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  1. Benzo [a]pyrene (B[a]P) exposure induces DNA adducts at all stages of spermatogenesis and in testis, and removal of these lesions is less efficient in nucleotide excision repair deficient Xpc-/- mice than in wild...

    Authors: Nicole Verhofstad, Jeroen LA Pennings, Conny ThM van Oostrom, Jan van Benthem, Frederik J van Schooten, Harry van Steeg and Roger WL Godschalk
    Citation: BMC Genomics 2010 11:333
    Content type: Research article Published on:

  2. The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate ...

    Authors: Luis David Alcaraz, Gabriel Moreno-Hagelsieb, Luis E Eguiarte, Valeria Souza, Luis Herrera-Estrella and Gabriela Olmedo
    Citation: BMC Genomics 2010 11:332
    Content type: Research article Published on:

  3. The neonatal bovine mammary fat pad (MFP) surrounding the mammary parenchyma (PAR) is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones...

    Authors: Paola Piantoni, Massimo Bionaz, Daniel E Graugnard, Kristy M Daniels, Robin E Everts, Sandra L Rodriguez-Zas, Harris A Lewin, Hurley L Hurley, Michael Akers and Juan J Loor
    Citation: BMC Genomics 2010 11:331
    Content type: Research article Published on:

  4. Although analysis of microRNAs (miRNAs) by DNA microarrays is gaining in popularity, these new technologies have not been adequately validated. We examined within and between platform reproducibility of four m...

    Authors: Carole L Yauk, Andrea Rowan-Carroll, John DH Stead and Andrew Williams
    Citation: BMC Genomics 2010 11:330
    Content type: Research article Published on:

  5. The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3)-β-linked glucose with a (1 → 6)-β-glycosyl branch on ev...

    Authors: Jochen Schmid, Dirk Müller-Hagen, Thomas Bekel, Laura Funk, Ulf Stahl, Volker Sieber and Vera Meyer
    Citation: BMC Genomics 2010 11:329
    Content type: Research article Published on:

  6. Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD ...

    Authors: Minghui Wang, Tianye Jia, Ning Jiang, Lin Wang, Xiaohua Hu and Zewei Luo
    Citation: BMC Genomics 2010 11:328
    Content type: Methodology article Published on:

  7. Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expec...

    Authors: Michael Hackenberg, Guillermo Barturen, Pedro Carpena, Pedro L Luque-Escamilla, Christopher Previti and José L Oliver
    Citation: BMC Genomics 2010 11:327
    Content type: Research article Published on:

  8. Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias.

    Authors: Javier Gayán, José J Galan, Antonio González-Pérez, María Eugenia Sáez, María Teresa Martínez-Larrad, Carina Zabena, M Carmen Rivero, Ana Salinas, Reposo Ramírez-Lorca, Francisco J Morón, Jose Luis Royo, Concha Moreno-Rey, Juan Velasco, José M Carrasco, Eva Molero, Carolina Ochoa…
    Citation: BMC Genomics 2010 11:326
    Content type: Research article Published on:

  9. Rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic N2-fixing environment. It is emerging as a genetically amenable model organism for molec...

    Authors: Yih-Kuang Lu, Jeremiah Marden, Mira Han, Wesley D Swingley, Stephen D Mastrian, Sugata Roy Chowdhury, Jicheng Hao, Tamer Helmy, Sun Kim, Ahmet A Kurdoglu, Heather J Matthies, David Rollo, Paul Stothard, Robert E Blankenship, Carl E Bauer and Jeffrey W Touchman
    Citation: BMC Genomics 2010 11:325
    Content type: Research article Published on:

  10. The cancer stem cell (CSC) hypothesis proposes that a population of tumor cells bearing stem cell properties is responsible for the origin and maintenance of tumors. Normal and cancer stem cells possess the ab...

    Authors: Maria Ana Duhagon, Elaine M Hurt, Jose R Sotelo-Silveira, Xiaohu Zhang and William L Farrar
    Citation: BMC Genomics 2010 11:324
    Content type: Research article Published on:

  11. The GeneChip®Medicago Genome Array, developed for Medicago truncatula, is a suitable platform for transcript profiling in tetraploid alfalfa [Medicago sativa (L.) subsp. sativa]. However, previous research involv...

    Authors: S Samuel Yang, Wayne Wenzhong Xu, Mesfin Tesfaye, JoAnn FS Lamb, Hans-Joachim G Jung, Kathryn A VandenBosch, Carroll P Vance and John W Gronwald
    Citation: BMC Genomics 2010 11:323
    Content type: Research article Published on:

  12. The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple pr...

    Authors: Shuwei Li, Ching-Hua Shih and Michael H Kohn
    Citation: BMC Genomics 2010 11:322
    Content type: Research article Published on:

  13. Invasive amoebiasis, caused by infection with the human parasite Entamoeba histolytica remains a major cause of morbidity and mortality in some less-developed countries. Genetically E. histolytica exhibits a numb...

