Units of genetic transfer in prokaryotes (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
The transfer of genetic materials across species (lateral genetic transfer, LGT) contributes to genomic and physiological innovation in prokaryotes. The extent of LGT in prokaryotes has been examined...
Protein domains as units of genetic transfer (2007)
Chan, Cheong Xin, Beiko, Robert G., Darling, Aaron E., Ragan, Mark A.
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There...
Genetic transfer in Staphylococcus: a case study of 13 genomes (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there...
A two-phase approach for detecting recombination in nucleotide sequences (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
A two-phase strategy for detecting recombination in nucleotide sequences (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
Andersson, Jan O, Sjögren, Åsa M, Horner, David S, Murphy, Colleen A, Dyal, Patricia L, Svärd, Staffan G, ...
Abstract Background Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have...
A two-phase approach for detecting recombination in nucleotide sequences (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
A two-phase approach for detecting recombination in nucleotide sequences (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
A two-phase strategy for detecting recombination in nucleotide sequences (2007)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
DELETE - Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny? (2007)
Hoehl, Michael, Ragan, Mark A.
The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple...
DELETE - Japan's language policy and the "Lost Decade" (2007)
Hashimoto, Kayoko, Beeson, Mark K., Ragan, Mark A., Smith, C. A., Jones, R. J., Moe, C., ...
Detecting recombination in evolving nucleotide sequences (2006)
Chan, Cheong, Beiko, Robert G, Ragan, Mark A
Abstract Background Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue...
Detecting Recombination in Evolving Nucleotide Sequences (2006)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Background Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions,...
Detecting Recombination in Evolving Nucleotide Sequences (2006)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Background Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions,...
Castro, Alexander, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
Abstract Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks...
Pattern-based phylogenetic distance estimation and tree reconstruction (2006)
Höhl, Michael, Rigoutsos, Isidore, Ragan, Mark A.
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned...
Searching for Convergence in Phylogenetic Markov Chain Monte Carlo (2006)
Beiko, Robert G., Keith, Jonathan M., Harlow, Timothy J., Ragan, Mark A
Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for...
Searching for Convergence in Phylogenetic Markov Chain Monte Carlo (2006)
Beiko, Robert G., Keith, Jonathan M., Harlow, Timothy J., Ragan, Mark A
Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogeneticscommunity and is central to phylogenetic software packages such as MrBayes. An important issue for...
Detecting Recombination in Evolving Nucleotide Sequences (2006)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Background Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions,...
Advanced computing for systems biology (2006)
Burrage, Kevin, Hood, Lindsay, Ragan, Mark A.
Systems biology is based on computational modelling and simulation of large networks of interacting components. Models may be intended to capture processes, mechanisms, components and interactions at...
Searching for Convergence in Phylogenetic Markov Chain Monte Carlo (2006)
Beiko, Robert G., Keith, Jonathan M., Harlow, Timothy J., Ragan, Mark A
Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for...
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction (2006)
Michael Höhl, Isidore Rigoutsos, Mark A. Ragan
We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned...
Garcia Castro, Alexander, Thoraval, Samuel, Garcia, Leyla J, Ragan, Mark A
Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are...
Garcia, Alexander C., Thoraval, Samuel, Garcia, Leyla J., Ragan, Mark A.
Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a...
Garcia, Alexander C., Thoraval, Samuel, Garcia, Leyla J., Ragan, Mark A.
Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a...
Sampling phylogenetic tree space with the generalized Gibbs sampler (2005)
Keith, Jonathan M., Adams, Peter, Ragan, Mark A., Bryant, Darryn
The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms...
A Word-Oriented Approach to Alignment Validation (2005)
Beiko, Robert G., Chan, Cheong Xin, Ragan, Mark A.
Motivation: Multiple sequence alignment at the level of whole proteomes requires a high degree of automation, precluding the use of traditional validation methods such as manual curation. Since...
A Word-Oriented Approach to Alignment Validation (2005)
Beiko, Robert G., Chan, Cheong Xin, Ragan, Mark A.
Motivation: Multiple sequence alignment at the level of whole proteomes requires a high degree of automation, precluding the use of traditional validation methods such as manual curation. Since...
Mar, Jessica C, Harlow, Timothy J, Ragan, Mark A
Abstract Background Bayesian phylogenetic inference holds promise as an alternative to maximum likelihood, particularly for large molecular-sequence data sets. We have investigated the performance of...
Garcia, Alexander C., Thoraval, Samuel, Garcia, Leyla J., Ragan, Mark A.
Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a...
A Word-Oriented Approach to Alignment Validation (2005)
Beiko, Robert G., Chan, Cheong Xin, Ragan, Mark A.
Motivation: Multiple sequence alignment at the level of whole proteomes requires a high degree of automation, precluding the use of traditional validation methods such as manual curation. Since...
Sampling phylogenetic tree space with the generalized Gibbs sampler (2005)
Keith, Jonathan M., Adams, Peter, Ragan, Mark A., Bryant, Darryn
The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms...
A word-oriented approach to alignment validation (2005)
Beiko, Robert G., Chan, Cheong Xin, Ragan, Mark A.
Motivation: Multiple sequence alignment at the level of whole proteomes requires a high degree of automation, precluding the use of traditional validation methods such as manual curation. Since...
