Genome trees constructed using five different approaches suggest new major bacterial clades
BMC Evolutionary Biology 2001, 1:8 (23 October 2001)
Five different methods of phylogenetic reconstruction suggest novel high-level bacterial clades, despite confounding factors such as lateral gene transfer and gene loss.
Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria
Journal of Biology 2009, 8:29 (15 April 2009)
Venancio and Aravind review recent studies, including one in BMC Systems Biology, that offer new ways to reconstruct transcriptional regulatory networks in previously uncharacterised prokaryotes, such as the actinobacteria.
Predicting domain-domain interactions using a parsimony approach
Genome Biology 2006, 7:R104 (9 November 2006)
A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics
Biology Direct 2006, 1:30 (3 October 2006)
Duplicated genes evolve slower than singletons despite the initial rate increase
BMC Evolutionary Biology 2004, 4:22 (6 July 2004)
Following gene duplication there is a period of rapid evolution, which then slows down in cases where the original gene has an important biological function and the duplicate is retained.
Identification and characterization of pseudogenes in the rice gene complement
BMC Genomics 2009, 10:317 (16 July 2009)
Detection of co-eluted peptides using database search methods
Biology Direct 2008, 3:27 (2 July 2008)
The "one peptide per spectrum" dogma cannot hold true due to limited chromatographic separation resulting in
mass spectra containing co-eluted peptides with high probability; this issue is numerically investigated.
Constructing a semantic predication gold standard from the biomedical literature
BMC Bioinformatics 2011, 12:486 (20 December 2011)
Exceptional error minimization in putative primordial genetic codes
Biology Direct 2009, 4:44 (19 November 2009)
Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
Genome Biology 2009, 10:R33 (30 March 2009)
A computational model of the yeast Ubiquitin system highlights interesting biological features including functional interactions between components and interplay with other regulatory mechanisms.
Novel eukaryotic enzymes modifying cell-surface biopolymers
Biology Direct 2010, 5:1 (7 January 2010)
Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea
Biology Direct 2009, 4:39 (14 October 2009)
While Archaea are thought to possess a single RNA polymerase type resembling in its subunit composition eukaryotic RNAP II, the identified archaeal RPC34 orhtolog implicates functional specialization of archaeal RNAPs.
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
Genome Biology 2001, 2:research0007-research0007.8 (19 February 2001)
Sequence-profile analysis shows that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. This allows the prediction of catalytic activity for a wide range of biochemically uncharacterized proteins from eukaryotes and bacteria.
A unified framework for managing provenance information in translational research
BMC Bioinformatics 2011, 12:461 (29 November 2011)
GeneRIF indexing: sentence selection based on
BMC Bioinformatics 2013, 14:171 (31 May 2013)
Clustering cliques for graph-based summarization of the biomedical research literature
BMC Bioinformatics 2013, 14:182 (7 June 2013)
OST-HTH: a novel predicted RNA-binding domain
Biology Direct 2010, 5:13 (19 March 2010)
Accumulation of GC donor splice signals in mammals
Biology Direct 2008, 3:30 (9 July 2008)
Reconstruction of the evolution of donor splice sites in mammals reveals accumulation of minor GC sites that could contribute to the evolution of alternative splicing.
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.
Overview of the BioCreative III Workshop
BMC Bioinformatics 2011, 12(Suppl 8):S1 (3 October 2011)
Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
Biology Direct 2008, 3:7 (17 March 2008)
Homoplasy denotes the same (parallel) mutations occurring independently in different lineages. It is a scourge of phylogenetic methods. Here, however, it is shown that homoplasy is also an interesting evolutionary phenomenon. Homplasy seems, at least, in part, to underlie the so-called homologous series of phenotypic variation occurring in different, particularly, closely related lineages, an effect first described by the famous Russian geneticict Vavilov some 90 years ago.
Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains
Biology Direct 2010, 5:43 (30 June 2010)
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases
BMC Structural Biology 2003, 3:1 (28 January 2003)
The discovery that RNA-dependent RNA polymerases, which are solely eukaryotic, share a domain with a subunit of DNA-dependent RNA polymerases, which are universal, sheds light on the evolutionary relationships and origins of polymerases.
A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain
Genome Biology 2004, 5:R30 (16 April 2004)
This study characterizes the KAP protein family - a newly identified sub-group of the P-loop NTPases, which have transmembrane helices inserted into the P-loop NTPase domain. Their unusual phyletic distribution suggests KAP proteins were transferred from bacteria to animals by horizontal gene transfer.
Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem
BMC Bioinformatics 2008, 9:401 (25 September 2008)