M A Ragan

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. pmc Highways of gene sharing in prokaryotes
    Robert G Beiko
    Institute for Molecular Bioscience and Australian Research Council Centre in Bioinformatics, The University of Queensland, Brisbane 4072, Australia
    Proc Natl Acad Sci U S A 102:14332-7. 2005
  2. pmc The mammalian PYHIN gene family: phylogeny, evolution and expression
    Jasmyn A Cridland
    The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia
    BMC Evol Biol 12:140. 2012
  3. pmc mCOPA: analysis of heterogeneous features in cancer expression data
    Chenwei Wang
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
    J Clin Bioinforma 2:22. 2012
  4. pmc Protein-protein interaction as a predictor of subcellular location
    Chang Jin Shin
    The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, QLD, Australia
    BMC Syst Biol 3:28. 2009
  5. pmc A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
    Jan O Andersson
    Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
    BMC Genomics 8:51. 2007
  6. pmc Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation
    Jessica C Mar
    1Department of Mathematics, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Evol Biol 5:8. 2005
  7. pmc A hybrid clustering approach to recognition of protein families in 114 microbial genomes
    Timothy J Harlow
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 5:45. 2004
  8. pmc The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case
    Alexander Garcia Castro
    Microarray Informatics Team, The European Bioinformatics Institute European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK
    BMC Bioinformatics 7:267. 2006
  9. pmc Detecting recombination in evolving nucleotide sequences
    Cheong Xin Chan
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 7:412. 2006
  10. pmc Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
    Alexander Garcia Castro
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 6:87. 2005

