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  1. Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metal...

    Authors: Jessica E Butler, Qiang He, Kelly P Nevin, Zhili He, Jizhong Zhou and Derek R Lovley
    Citation: BMC Genomics 2007 8:180
    Content type: Research article Published on:

  2. It has become evident that host cells react to recombinant protein production with a variety of metabolic and intrinsic stresses such as the unfolded protein response (UPR) pathway. Additionally, environmental...

    Authors: Brigitte Gasser, Michael Maurer, Jari Rautio, Michael Sauer, Anamitra Bhattacharyya, Markku Saloheimo, Merja Penttilä and Diethard Mattanovich
    Citation: BMC Genomics 2007 8:179
    Content type: Research article Published on:

  3. Cotton, as an allopolyploid species, contains homoeologous A and D subgenomes. The study of the homoeologous (duplicated) segments or chromosomes can facilitate insight into the evolutionary process of polyplo...

    Authors: Kai Wang, Wangzhen Guo and Tianzhen Zhang
    Citation: BMC Genomics 2007 8:178
    Content type: Research article Published on:

  4. EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. ...

    Authors: Ping Li, Eric Peatman, Shaolin Wang, Jinian Feng, Chongbo He, Puttharat Baoprasertkul, Peng Xu, Huseyin Kucuktas, Samiran Nandi, Benjaporn Somridhivej, Jerry Serapion, Micah Simmons, Cemal Turan, Lei Liu, William Muir, Rex Dunham…
    Citation: BMC Genomics 2007 8:177
    Content type: Research article Published on:

  5. The ciliate protozoan Ichthyophthirius multifiliis (Ich) is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of t...

    Authors: Jason W Abernathy, Peng Xu, Ping Li, De-Hai Xu, Huseyin Kucuktas, Phillip Klesius, Covadonga Arias and Zhanjiang Liu
    Citation: BMC Genomics 2007 8:176
    Content type: Research article Published on:

  6. Plants respond to low temperature through an intricately coordinated transcriptional network. The CBF/DREB-regulated network of genes has been shown to play a prominent role in freeze-tolerance of Arabidopsis thr...

    Authors: Chen Cheng, Kil-Young Yun, Habtom W Ressom, Bijayalaxmi Mohanty, Vladimir B Bajic, Yulin Jia, Song Joong Yun and Benildo G de los Reyes
    Citation: BMC Genomics 2007 8:175
    Content type: Research article Published on:

  7. The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful t...

    Authors: Linda A Raubeson, Rhiannon Peery, Timothy W Chumley, Chris Dziubek, H Matthew Fourcade, Jeffrey L Boore and Robert K Jansen
    Citation: BMC Genomics 2007 8:174
    Content type: Research article Published on:

  9. MicroRNAs (miRNAs) are a novel class of short double stranded RNA that mediate the post-transcriptional regulation of gene expression. Previous studies have implicated changes in miRNA expression in the regula...

    Authors: Andrew E Williams, Mark M Perry, Sterghios A Moschos and Mark A Lindsay
    Citation: BMC Genomics 2007 8:172
    Content type: Research article Published on:

  10. Staphylococcus aureus, a leading cause of chronic or acute infections, is traditionally considered an extracellular pathogen despite repeated reports of S. aureus internalization by a variety of non-myeloid cells...

    Authors: Christian Garzoni, Patrice Francois, Antoine Huyghe, Sabine Couzinet, Caroline Tapparel, Yvan Charbonnier, Adriana Renzoni, Sacha Lucchini, Daniel P Lew, Pierre Vaudaux, William L Kelley and Jacques Schrenzel
    Citation: BMC Genomics 2007 8:171
    Content type: Research article Published on:

  11. A number of studies have shown that peptidases and in particular cysteine peptidases constitute major pathogenicity factors in Entamoeba histolytica. Recent studies have suggested that a considerable number of ge...

