Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text
BMC Bioinformatics 2013, 14:146 (30 April 2013)
Biology direct: celebrating 7 years of open, published peer review
Biology Direct 2013, 8:11 (30 April 2013)
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
Biology Direct 2013, 8:9 (22 April 2013)
The genome of the first terrestrial member of the
Nanoarchaeota and comparisons with the marine Nanoarchaeum equitans reveals stages in the evolution of archaeal symbiosis and parasitism
Seeing the Tree of Life behind the phylogenetic forest
BMC Biology 2013, 11:46 (15 April 2013)
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites
Plant Methods 2013, 9:12 (11 April 2013)
This article describes a software tool that can identify transcription factor binding sites from amongst large collections of promoter sequences by integrating a number of different approaches. The method is able to identify more over-represented binding site sequences than other common approaches.
Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family
Virology Journal 2013, 10:106 (4 April 2013)
Clusters of orthologous genes for mimiviruses (mimiCOGs) were constructed and used for comprehensive phylogenetic analysis of large dsDNA viruses, finding that two Phycodnaviruses actually belong in the Mimiviridae.
Genome-wide associations of signaling pathways in glioblastoma multiforme
BMC Medical Genomics 2013, 6:11 (28 March 2013)
PubChem3D: conformer ensemble accuracy
Journal of Cheminformatics 2013, 5:1 (7 January 2013)
Lower short- and long-term mortality associated with overweight and obesity in a large cohort study of adult intensive care unit patients
Critical Care 2012, 16:R235 (18 December 2012)
Overweight and obese patients have significantly lower mortality rates than normal weight patients, both 30 days and one year after ICU admission, supporting the theory that obesity has a “protective effect”.
AID/APOBEC cytosine deaminase induces genome-wide kataegis
Biology Direct 2012, 7:47 (18 December 2012)
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
Biology Direct 2012, 7:46 (14 December 2012)
Analysis of the updated set of orthologs in 120 archaeal genomes reveals a complex history of gene exchange with no major "highways" of horizontal gene transfer.
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes
Biology Direct 2012, 7:40 (14 November 2012)
ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons
Biology Direct 2012, 7:39 (12 November 2012)
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
Journal of Cheminformatics 2012, 4:28 (7 November 2012)
In the latest article in the PubChem3D series, the effects of employing multiple diverse conformers per compound on 3D similarity computation are investigated, which may help to build search and analysis tools that exploit 3D molecular similarity between compounds in PubChem
Thematic clustering of text documents using an EM-based approach
Journal of Biomedical Semantics 2012, 3(Suppl 3):S6 (5 October 2012)
Finding biomedical categories in Medline ®
Journal of Biomedical Semantics 2012, 3(Suppl 3):S3 (5 October 2012)
Proteorhodopsin genes in giant viruses
Biology Direct 2012, 7:34 (4 October 2012)
Some giant viruses encode previously unknown proteorhodopsins that are predicted to affect signal transduction in infected protists and might have substantial ecological impact.
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory
BMC Bioinformatics 2012, 13:257 (3 October 2012)
In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex
BMC Structural Biology 2012, 12:25 (3 October 2012)
Does the central dogma still stand?
Biology Direct 2012, 7:27 (23 August 2012)
Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes
Virology Journal 2012, 9:161 (14 August 2012)
Research confirming that the Nucleo-Cytoplasmic Large DNA viruses, from smallpox to mimivirus, evolved from a single common ancestor. Interestingly a number of core genes, carrying out the same function in these diverse viruses, were unrelated to each other but were instead independently acquired from their eukaryotic hosts. This remarkable example of convergent evolution reveals a complex genetic history for an important group of viruses.
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
Biology Direct 2012, 7:18 (25 June 2012)
Comprehensive dissection of polymorphic and related secreted toxin systems uncovers nearly 240 toxin and immunity domains with implications for intra-organismal conflict, kin discrimination, pathogenesis and emergence of eukaryotic sub-cellular systems.
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
BMC Bioinformatics 2012, 13:144 (22 June 2012)
Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots
Proteome Science 2012, 10(Suppl 1):S11 (21 June 2012)
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
BMC Bioinformatics 2012, 13:134 (18 June 2012)