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.
Evolution of gene fusions: horizontal transfer versus independent events
Genome Biology 2002, 3:research0024-research0024.13 (26 April 2002)
The evolutionary history of gene fusions was studied by phylogenetic analysis. Of the 51 gene fusions studied, 31 were most probably disseminated by cross-kingdom horizontal gene transfer, 14 appeared to have evolved independently in different kingdoms and two were probably inherited from a common ancestor.
A virtual computer lab for distance biomedical technology education
BMC Medical Education 2008, 8:12 (13 March 2008)
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
BMC Genomics 2008, 9:226 (17 May 2008)
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation
BMC Bioinformatics 2008, 9:237 (16 May 2008)
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.
Overview of the BioCreative III Workshop
BMC Bioinformatics 2011, 12(Suppl 8):S1 (3 October 2011)
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.
A highly conserved family of inactivated archaeal B family DNA polymerases
Biology Direct 2008, 3:32 (6 August 2008)
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts
BMC Bioinformatics 2011, 12:355 (26 August 2011)
The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains
Biology Direct 2009, 4:25 (14 August 2009)
The Anabaena sensory rhodopsin signal transducer defines a novel class of small molecule binding beta-sandwich domains that are involved in carbohydrate recognition.
New directions in biomedical text annotation: definitions, guidelines and corpus construction
BMC Bioinformatics 2006, 7:356 (25 July 2006)
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
Genome Biology 2000, 1:research0009-research0009.19 (6 November 2000)
The database of Clusters of Orthologous Groups of proteins (COGs) was used to reannotate the genomes of
Aeropyrum pernix and Pyrococcus abyssi. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange.
OST-HTH: a novel predicted RNA-binding domain
Biology Direct 2010, 5:13 (19 March 2010)
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
BMC Bioinformatics 2007, 8:173 (23 May 2007)
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)
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
BMC Biology 2006, 4:41 (7 December 2006)
The first description is now available of the updated TBLASTN, an implementation of the BLAST search that aligns protein sequences to a translated nucleotide database, revealing the composition-based statistics that give increased accuracy and reliability.
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors
Genome Biology 2002, 3:research0012-research0012.11 (13 February 2002)
Using computational analysis, the amino-terminal module of the D6R/N1R proteins is shown to define a novel, conserved DNA-binding domain (the KilA-N domain) found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. It is suggested to be homologous to the fungal DNA-binding APSES domain; analysis of these domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes.
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences
Genome Biology 2001, 2:research0051-research0051.11 (13 November 2001)
Six cases where application of novel or conventional computational methods for protein sequence and structure analysis led to non-trivial predictions that were subsequently supported by direct experiments were analyzed. On all occasions, the original prediction seemed unjustified, and in at least three cases an alternative, well-supported computational prediction, incompatible with the original one, could be derived.
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.
Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots
Proteome Science 2012, 10(Suppl 1):S11 (21 June 2012)
The GOLD domain, a novel protein module involved in Golgi function and secretion
Genome Biology 2002, 3:research0023-research0023.7 (24 April 2002)
Members of the p24 family of proteins have been shown to be components of the coated vesicles that are involved in the transportation of molecules from the endoplasmic reticulum to the Golgi complex. A sequence-profile analysis method was used to identify a β-strand-rich domain, the GOLD domain, in the p24 proteins and several other proteins with roles in Golgi dynamics and secretion.
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.
Thematic clustering of text documents using an EM-based approach
Journal of Biomedical Semantics 2012, 3(Suppl 3):S6 (5 October 2012)
Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
Genome Biology 2001, 2:research0033-research0033.14 (30 August 2001)
Bacterial genomes were searched for duplications of ribosomal proteins. Of the four ribosomal proteins for which paralogs were detected in several genomes, three come in two distinct versions. One form contains a metal-binding Zn-ribbon while in the second, the metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions. Lineage-specific gene loss and horizontal gene transfer therefore seem to make major contributions to the evolution of bacterial ribosomal proteins.