    Authors: Derek M Huntley, Ioannis Pandis, Sarah A Butcher and John P Ackers
    Citation: BMC Genomics 2010 11:321
    Content type: Research article Published on:

  14. MicroRNAs (miRNAs) are a large class of tiny non-coding RNAs (~22-24 nt) that regulate diverse biological processes at the posttranscriptional level by controlling mRNA stability or translation. As a molecular...

    Authors: Limei Qin, Yaosheng Chen, Yuna Niu, Weiquan Chen, Qiwei Wang, Shuqi Xiao, Anning Li, Ying Xie, Jing Li, Xiao Zhao, Zuyong He and Delin Mo
    Citation: BMC Genomics 2010 11:320
    Content type: Research article Published on:

  16. Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating e...

    Authors: Vladimir N Babenko, Igor V Makunin, Irina V Brusentsova, Elena S Belyaeva, Daniil A Maksimov, Stepan N Belyakin, Peter Maroy, Lyubov A Vasil'eva and Igor F Zhimulev
    Citation: BMC Genomics 2010 11:318
    Content type: Research article Published on:

  17. Powdery mildew and rust fungi are widespread, serious pathogens that depend on developing haustoria in the living plant cells. Haustoria are separated from the host cytoplasm by a plant cell-derived extrahaust...

    Authors: Dale Godfrey, Henrik Böhlenius, Carsten Pedersen, Ziguo Zhang, Jeppe Emmersen and Hans Thordal-Christensen
    Citation: BMC Genomics 2010 11:317
    Content type: Research article Published on:

  18. In bacteria, small non-coding RNAs (sRNAs) have been recognized as important regulators of various cellular processes. Approximately 200 bacterial sRNAs in total have been reported. However, very few sRNAs hav...

    Authors: Rui-Ping Jiang, Dong-Jie Tang, Xiao-Lin Chen, Yong-Qiang He, Jia-Xun Feng, Bo-Le Jiang, Guang-Tao Lu, Min Lin and Ji-Liang Tang
    Citation: BMC Genomics 2010 11:316
    Content type: Research article Published on:

  19. High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has be...

    Authors: Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi and Nori Kurata
    Citation: BMC Genomics 2010 11:315
    Content type: Research article Published on:

  20. One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological di...

    Authors: Yuki Ishikawa, Yasukazu Okada, Asano Ishikawa, Hitoshi Miyakawa, Shigeyuki Koshikawa and Toru Miura
    Citation: BMC Genomics 2010 11:314
    Content type: Research article Published on:

  22. Anopheles gambiae has been shown to change its global gene expression patterns upon Plasmodium infection. While many alterations are directly related to the mosquito's innate immune response, parasite invasion is...

    Authors: Rute C Félix, Pie Müller, Vera Ribeiro, Hilary Ranson and Henrique Silveira
    Citation: BMC Genomics 2010 11:312
    Content type: Research article Published on:

  23. Pseudomonas putida is a model organism for bioremediation because of its remarkable metabolic versatility, extensive biodegradative functions, and ubiquity in contaminated soil environments. To further the unders...

    Authors: Dorothea K Thompson, Karuna Chourey, Gene S Wickham, Stephanie B Thieman, Nathan C VerBerkmoes, Bing Zhang, Andrea T McCarthy, Matt A Rudisill, Manesh Shah and Robert L Hettich
    Citation: BMC Genomics 2010 11:311
    Content type: Research article Published on:

  24. Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversi...

    Authors: Shawn T O'Neil, Jason DK Dzurisin, Rory D Carmichael, Neil F Lobo, Scott J Emrich and Jessica J Hellmann
    Citation: BMC Genomics 2010 11:310
    Content type: Research article Published on:

  26. The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documen...

    Authors: Tatiana V Tatarinova, Nickolai N Alexandrov, John B Bouck and Kenneth A Feldmann
    Citation: BMC Genomics 2010 11:308
    Content type: Research article Published on:

  27. Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism...

    Authors: Zhengyuan Wang, Sahar Abubucker, John Martin, Richard K Wilson, John Hawdon and Makedonka Mitreva
    Citation: BMC Genomics 2010 11:307
    Content type: Research article Published on:

  28. The molecular mechanisms leading to a fully differentiated thyrocite are still object of intense study even if it is well known that thyroglobulin, thyroperoxidase, NIS and TSHr are the marker genes of thyroid...

    Authors: Roberto Nitsch, Valeria Di Dato, Alessandra di Gennaro, Tiziana de Cristofaro, Serena Abbondante, Mario De Felice, Mariastella Zannini and Roberto Di Lauro
    Citation: BMC Genomics 2010 11:306
    Content type: Research article Published on:

  31. The small brown planthopper (Laodelphax striatellus) is an important agricultural pest that not only damages rice plants by sap-sucking, but also acts as a vector that transmits rice stripe virus (RSV), which can...