Collaborators

Detail Information

Publications49

  1. pmc Highways of gene sharing in prokaryotes
    Robert G Beiko
    Institute for Molecular Bioscience and Australian Research Council Centre in Bioinformatics, The University of Queensland, Brisbane 4072, Australia
    Proc Natl Acad Sci U S A 102:14332-7. 2005
    ..The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments...
  2. pmc The mammalian PYHIN gene family: phylogeny, evolution and expression
    Jasmyn A Cridland
    The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia
    BMC Evol Biol 12:140. 2012
    ..To better understand the evolution, orthology and function of these genes, we have documented the range of PYHIN genes present in representative mammalian species, and undertaken phylogenetic and expression analyses...
  3. pmc mCOPA: analysis of heterogeneous features in cancer expression data
    Chenwei Wang
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
    J Clin Bioinforma 2:22. 2012
    ..abstract:..
  4. pmc Protein-protein interaction as a predictor of subcellular location
    Chang Jin Shin
    The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, QLD, Australia
    BMC Syst Biol 3:28. 2009
    ..Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity...
  5. pmc A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
    Jan O Andersson
    Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
    BMC Genomics 8:51. 2007
    ..barkhanus)...
  6. pmc Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation
    Jessica C Mar
    1Department of Mathematics, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Evol Biol 5:8. 2005
    ..We have investigated the performance of Bayesian inference with empirical and simulated protein-sequence data under conditions of relative branch-length differences and model violation...
  7. pmc A hybrid clustering approach to recognition of protein families in 114 microbial genomes
    Timothy J Harlow
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 5:45. 2004
    ..g. as the result of matches to so-called promiscuous domains. Use of the Markov Cluster algorithm avoids this non-specificity, but does not preserve topological or threshold information about protein families...
  8. pmc The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case
    Alexander Garcia Castro
    Microarray Informatics Team, The European Bioinformatics Institute European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK
    BMC Bioinformatics 7:267. 2006
    ....
  9. pmc Detecting recombination in evolving nucleotide sequences
    Cheong Xin Chan
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 7:412. 2006
    ..While there are many algorithms for the identification of recombination events, little is known about the effects of subsequent substitutions on the accuracy of available recombination-detection approaches...
  10. pmc Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
    Alexander Garcia Castro
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 6:87. 2005
    ..Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported...
  11. pmc Automatic, context-specific generation of Gene Ontology slims
    Melissa J Davis
    The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 11:498. 2010
    ..Decisions about which terms to include are necessarily subjective, and the creation process itself and subsequent curation are time-consuming and largely manual...
  12. pmc Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
    Elizabeth Skippington
    The University of Queensland, Institute for Molecular Bioscience and Australian Research Council Centre of Excellence in Bioinformatics, Brisbane, Queensland 4072, Australia
    BMC Genomics 12:532. 2011
    ..coli transcriptional regulatory network (TRN)...
  13. ncbi request reprint Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota
    M A Ragan
    Institute for Marine Biosciences, National Research Council of Canada, Halifax, Nova Scotia
    Dis Aquat Organ 42:185-90. 2000
    ..These results confirm the provisional assignment of QPX to the Labyrinthulomycota made previously on the basis of morphological and ultrastructural characters found in some, but not all, geographic isolates...
  14. ncbi request reprint On surrogate methods for detecting lateral gene transfer
    M A Ragan
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    FEMS Microbiol Lett 201:187-91. 2001
    ..Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees...
  15. pmc Lateral genetic transfer: open issues
    Mark A Ragan
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
    Philos Trans R Soc Lond B Biol Sci 364:2241-51. 2009
    ..Here we identify and consider significant open questions concerning the role of LGT in genome evolution...
  16. ncbi request reprint Detection of lateral gene transfer among microbial genomes
    M A Ragan
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Curr Opin Genet Dev 11:620-6. 2001
    ..These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently...
  17. ncbi request reprint Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1alpha of Ichthyophonus irregularis
    Mark A Ragan
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Canada
    Mol Phylogenet Evol 29:550-62. 2003
    ..irregularis is a specific relative of animals or of fungi. However, the EF-1alpha of I. irregularis exhibits a two amino acid deletion heretofore reported only among fungi...
  18. pmc Trees and networks before and after Darwin
    Mark A Ragan
    The University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, Queensland, Australia
    Biol Direct 4:43; discussion 43. 2009
    ..In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it...
  19. ncbi request reprint Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission
    Mark A Ragan
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
    Int J Syst Evol Microbiol 52:777-87. 2002
    ..ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes...
  20. ncbi request reprint Do different surrogate methods detect lateral genetic transfer events of different relative ages?
    Mark A Ragan
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Trends Microbiol 14:4-8. 2006
    ..This conjecture is supported by a rigorous phylogenetic analysis of 3776 proteins in Escherichia coli K12 MG1655 to map the ages of transfer events relative to one another...
  21. ncbi request reprint Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea from the Nova Scotia shelf
    T G Rand
    Biology Department, Saint Mary s University, Halifax, Nova Scotia, Canada
    Dis Aquat Organ 41:31-6. 2000
    ....
  22. ncbi request reprint Completing the sequence of the Sulfolobus solfataricus P2 genome
    C W Sensen
    National Research Council of Canada, Institute for Marine Biosciences, Halifax, NS, Canada
    Extremophiles 2:305-12. 1998
    ..After an overview of the general sequence features, metabolic pathway studies are explained, using sugar metabolism as an example. The paper closes with an overview of repetitive elements in S. solfataricus...
  23. ncbi request reprint The Sulfolobus solfataricus P2 genome project
    R L Charlebois
    Canadian Institute for Advanced Research, University of Ottawa, ON, Canada
    FEBS Lett 389:88-91. 1996
    ..An examination of completely sequenced cosmids suggests a clustering of genes by function in the S. solfataricus genome...
  24. pmc Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates
    Karin S Kassahn
    The University of Queensland, Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, QLD, Australia