    Authors: Manuela Tillack, Laura Biller, Henriette Irmer, Michelle Freitas, Maria A Gomes, Egbert Tannich and Iris Bruchhaus
    Citation: BMC Genomics 2007 8:170
    Content type: Research article Published on:

  12. Currently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and particularly plants. Using gender-spec...

    Authors: Carrie-Ann Whittle, Meghna R Malik and Joan E Krochko
    Citation: BMC Genomics 2007 8:169
    Content type: Research article Published on:

  14. Genomic copy number variants (CNVs) involving >1 kb of DNA have recently been found to be widely distributed throughout the human genome. They represent a newly recognized form of DNA variation in normal popul...

    Authors: Ying Qiao, Xudong Liu, Chansonette Harvard, Sarah L Nolin, W Ted Brown, Maryam Koochek, Jeanette JA Holden, ME Suzanne Lewis and Evica Rajcan-Separovic
    Citation: BMC Genomics 2007 8:167
    Content type: Research article Published on:

  16. Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, th...

    Authors: Vincent A Funari, Allen Day, Deborah Krakow, Zachary A Cohn, Zugen Chen, Stanley F Nelson and Daniel H Cohn
    Citation: BMC Genomics 2007 8:165
    Content type: Research article Published on:

  18. The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however ha...

    Authors: Joanna Kiraga, Pawel Mackiewicz, Dorota Mackiewicz, Maria Kowalczuk, Przemysław Biecek, Natalia Polak, Kamila Smolarczyk, Miroslaw R Dudek and Stanislaw Cebrat
    Citation: BMC Genomics 2007 8:163
    Content type: Research article Published on:

  19. Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and...

    Authors: Ozan Gundogdu, Stephen D Bentley, Matt T Holden, Julian Parkhill, Nick Dorrell and Brendan W Wren
    Citation: BMC Genomics 2007 8:162
    Content type: Research article Published on:

  22. New technologies have enabled genome-wide association studies to be conducted with hundreds of thousands of genotyped SNPs. Several different first-generation genome-wide panels of SNPs have been commercialize...

    Authors: Reedik Mägi, Arne Pfeufer, Mari Nelis, Alexandre Montpetit, Andres Metspalu and Maido Remm
    Citation: BMC Genomics 2007 8:159
    Content type: Research article Published on:

  23. Filamentous fungi such as Aspergillus niger have a high capacity secretory system and are therefore widely exploited for the industrial production of native and heterologous proteins. However, in most cases the y...

    Authors: Thomas Guillemette, Noël NME van Peij, Theo Goosen, Karin Lanthaler, Geoffrey D Robson, Cees AMJJ van den Hondel, Hein Stam and David B Archer
    Citation: BMC Genomics 2007 8:158
    Content type: Research article Published on:

  24. The eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding...

    Authors: Jonas Quilang, Shaolin Wang, Ping Li, Jason Abernathy, Eric Peatman, Yongping Wang, Lingling Wang, Yaohua Shi, Richard Wallace, Ximing Guo and Zhanjiang Liu
    Citation: BMC Genomics 2007 8:157
    Content type: Research article Published on:

  25. Phosphorus is an essential element for all life forms. However, it is limiting in most ecological environments where cyanobacteria inhabit. Elucidation of the phosphorus assimilation pathways in cyanobacteria ...

    Authors: Zhengchang Su, Victor Olman and Ying Xu
    Citation: BMC Genomics 2007 8:156
    Content type: Research article Published on:

  26. Meat technological traits (i.e. meat pH, water retention and color) are important considerations for improving further processing of chicken meat. These quality traits were originally characterized in experime...

    Authors: Javad Nadaf, Hélène Gilbert, Frédérique Pitel, Cécile M Berri, Katia Feve, Catherine Beaumont, Michel J Duclos, Alain Vignal, Tom E Porter, Jean Simon, Samuel E Aggrey, Larry A Cogburn and Elisabeth Le Bihan-Duval
    Citation: BMC Genomics 2007 8:155
    Content type: Research article Published on:

  27. Individuals in the same species are assumed to share the same genomic set. However, it is not unusual to find an orthologous gene only in small subset of the species, and recent genomic studies suggest that st...

