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A selection of evaluations from Faculty of 1000 covering gene expression patterns in the Xenopus embryo; detecting SNPs; circadian clock mutations in Arabidopsis; radiation resistant genes in Deinococcus; Mycobac...
The abnormalities found in human Down syndrome (trisomy 21) have been thought to result from increased expression of genes on chromosome 21 because of their higher gene dosage. Now, several groups have shown t...
Recent studies show that active regulatory regions of the yeast genome have a lower density of nucleosomes than other regions, and that there is an inverse correlation between nucleosome density and the transc...
Most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. But as well as acting on the information content of genes, natural selection may also act directly on nu...
We have developed a systematic approach to generating cDNA clones containing full-length open reading frames (ORFs), exploiting knowledge of gene structure from genomic sequence. Each ORF was amplified by PCR ...
Analyzing proteins in the context of all available genome and transcript sequence data has the potential to reveal functional properties not accessible through protein sequence analysis alone. To analyze the i...
Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy ...
Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explor...
A report on The Biology of Genomes meeting, Cold Spring Harbor, USA, 12-16 May 2004.
Homologous recombination between alleles or non-allelic paralogous sequences does not occur uniformly but is concentrated in 'hotspots' with high recombination rates. Recent studies of these hotspots show that...
We report the use of the cross-linking drug hexamethylphosphoramide (HMPA), which introduces small deletions, as a mutagen suitable for reverse genetics in the model organism Drosophila melanogaster. A compatible...
We have developed a screening technology for the identification of short-lived proteins. A green fluorescent protein (GFP)-fusion cDNA library was generated for monitoring degradation kinetics. Cells expressin...
Transcripts in a GeneChip type microarray is represented by multiple independent short oligonucleotide probes. One widely used approach is to compute a model based unified expression index for the transcript w...
Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled w...
Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predi...
A report on the third Complex Trait Consortium meeting, Bar Harbor, USA, 6-9 July 2004.
A report on the second International Conference on Legume Genomics and Genetics, organized jointly with the fifth AEP European Conference on Grain Legumes "Legumes for the benefit of agriculture, nutrition and...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative developme...
Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of actual sequences. This only re...
Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely ...
Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human tissues, we analyzed the splici...
Given that microRNAs select their targets by nucleotide base-pairing, it follows that it should be possible to find microRNA targets computationally. There has been considerable progress, but assessing success...
We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We se...
MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates mic...
A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some miRNAs and their time- and tissue-...
A report of the 29th Congress of the Federation of European Biochemical Societies (FEBS), Warsaw, Poland, 26 June-1 July 2004.
Cyclooxygenases (COXs) catalyze the rate-limiting step in the production of prostaglandins, bioactive compounds involved in processes such as fever and sensitivity to pain, and are the target of aspirin-like d...
Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, hav...
We demonstrate that the process of identifying differentially expressed genes in microarray studies with small sample sizes can be substantially improved by extracting information from a large number of datase...
Comprehensive, tissue-specific, microarray analysis is a potent tool for the identification of tightly defined expression patterns that might be missed in whole-organism scans. We applied such an analysis to Dros...
Pseudogenes often manifest themselves as disabled copies of known genes. In prokaryotes, it was generally believed (with a few well-known exceptions) that they were rare.
A report on the Keystone Symposium 'Structural Genomics', held concurrently with the 'Frontiers in Structural Biology' symposium, Snowbird, USA, 13-19 April 2004.
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