    Genome Res 19:1404-18. 2009
    ..We find limited evidence that reciprocal gene loss led to reproductive isolation and speciation in this lineage...
  25. ncbi request reprint Searching for convergence in phylogenetic Markov chain Monte Carlo
    Robert G Beiko
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Syst Biol 55:553-65. 2006
    ..Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely...
  26. pmc Seevolution: visualizing chromosome evolution
    Andrés Esteban-Marcos
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
    Bioinformatics 25:960-1. 2009
    ....
  27. pmc MACHOS: Markov clusters of homologous subsequences
    Simon Wong
    ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 24:i77-85. 2008
    ....
  28. doi request reprint Detecting lateral genetic transfer : a phylogenetic approach
    Robert G Beiko
    Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
    Methods Mol Biol 452:457-69. 2008
    ..This chapter outlines how bioinformatic and phylogenetic analyses can be built into a workflow to identify LGT among microbial genomes...
  29. pmc Dynamics of genome rearrangement in bacterial populations
    Aaron E Darling
    ARC Center of Excellence in Bioinformatics, The University of Queensland, St Lucia, Queensland, Australia
    PLoS Genet 4:e1000128. 2008
    ..Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes...
  30. ncbi request reprint Information integration in molecular bioscience
    Alexander Garcia Castro
    ARC Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
    Appl Bioinformatics 4:157-73. 2005
    ....
  31. ncbi request reprint The lobster parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): nuclear 18S rDNA sequence, phylogeny and detection using oligonucleotide primers
    M A Ragan
    Institute for Marine Biosciences, National Research Council of Canada, Halifax, Nova Scotia, Canada
    J Eukaryot Microbiol 43:341-6. 1996
    ..haemophila deoxyribonucleic acid against at least a 1600-fold excess of total deoxyribonucleic acid from H. americanus. GENBANK/U51554..
  32. ncbi request reprint Protein contact prediction using patterns of correlation
    Nicholas Hamilton
    Advanced Computational Modelling Centre, Department of Mathematics, The University of Queensland, St Lucia, Queensland, Australia
    Proteins 56:679-84. 2004
    ..Predictive accuracy is also found to improve by using multiple sequence alignments containing many sequences to calculate the correlations...
  33. ncbi request reprint Sampling phylogenetic tree space with the generalized Gibbs sampler
    Jonathan M Keith
    Department of Mathematics, University of Queensland, St Lucia, QLD 4072, Australia
    Mol Phylogenet Evol 34:459-68. 2005
    ..The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package...
  34. doi request reprint Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction
    Robert G Beiko
    Department of Computer Science, Dalhousie University, Halifax, NS, Canada
    Methods Mol Biol 532:241-56. 2009
    ..In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method...
  35. pmc Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data
    Tim McComb
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Bioinformatics 25:1208-10. 2009
    ..AVAILABILITY: http://www.visiblecell.com/illoura. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  36. ncbi request reprint A word-oriented approach to alignment validation
    Robert G Beiko
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD 4072, Australia
    Bioinformatics 21:2230-9. 2005
    ..We present WOOF, a novel 'word-oriented' objective function that relies on the identification and scoring of conserved amino acid patterns (words) between pairs of sequences...
  37. ncbi request reprint Is multiple-sequence alignment required for accurate inference of phylogeny?
    Michael Hohl
    Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Syst Biol 56:206-21. 2007
    ..Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences...
  38. ncbi request reprint Thinking laterally about genomes
    Mark A Ragan
    The University of Queensland, Institute for Molecular Bioscience, 306 Carmody Rd, St Lucia, Brisbane, Queensland 4072, Australia
    Genome Inform 23:221-2. 2009
    ..Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT...
  39. pmc Are protein domains modules of lateral genetic transfer?
    Cheong Xin Chan
    The University of Queensland, Institute for Molecular Biosciences, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia
    PLoS ONE 4:e4524. 2009
    ..e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins...
  40. doi request reprint A semantic web ontology for small molecules and their biological targets
    Jooyoung Choi
    Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia
    J Chem Inf Model 50:732-41. 2010
    ..These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery...
  41. doi request reprint A visual framework for sequence analysis using n-grams and spectral rearrangement
    Stefan R Maetschke
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 26:737-44. 2010
    ..New approaches are required to discover, visualize and analyze these sequence regions and thus enable a better understanding of protein evolution...
  42. ncbi request reprint An archaebacterial homolog of pelota, a meiotic cell division protein in eukaryotes
    M A Ragan
    Program in Evolutionary Biology, Canadian Institue for Advanced Research, National Research Council of Canada, Halifax, Nova Scotia, Canada
    FEMS Microbiol Lett 144:151-5. 1996
    ..The nuclear localization signal and negatively charged carboxy-terminus characteristic of eukaryotic pelota-like proteins are absent from the S. solfataricus homolog, and hence may be indicative of the acquired eukaryotic function(s)...
  43. ncbi request reprint Advanced computing for systems biology
    Kevin Burrage
    ARC Centre in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
    Brief Bioinform 7:390-8. 2006
    ..Challenges remain in providing lightweight standards to facilitate the penetration of robust, scalable grid-type computing into diverse user communities to meet the evolving demands of systems biology...
  44. pmc Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH
    Chikako Ragan
    The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia
    PLoS ONE 4:e5745. 2009
    ..These results confirm and extend the scope of miRNA-mediated species- and transcript-specific regulation in different cell types, tissues and developmental conditions...
  45. doi request reprint Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse
    Chang Jin Shin
    The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
    Proteomics 9:5256-66. 2009
    ....
  46. pmc Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts
    Siew Ping Han
    School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
    RNA 16:1760-8. 2010
    ....
  47. doi request reprint Identification of human haploinsufficient genes and their genomic proximity to segmental duplications
    Vinh T Dang
    ARC Centre of Excellence in Bioinformatics, Brisbane, Queensland, Australia
    Eur J Hum Genet 16:1350-7. 2008
    ....
  48. pmc Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
    G D Paul Clarke
    NeuroGadgets Inc, Ottawa, Ontario K1G 4B5, Canada
    J Bacteriol 184:2072-80. 2002
    ..Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree...
  49. ncbi request reprint Microbial phylogenomics: Branching out
    Robert L Charlebois
    Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
    Nature 421:217. 2003