Castro, Alexander Garcia, Thoraval, Samuel, Garcia, Leyla J., Ragan, Mark A.
Background: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a...
Protein contact prediction using patterns of correlation (2004)
Nicholas Hamilton, Kevin Burrage, Mark A. Ragan, Thomas Huber
In this paper a novel method for protein contact prediction is developed by using neural networks to find patterns of correlation in multiple sequence alignments. The results obtained are among the...
A hybrid clustering approach to recognition of protein families in 114 microbial genomes (2004)
Harlow, Timothy J, Gogarten, J Peter, Ragan, Mark A
Abstract Background Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses ( e.g. , homology-based prediction of structure or function). Standard...
Benchmarking the Detection and Analysis of Recombination (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic sequences in the course of molecular evolution. Given the possibilities of multiple events...
Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic relationships among genetic sequences in the course of molecular evolution. Problems in...
Position Paper for Semantic Web Life Sciences Workshop (2004)
Hunter, Jane, Ragan, Mark A., Little, Suzanne
The "Visible Cell" project is a research project being undertaken at the ARC Centre in Bioinformatics at the University of Queensland. The aim of this project is to significantly progress our...
Position Paper for Semantic Web Life Sciences Workshop (2004)
Hunter, Jane, Ragan, Mark A., Little, Suzanne
The "Visible Cell" project is a research project being undertaken at the ARC Centre in Bioinformatics at the University of Queensland. The aim of this project is to significantly progress our...
Position Paper for Semantic Web Life Sciences Workshop (2004)
Hunter, Jane, Ragan, Mark A., Little, Suzanne
The "Visible Cell" project is a research project being undertaken at the ARC Centre in Bioinformatics at the University of Queensland. The aim of this project is to significantly progress our...
Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic relationships among genetic sequences in the course of molecular evolution. Problems in...
Benchmarking the Detection and Analysis of Recombination (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic sequences in the course of molecular evolution. Given the possibilities of multiple events...
Benchmarking the Detection and Analysis of Recombination (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic sequences in the course of molecular evolution. Given the possibilities of multiple events...
Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events (2004)
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Recombination events can have a substantial impact in determining phylogenetic relationships among genetic relationships among genetic sequences in the course of molecular evolution. Problems in...
Position Paper for Semantic Web Life Sciences Workshop (2004)
Hunter, Jane, Ragan, Mark A., Little, Suzanne
The "Visible Cell" project is a research project being undertaken at the ARC Centre in Bioinformatics at the University of Queensland. The aim of this project is to significantly progress our...
Gene Content and Organization of a 281-Kbp (2000)
Robert L. Charlebois, Rama K. Singh, Ghislaine Allard, Cynthia Chow, Fabrice Confalonieri, ...
The sequence of a 281-kbp contig from the crenarchaeote Sulfolobus solfataricus P2 was determined and analysed. Notable features in this region include 29 ribosomal protein genes, 12 tRNA genes (four...
Christoph W. Sensen, Robert L. Charlebois, Cynthia Chow, Ib Groth, Clausen Bruce Curtis, W. Ford, ...
The Sulfolobus solfataricus P2 genome collaborators are poised to sequence the entire 3-Mbp genome of this crenarchaeote archaeon. About 80% of the genome has been sequenced to date, with the rest of...
Physodes and the phenolic compounds of brown algae [microform] / (1976)
Thesis (Ph. D.)--Dalhousie University, 1976.
Berger, Lee, Speare, Rick, Daszak, Peter, Green, D. Earl, Cunningham, Andrew A., Goggin, C. Louise, ...
Epidermal changes caused by a chytridiomycete fungus (Chytridiomycota; Chytridiales) were found in sick and dead adult anurans collected from montane rain forests in Queensland (Australia) and Panama...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Clarke, G. D. Paul, Beiko, Robert G., Ragan, Mark A., Charlebois, Robert L.
Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are...
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
Garcia Castro, Alexander, Thoraval, Samuel, Garcia, Leyla J, Ragan, Mark A
Highways of gene sharing in prokaryotes
Beiko, Robert G., Harlow, Timothy J., Ragan, Mark A.
The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of...
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
Berger, Lee, Speare, Rick, Daszak, Peter, Green, D. Earl, Cunningham, Andrew A., Goggin, C. Louise, ...
Epidermal changes caused by a chytridiomycete fungus (Chytridiomycota; Chytridiales) were found in sick and dead adult anurans collected from montane rain forests in Queensland (Australia) and Panama...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Clarke, G. D. Paul, Beiko, Robert G., Ragan, Mark A., Charlebois, Robert L.
Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are...
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
Garcia Castro, Alexander, Thoraval, Samuel, Garcia, Leyla J, Ragan, Mark A
Highways of gene sharing in prokaryotes
Beiko, Robert G., Harlow, Timothy J., Ragan, Mark A.
The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of...
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
Andersson, Jan O, Sjögren, Åsa M, Horner, David S, Murphy, Colleen A, Dyal, Patricia L, Svärd, Staffan G, ...
A two-phase approach for detecting recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
A two-phase approach for detecting recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G., Ragan, Mark A.
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as...
Dynamics of Genome Rearrangement in Bacterial Populations
Darling, Aaron E., Miklós, István, Ragan, Mark A.
Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic...