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.
Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection
Biology Direct 2006, 1:4 (31 January 2006)
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
BMC Bioinformatics 2008, 9:78 (31 January 2008)
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory
BMC Bioinformatics 2012, 13:257 (3 October 2012)
Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity
Biology Direct 2009, 4:51 (18 December 2009)
Female Anopheles gambiae antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2
Parasites & Vectors 2012, 5:27 (6 February 2012)
The odorant binding protein, OBP2, had increased transcript accumulation in the antennae of female vs. male Anopheles gambiae. suggesting it may play a role in female feeding and breeding behavior. Image: Heads, mouthparts and antennae of female (left) and male (right) Anopheles gambiae
Evolutionary primacy of sodium bioenergetics
Biology Direct 2008, 3:13 (1 April 2008)
Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis
Biology Direct 2010, 5:48 (2 August 2010)
Two class-I aminoacyl-tRNA-synthetase homologs, the cyclic dipeptide synthases and a paralogous Met-tRNA-synthetase, are shown to be involved as peptide ligases in non-ribosomal biosynthesis of novel peptide metabolites.
The relationship of protein conservation and sequence length
BMC Evolutionary Biology 2002, 2:20 (1 November 2002)
Proteins conserved across kingdoms are likely to be longer than more divergent proteins, suggesting evolutionary trends in favour of shortness.
Fast 3D shape screening of large chemical databases through alignment-recycling
Chemistry Central Journal 2007, 1:12 (6 June 2007)
Back to Bermuda: how is science best served?
Genome Biology 2009, 10:105 (24 April 2009)
Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families
BMC Structural Biology 2008, 8:55 (26 December 2008)
Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea
Biology Direct 2010, 5:33 (7 May 2010)
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.
The mammalian transcriptome and the function of non-coding DNA sequences
Genome Biology 2004, 5:105 (25 March 2004)
Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation
BMC Bioinformatics 2011, 12:223 (2 June 2011)
Virus variation resources at the National Center for Biotechnology Information: dengue virus
BMC Microbiology 2009, 9:65 (2 April 2009)
Transposable element derived DNaseI-hypersensitive sites in the human genome
Biology Direct 2006, 1:20 (20 July 2006)
Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes
Genome Biology 2003, 4:R11 (3 February 2003)
Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them.
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
BMC Genomics 2008, 9:226 (17 May 2008)
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.
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.
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
Genome Biology 2003, 4:R55 (29 August 2003)
Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.
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 tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs
BMC Bioinformatics 2012, 13:25 (7 February 2012)