Genome Biology - Most viewed articlesMost viewed articles in last 30 days from Genome Biology (ISSN 1465-6906) published by BioMed CentralCalling on a million minds for community annotation in WikiProteins- May 28, 2008 WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and.http://genomebiology.com/2008/9/5/R89 Sequence-based prediction of protein-protein interactions by means of codon usage- May 23, 2008 We introduce a novel approach to predict interaction of two proteins solely by analyzing their coding sequences. We found that similarity in codon usage is a strong predictor of protein-protein interactions and, for high specificity values, is as sensitive as the most powerful current prediction methods. Furthermore, combining codon usage with other predictors results in a 75% increase in sensitivity at a precision of 50%, compared to prediction without considering codon usage.http://genomebiology.com/2008/9/5/R87 Gene expression profiling of human prostate cancer stem cells reveals a pro-inflammatory phenotype and the importance of extracellular matrix interact- May 20, 2008 Background: The tumor-initiating capacity of many cancers is considered to reside in a small subpopulation of cells (cancer stem cells). We have previously shown that rare prostate epithelial cells with a CD133+21hi phenotype have the properties of prostate cancer stem cells. We have compared gene expression in these cells relative to their normal and differentiated (CD133-21low) counterparts, resulting in an informative cancer stem cell gene-expression signature. Results: Cell cultures were...http://genomebiology.com/2008/9/5/R83 Individual mRNA expression profiles reveal the effects of specific microRNAs- May 16, 2008 Background: MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level. We sought, therefore, to determine whether a general lowering of predicted target gene mRNA expression by endogenous miRNAs was detectable within microarray gene expression...http://genomebiology.com/2008/9/5/R82 Loss of genes implicated in gastric function during platypus evolution- May 15, 2008 Background: The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria, which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique opportunity to illuminate some aspects of the biology and evolution of these animals. Results: We show that several genes implicated in food digestion in the stomach have been deleted or inactivated in platypus. Comparison with other vertebrate genomes revealed that the main.http://genomebiology.com/2008/9/5/R81 CpG island density and its correlations with genomic features in mammalian genomes- May 13, 2008 Background: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level among mammalian genomes and of their correlations with other genome features. Results: In this study, we performed a systematic...http://genomebiology.com/2008/9/5/R79 The genome sequence of the model ascomycete fungus Podospora anserina- May 6, 2008 Background: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. Results: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcriptionsplicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and...http://genomebiology.com/2008/9/5/R77 |