    Authors: Fujie Zhang, Hongyan Guo, Huajun Zheng, Tong Zhou, Yijun Zhou, Shengyue Wang, Rongxiang Fang, Wei Qian and Xiaoying Chen
    Citation: BMC Genomics 2010 11:303
    Content type: Research article Published on:

  33. The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries i...

    Authors: Giang TH Vu, Peter DS Caligari and Mike J Wilkinson
    Citation: BMC Genomics 2010 11:301
    Content type: Methodology article Published on:

  34. Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we...

    Authors: Julie Lamontagne, Maxime Béland, Anik Forest, Alexandra Côté-Martin, Najib Nassif, Fadi Tomaki, Ignacio Moriyón, Edgardo Moreno and Eustache Paramithiotis
    Citation: BMC Genomics 2010 11:300
    Content type: Research article Published on:

  35. Anaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute ~50% of t...

    Authors: Marnix H Medema, Miaomiao Zhou, Sacha AFT van Hijum, Jolein Gloerich, Hans JCT Wessels, Roland J Siezen and Marc Strous
    Citation: BMC Genomics 2010 11:299
    Content type: Research article Published on:

  36. Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of co...

    Authors: Candy Kumps, Nadine Van Roy, Lien Heyrman, Dirk Goossens, Jurgen Del-Favero, Rosa Noguera, Jo Vandesompele, Frank Speleman and Katleen De Preter
    Citation: BMC Genomics 2010 11:298
    Content type: Research article Published on:

  37. Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play...

    Authors: Patricia Jumbo-Lucioni, Julien F Ayroles, Michelle Moses Chambers, Katherine W Jordan, Jeff Leips, Trudy FC Mackay and Maria De Luca
    Citation: BMC Genomics 2010 11:297
    Content type: Research article Published on:

  38. High-throughput sequencing technologies offer new perspectives for biomedical, agronomical and evolutionary research. Promising progresses now concern the application of these technologies to large-scale studi...

    Authors: Maxime Galan, Emmanuel Guivier, Gilles Caraux, Nathalie Charbonnel and Jean-François Cosson
    Citation: BMC Genomics 2010 11:296
    Content type: Methodology article Published on:

  39. The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource. Though valuable information is available, data can be difficult to access, compare and integrate ...

    Authors: Giulietta M Spudich and Xosé M Fernández-Suárez
    Citation: BMC Genomics 2010 11:295
    Content type: Correspondence Published on:

  40. Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating t...

    Authors: Benoît Ballester, Nathan Johnson, Glenn Proctor and Paul Flicek
    Citation: BMC Genomics 2010 11:294
    Content type: Methodology article Published on:

  41. The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derive...

    Authors: Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney and Paul Flicek
    Citation: BMC Genomics 2010 11:293
    Content type: Database Published on:

  42. Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig...

    Authors: Yu Gao, Laurence Flori, Jérome Lecardonnel, Diane Esquerré, Zhi-Liang Hu, Angélique Teillaud, Gaëtan Lemonnier, Francois Lefèvre, Isabelle P Oswald and Claire Rogel-Gaillard
    Citation: BMC Genomics 2010 11:292
    Content type: Research article Published on:

  43. Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known...

    Authors: Xizeng Mao, Victor Olman, Rhona Stuart, Ian T Paulsen, Brian Palenik and Ying Xu
    Citation: BMC Genomics 2010 11:291
    Content type: Research article Published on:

  44. Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (C...

    Authors: David A Fitzpatrick, Peadar O'Gaora, Kevin P Byrne and Geraldine Butler
    Citation: BMC Genomics 2010 11:290
    Content type: Research article Published on:

  45. Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, becau...

    Authors: Liang Jiang, Qiong Liu and Jiazuan Ni
    Citation: BMC Genomics 2010 11:289
    Content type: Research article Published on:

  46. MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post - transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polyme...

    Authors: Candida Vaz, Hafiz M Ahmad, Pratibha Sharma, Rashi Gupta, Lalit Kumar, Ritu Kulshreshtha and Alok Bhattacharya
    Citation: BMC Genomics 2010 11:288
    Content type: Research article Published on:

  47. AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP da...

    Authors: Margot Paris, Benjamin Bonnes, Gentile Francesco Ficetola, Bénédicte N Poncet and Laurence Després
    Citation: BMC Genomics 2010 11:287
    Content type: Methodology article Published on:

  49. The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by m...

    Authors: Soumya A Vemuganti, Fernando Pardo-Manuel de Villena and Deborah A O'Brien
    Citation: BMC Genomics 2010 11:285
    Content type: Research article Published on:

  50. Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwi...

    Authors: João Fadista, Bo Thomsen, Lars-Erik Holm and Christian Bendixen
    Citation: BMC Genomics 2010 11:284
    Content type: Research article Published on:

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BMC Genomics

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