New directions in biomedical text annotation: definitions, guidelines and corpus construction
BMC Bioinformatics 2006, 7:356 (25 July 2006)
Transposable element derived DNaseI-hypersensitive sites in the human genome
Biology Direct 2006, 1:20 (20 July 2006)
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains
Genome Biology 2006, 7:R60 (19 July 2006)
A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history.
PHOG: a database of supergenomes built from proteome complements
BMC Evolutionary Biology 2006, 6:52 (22 June 2006)
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease
BMC Bioinformatics 2006, 7:291 (8 June 2006)
Method of predicting Splice Sites based on signal interactions
Biology Direct 2006, 1:10 (3 April 2006)
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
Biology Direct 2006, 1:7 (16 March 2006)
Computational analysis shows that CRISPR repeats and associated Cas proteins in prokaryotes might act in conjunction as a RNA-silencing mechanism against plasmids and viruses, similar to the eukaryotic RNA-interference system.
Fold classification based on secondary structure – how much is gained by including loop topology?
BMC Structural Biology 2006, 6:3 (8 March 2006)
Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models
Biology Direct 2006, 1:6 (17 February 2006)
Computational models with thermodynamic and composition features improve siRNA design
BMC Bioinformatics 2006, 7:65 (12 February 2006)
Analyzing siRNAs from the literature generated a model for silencing efficiency based on three key thermodynamic and compositional parameters including U-rich 5' ends, which was used to predict optimal targets across the human transcriptome.
Rate of promoter class turn-over in yeast evolution
BMC Evolutionary Biology 2006, 6:14 (10 February 2006)
Analysis of sequence data from five yeast species indicates that promoter sequences of genes evolve at surprising rates, with some switching class from TATA-containing to non-TATA containing, while in others the position of the TATA box changes.
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
BMC Cancer 2006, 6:36 (9 February 2006)
Genome-wide analysis of probable somatic mutations in normal and malignant tissue suggests that positive selection for gain of function may affect a number of genes during tumorigenesis.
A novel cell immunoassay to measure survival of motor neurons protein in blood cells
BMC Neurology 2006, 6:6 (1 February 2006)
Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection
Biology Direct 2006, 1:4 (31 January 2006)
A community experiment with fully open and published peer review
Biology Direct 2006, 1:1 (31 January 2006)
SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study
BMC Medical Informatics and Decision Making 2005, 5:37 (1 December 2005)
SLIM, a slider-bar web interface for searching PubMed and MEDLINE, allows users easily to vary limits, filters and MeSH terms, thereby significantly enhancing search focus and refinement
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
BMC Evolutionary Biology 2005, 5:57 (20 October 2005)
A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts
BMC Microbiology 2005, 5:35 (14 June 2005)
A comprehensive census of bacterial and archaeal signal transduction sequences reveals that the complexity of signalling systems can generally be correlated with the phylogenetic position and lifestyle of the organism, and that Wolinella succinogenes has the highest 'IQ' as measured by the number of encoded signal transducers.
A draft framework for measuring progress towards the development of a national health information infrastructure
BMC Medical Informatics and Decision Making 2005, 5:14 (13 June 2005)
Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes
BMC Immunology 2005, 6:10 (10 June 2005)
Expression in yeast of human activation-induced deaminase (AID), which is involved in the generation of antibody diversity, results in mutations that are mainly at G-C base pairs and in sequence contexts that are similar to those of somatically mutated G-C pairs in immunoglobulin genes.
GENETAG: a tagged corpus for gene/protein named entity recognition
BMC Bioinformatics 2005, 6(Suppl 1):S3 (24 May 2005)
askMEDLINE: a free-text, natural language query tool for MEDLINE/PubMed
BMC Medical Informatics and Decision Making 2005, 5:5 (10 March 2005)
A new plain text search tool for clinicians, researchers and other information seekers which will translate a question into an efficient search of MEDLINE/PubMed.
Structural similarity of loops in protein families: toward the understanding of protein evolution
BMC Evolutionary Biology 2005, 5:10 (3 February 2005)
Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
Genome Biology 2004, 6:R4 (20 December 2004)
Acetylcholine receptor type ligand-gated ion channels are well known in animals. Homologs are identified in prokaryotes that may act as chemotactic receptors.
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models
BMC Evolutionary Biology 2004, 4:32 (9 September 2004)