Darby, Zijin Du, Steve Forst, Sophie Gaudriault, Brad Goodner, Heidi Goodrich-Blair and Steven Slater
    Citation: BMC Genomics 2007 8:321
    Content type: Methodology article Published on:

  34. Leucine-rich repeats (LRRs) are highly versatile and evolvable protein-ligand interaction motifs found in a large number of proteins with diverse functions, including innate immunity and nervous system develop...

    Authors: Jackie Dolan, Karen Walshe, Samantha Alsbury, Karsten Hokamp, Sean O'Keeffe, Tatsuya Okafuji, Suzanne FC Miller, Guy Tear and Kevin J Mitchell
    Citation: BMC Genomics 2007 8:320
    Content type: Research article Published on:

  35. Marfan syndrome (MFS) is a heritable connective tissue disorder caused by mutations in the fibrillin-1 gene. This syndrome constitutes a significant identifiable subtype of aortic aneurysmal disease, accountin...

    Authors: Zizhen Yao, Jochen C Jaeger, Walter L Ruzzo, Cecile Z Morale, Mary Emond, Uta Francke, Dianna M Milewicz, Stephen M Schwartz and Eileen R Mulvihill
    Citation: BMC Genomics 2007 8:319
    Content type: Research article Published on:

  36. The transforming growth factors (TGF)-β, TGF-β1, TGF-β2 and TGF-β3, and their receptors [TβRI, TβRII, TβRIII (betaglycan)] elicit pleiotropic functions in the prostate. Although expression of the ligands and r...

    Authors: Lutz Konrad, Jonas A Scheiber, Elke Völck-Badouin, Marcel M Keilani, Leslie Laible, Heidrun Brandt, Ansgar Schmidt, Gerhard Aumüller and Rainer Hofmann
    Citation: BMC Genomics 2007 8:318
    Content type: Research article Published on:

  37. Teleost fish have seven paralogous clusters of Hox genes stemming from two complete genome duplications early in vertebrate evolution, and an additional genome duplication during the evolution of ray-finned fi...

    Authors: Simone Hoegg, Jeffrey L Boore, Jennifer V Kuehl and Axel Meyer
    Citation: BMC Genomics 2007 8:317
    Content type: Research article Published on:

  38. Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and mRNA like ncRNAs in eukaryotes. T...

    Authors: Stefan E Seemann, Michael J Gilchrist, Ivo L Hofacker, Peter F Stadler and Jan Gorodkin
    Citation: BMC Genomics 2007 8:316
    Content type: Research article Published on:

  39. Giant panda is rare and endangered species endemic to China. The low rates of reproductive success and infectious disease resistance have severely hampered the development of captive and wild populations of th...

    Authors: Chang-Jun Zeng, Hui-Juan Pan, Shao-Bin Gong, Jian-Qiu Yu, Qiu-Hong Wan and Sheng-Guo Fang
    Citation: BMC Genomics 2007 8:315
    Content type: Research article Published on:

  40. We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an Eco RI- and a Bam HI-digested library) and conducted an in silico analysis to characterize the obtained seque...

    Authors: Yoshitaka Suetsugu, Hiroshi Minami, Michihiko Shimomura, Shun-ichi Sasanuma, Junko Narukawa, Kazuei Mita and Kimiko Yamamoto
    Citation: BMC Genomics 2007 8:314
    Content type: Research article Published on:

  41. The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses,...

    Authors: Jonathan J Rios, Andrey A Perelygin, Maureen T Long, Teri L Lear, Andrey A Zharkikh, Margo A Brinton and David L Adelson
    Citation: BMC Genomics 2007 8:313
    Content type: Research article Published on:

  42. The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (ter...

    Authors: Nicol Siegel, Simone Hoegg, Walter Salzburger, Ingo Braasch and Axel Meyer
    Citation: BMC Genomics 2007 8:312
    Content type: Research article Published on:

  43. Lungworms of the genus Dictyocaulus (family Dictyocaulidae) are parasitic nematodes of major economic importance. They cause pathological effects and clinical disease in various ruminant hosts, particularly in yo...

    Authors: Shoba Ranganathan, Shivashankar H Nagaraj, Min Hu, Christina Strube, Thomas Schnieder and Robin B Gasser
    Citation: BMC Genomics 2007 8:311
    Content type: Research article Published on:

  44. High resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high res...

    Authors: Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang, James E Womack, Paul Stothard and Stephen S Moore
    Citation: BMC Genomics 2007 8:310
    Content type: Research article Published on:

  45. Microsporidia, parasitic fungi-related eukaryotes infecting many cell types in a wide range of animals (including humans), represent a serious health threat in immunocompromised patients. The 2.9 Mb genome of ...

    Authors: Diego Miranda-Saavedra, Michael JR Stark, Jeremy C Packer, Christian P Vivares, Christian Doerig and Geoffrey J Barton
    Citation: BMC Genomics 2007 8:309
    Content type: Research article Published on:

  46. The Burkholderia cepacia complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cyst...

    Authors: Aymeric Menard, Paulina Estrada de los Santos, Arnault Graindorge and Benoit Cournoyer
    Citation: BMC Genomics 2007 8:308
    Content type: Research article Published on:

  47. Synthesis of the Staphylococcus aureus peptidoglycan pentaglycine interpeptide bridge is catalyzed by the nonribosomal peptidyl transferases FemX, FemA and FemB. Inactivation of the femAB operon reduces the inter...

    Authors: Judith Hübscher, Andrea Jansen, Oliver Kotte, Juliane Schäfer, Paul A Majcherczyk, Llinos G Harris, Gabriele Bierbaum, Matthias Heinemann and Brigitte Berger-Bächi
    Citation: BMC Genomics 2007 8:307
    Content type: Research article Published on:

  48. Melon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential tra...

    Authors: Daniel Gonzalez-Ibeas, José Blanca, Cristina Roig, Mireia González-To, Belén Picó, Verónica Truniger, Pedro Gómez, Wim Deleu, Ana Caño-Delgado, Pere Arús, Fernando Nuez, Jordi Garcia-Mas, Pere Puigdomènech and Miguel A Aranda
    Citation: BMC Genomics 2007 8:306
    Content type: Research article Published on:

  49. Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease...

    Authors: Gui Youn Lee, Woo Ick Yang, Hei Cheul Jeung, Sang Chul Kim, Min Young Seo, Chan Hee Park, Hyun Cheol Chung and Sun Young Rha
    Citation: BMC Genomics 2007 8:305
    Content type: Research article Published on:

  50. Cultivated chickpea (Cicer arietinum) has a narrow genetic base making it difficult for breeders to produce new elite cultivars with durable resistance to major biotic and abiotic stresses. As an alternative to g...

    Authors: Nitin L Mantri, Rebecca Ford, Tristan E Coram and Edwin CK Pang
    Citation: BMC Genomics 2007 8:303
    Content type: Research article Published on:

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BMC Genomics

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