Affiliation: Center for Biological Sequence Analysis
- Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representationRodrigo Gouveia-Oliveira
Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
Algorithms Mol Biol 2:12. 2007..Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues - coevolution. Our goal is to find these coevolving residues...
- MaxAlign: maximizing usable data in an alignmentRodrigo Gouveia-Oliveira
Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
BMC Bioinformatics 8:312. 2007..The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment...
- Higher variability in the number of sexual partners in males can contribute to a higher prevalence of sexually transmitted diseases in femalesRodrigo Gouveia-Oliveira
Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
J Theor Biol 261:100-6. 2009..We suggest that this pattern may be caused by the effect described above in highly prevalent sexually transmitted diseases, while its impact in low-prevalence epidemics is surpassed by the action of high-risk individuals (mostly males)...
- Genome update: DNA repeats in bacterial genomesDavid W Ussery
Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
Microbiology 150:3519-21. 2004
- InterMap3D: predicting and visualizing co-evolving protein residuesRodrigo Gouveia-Oliveira
Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
Bioinformatics 25:1963-5. 2009..Finally, InterMap3D generates high-quality images of the protein with the predicted co-evolving residues highlighted...
- Comparative evaluation of word composition distances for the recognition of SCOP relationshipsSusana Vinga
Biomathematics Group, ITQB, Universidade Nova de Lisboa, Rua da Quinta Grande, N 6, 2780 156 Oeiras, Portugal
Bioinformatics 20:206-15. 2004....
- Phylogenetic relationships between Sarcocystis species from reindeer and other Sarcocystidae deduced from ssu rRNA gene sequencesStina S Dahlgren
Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Section of Microbiology, Immunology and Parasitology, Oslo, Norway
Vet Parasitol 151:27-35. 2008..This study suggests that phylogentic analysis can be a useful tool in the search for possible definitive hosts for those Sarcocystis species for which they are unknown and difficult to find solely by other methods...