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Eukaryotic genomes are full of long terminal repeat (LTR) retrotransposons. Although most LTR retrotransposons have common structural features and encode similar genes, there is nonetheless considerable divers...
Optimal use of genome sequences and gene-expression resources requires powerful phenotyping platforms, including those for systematic analysis of metabolite composition. The most used technologies for metaboli...
By comparing two fully sequenced genomes of Chlamydia trachomatis using competitive hybridization on DNA microarrays, a logarithmic correlation was demonstrated between the signal ratio of the arrays and the 75-9...
Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable...
A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
The availability of the rat genome sequence, and detailed three-way comparison of the rat, mouse and human genomes, is revealing a great deal about mammalian genome evolution. Together with recent developments...
Multiprotein complexes play an essential role in many cellular processes. But our knowledge of the mechanism of their formation, regulation and lifetimes is very limited. We investigated transcriptional regula...
Although the precise aims differ between the various international structural genomics initiatives currently aiming to illuminate the universe of protein folds, many selectively target protein families for whi...
Resistance to thyroid hormone (RTH) is caused by mutations of the thyroid hormone receptor β (TRβ) gene. To understand the transcriptional program underlying TRβ mutant-induced phenotypic expression of RTH, cD...
The importance of alternative splicing in many genomes has raised interesting questions about its role in evolution. We previously reported that alternative splicing appears to be associated with an increased ...
Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and are found in organisms ranging from bacteria to humans. In eukaryotes,...
ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-...
A selection of evaluations from Faculty of 1000 covering chromosomal rearrangements and mental retardation, peptide-MHC microarrays, antimicrobial drug discovery, a core set of Arabidopsis accessions and comparin...
Microarray-driven gene-expression profiles are generally produced and analyzed for a single specific experimental model. We have assessed an analytical approach that simultaneously evaluates multi-species expe...
Phyletic patterns denote the presence and absence of orthologous genes in completely sequenced genomes and are used to infer functional links between genes, on the assumption that genes involved in the same pa...
A report on the Keystone Symposium 'Comparative Genomics of Plants', Taos, USA, 4-9 March 2004.
Studies of mammalian prion diseases such as bovine spongiform encephalopathy have suggested that different strains consist of prion proteins with different conformations. Two recent studies of yeast prions hav...
A selection of evaluations from Faculty of 1000 covering microarrays to study antibiotic resistance, identifying SUMO substrate proteins, parallel SNP genotyping, intron origin and evolution and variation in CpG-...
A report on the First International Symposium of the Austrian Proteomics Platform, Seefeld, Austria, 26-29 January 2004.
A large amount of repetitive DNA complicates the assembly of the maize genome sequence. Genome-filtration techniques, such as methylation-filtration and high-CoT separation, enrich gene sequences in genomic li...
The advent of whole-genome sequencing has led to methods that infer protein function and linkages. We have combined four such algorithms (phylogenetic profile, Rosetta Stone, gene neighbor and gene cluster) in...
Recent sequence-structure studies on P-loop-fold NTPases have substantially advanced the existing understanding of their evolution and functional diversity. These studies provide a framework for characterizati...
Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect...
Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the an...
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