    Authors: Jing Ding, Hitoshi Araki, Qiang Wang, Pengfei Zhang, Sihai Yang, Jian-Qun Chen and Dacheng Tian
    Citation: BMC Genomics 2007 8:154
    Content type: Research article Published on:

  28. High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing...

    Authors: Fang Liu, Tor-Kristian Jenssen, Jeff Trimarchi, Claudio Punzo, Connie L Cepko, Lucila Ohno-Machado, Eivind Hovig and Winston Patrick Kuo
    Citation: BMC Genomics 2007 8:153
    Content type: Research article Published on:

  30. Uterine temporal and dose-dependent histopathologic, morphometric and gene expression responses to the selective estrogen receptor modulator tamoxifen (TAM) were comprehensively examined to further elucidate i...

    Authors: Cora J Fong, Lyle D Burgoon, Kurt J Williams, Agnes L Forgacs and Timothy R Zacharewski
    Citation: BMC Genomics 2007 8:151
    Content type: Research article Published on:

  31. The early stages of the immune response are regulated by key cytokines including both interleukin 1β (IL-1β) and interferon-γ (IFN-γ) which stimulate panels of responsive genes via conserved signal transductio...

    Authors: Samuel AM Martin, Jun Zou, Dominic F Houlihan and Christopher J Secombes
    Citation: BMC Genomics 2007 8:150
    Content type: Research article Published on:

  32. Vitellogenin is a well established biomarker for estrogenic exposure in fish. However, effects on gonadal differentiation at concentrations of estrogen not sufficient to give rise to a measurable vitellogenin ...

    Authors: Lina Gunnarsson, Erik Kristiansson, Lars Förlin, Olle Nerman and D G Joakim Larsson
    Citation: BMC Genomics 2007 8:149
    Content type: Research article Published on:

  33. The increasing use of DNA microarrays in biomedical research, toxicogenomics, pharmaceutical development, and diagnostics has focused attention on the reproducibility and reliability of microarray measurements...

    Authors: Robert A Ach, Arno Floore, Bo Curry, Vladimir Lazar, Annuska M Glas, Rob Pover, Anya Tsalenko, Hugues Ripoche, Fatima Cardoso, Mahasti Saghatchian d'Assignies, Laurakay Bruhn and Laura J Van't Veer
    Citation: BMC Genomics 2007 8:148
    Content type: Research article Published on:

  34. It has been estimated that more than 1 million workers in the United States are exposed to cobalt. Occupational exposure to 59 Co occurs mainly via inhalation and leads to various lung diseases. Cobalt is classif...

    Authors: Veronique Malard, Frederic Berenguer, Odette Prat, Sylvie Ruat, Gerard Steinmetz and Eric Quemeneur
    Citation: BMC Genomics 2007 8:147
    Content type: Research article Published on:

  35. Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two acr...

    Authors: Raazesh Sainudiin, Andrew G Clark and Richard T Durrett
    Citation: BMC Genomics 2007 8:146
    Content type: Research article Published on:

  36. Puccinia striiformis is a plant pathogenic fungus causing stripe rust, one of the most important diseases on cereal crops and grasses worldwide. However, little is know about its genome and genes involved in the ...

    Authors: Peng Ling, Meinan Wang, Xianming Chen and Kimberly Garland Campbell
    Citation: BMC Genomics 2007 8:145
    Content type: Research article Published on:

  37. An essential first step in the genomic characterisation of a new species, in this case Atlantic halibut (Hippoglossus hippoglossus), is the generation of EST information. This forms the basis for subsequent micro...

    Authors: Susan E Douglas, Leah C Knickle, Jennifer Kimball and Michael E Reith
    Citation: BMC Genomics 2007 8:144
    Content type: Research article Published on:

  38. Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. Moreover, transcriptomic analyses have demonstrate...

    Authors: José Viñuelas, Federica Calevro, Didier Remond, Jacques Bernillon, Yvan Rahbé, Gérard Febvay, Jean-Michel Fayard and Hubert Charles
    Citation: BMC Genomics 2007 8:143
    Content type: Research article Published on:

  39. More than half of the approximately 500,000 women diagnosed with cervical cancer worldwide each year will die from this disease. Investigation of genes expressed in precancer lesions compared to those expresse...

