Toward Automatic Reconstruction of a Highly Resolved Tree of Life
An automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains is developed, revealing interdomain discrepancies in taxonomic classification and suggesting a thermophilic last universal common ancestor.
SMART 4.0: towards genomic data integration
Improvements in SMART are centred on the integration of data from completed metazoan genomes, and the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.
Recent improvements to the SMART domain-based sequence annotation resource
The SMART database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats and new advanced queries provide direct access to the SMART relational database using SQL.
Nonsense‐mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways
- D. Gatfield, Leonie Unterholzner, F. Ciccarelli, P. Bork, E. Izaurralde
- BiologyEMBO Journal
- 1 August 2003
The findings reveal that despite conservation of the NMD machinery, different mechanisms have evolved to discriminate premature from natural stop codons in metazoa.
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens
The Network of Cancer Genes is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles, and annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, and protein function and essentiality.
Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia
Comparative sequence analysis indicates that spartin shares similarity with molecules involved in endosomal trafficking and with spastin, a molecule implicated in microtubule interaction that is commonly mutated in HSP.
Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates
- I. Fumasoni, N. Meani, Davide Rambaldi, G. Scafetta, M. Alcalay, F. Ciccarelli
- BiologyBMC Evolutionary Biology
- 4 October 2007
Comparison of PRDM genes shows that molecular evolution of paralogs correlates with their expression pattern; gene diversification is obtained through massive genomic rearrangements; and splicing modification contributes to the functional specialization of novel genes.
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
The taxonomic specificity of this domain and its predicted extracellular position could make it an interesting target for designing new drugs against some highly pathogenic bacteria.