    Authors: Ashleen Shadeo, Raj Chari, Greg Vatcher, Jennifer Campbell, Kim M Lonergan, Jasenka Matisic, Dirk van Niekerk, Thomas Ehlen, Dianne Miller, Michele Follen, Wan L Lam and Calum MacAulay
    Citation: BMC Genomics 2007 8:142
    Content type: Research article Published on:

  40. Death receptors on the cell surface and the interacting cytosolic molecules, adaptors and initiator caspases, are essential as core components of the extrinsic apoptotic signaling pathway. While the apoptotic ...

    Authors: Kazuhiro Sakamaki, Masami Nozaki, Katsuya Kominami and Yutaka Satou
    Citation: BMC Genomics 2007 8:141
    Content type: Research article Published on:

  41. The development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most r...

    Authors: Li-Jen Su, Ching-Wei Chang, Yu-Chung Wu, Kuang-Chi Chen, Chien-Ju Lin, Shu-Ching Liang, Chi-Hung Lin, Jacqueline Whang-Peng, Shih-Lan Hsu, Chen-Hsin Chen and Chi-Ying F Huang
    Citation: BMC Genomics 2007 8:140
    Content type: Methodology article Published on:

  43. TSEs are a group of fatal neurodegenerative diseases occurring in man and animals. They are caused by prions, alternatively folded forms of the endogenous prion protein, encoded by PRNP. Since differences in the ...

    Authors: Evelyne Lampo, Mario Van Poucke, Karine Hugot, Hélène Hayes, Alex Van Zeveren and Luc J Peelman
    Citation: BMC Genomics 2007 8:138
    Content type: Research article Published on:

  44. The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represe...

    Authors: Monique Turmel, Christian Otis and Claude Lemieux
    Citation: BMC Genomics 2007 8:137
    Content type: Research article Published on:

  45. Basic region-leucine zipper (bZIP) proteins are a class of transcription factors (TFs) that play diverse roles in eukaryotes. Malfunctions in these proteins lead to cancer and various other diseases. For detai...

    Authors: Taewoo Ryu, Juhyun Jung, Sunjae Lee, Ho Jung Nam, Sun Woo Hong, Jae Wook Yoo, Dong-ki Lee and Doheon Lee
    Citation: BMC Genomics 2007 8:136
    Content type: Database Published on:

  46. EST-PCR markers normally represent specific products from target genes, and are therefore effective tools for genetic analysis. However, because wheat is an allohexaploid plant, PCR products derived from homoe...

    Authors: Goro Ishikawa, Junichi Yonemaru, Mika Saito and Toshiki Nakamura
    Citation: BMC Genomics 2007 8:135
    Content type: Research article Published on:

  47. With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST) sequence data available for both model and non-model organism is growing exponentially. While t...

    Authors: Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Lin Fang, Yuansheng Liu, Kikia Carter, Jason S Webb and Jeffrey FD Dean
    Citation: BMC Genomics 2007 8:134
    Content type: Database Published on:

  48. The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of ...

    Authors: Sean Thomas, LL Isadora Trejo Martinez, Scott J Westenberger and Nancy R Sturm
    Citation: BMC Genomics 2007 8:133
    Content type: Research article Published on:

  49. Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significa...

    Authors: Kankshita Swaminathan, Kranthi Varala and Matthew E Hudson
    Citation: BMC Genomics 2007 8:132
    Content type: Research article Published on:

  50. Previous studies of individual genes have shown that in a self-enforcing way, dimethylation at histone 3 lysine 9 (dimethyl-H3K9) and DNA methylation cooperate to maintain a repressive mode of inactive genes. ...

    Authors: Jiejun Wu, Shu-Huei Wang, Dustin Potter, Joseph C Liu, Laura T Smith, Yue-Zhong Wu, Tim H-M Huang and Christoph Plass
    Citation: BMC Genomics 2007 8:131
    Content type: Research article Published on:

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BMC Genomics

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