Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp. - Carolyn J. Bird; Ellen L. Rice; Colleen A. Murphy; Qing Yan Liu; Mark A. Ragan (Nucleic Acids Res., 1990)

A hybrid clustering approach to recognition of protein families in 114 microbial genomes. - Timothy J. Harlow; J. Peter Gogarten; Mark A. Ragan (BMC Bioinform., 2004)

A word-oriented approach to alignment validation. - Robert G. Beiko; Cheong Xin Chan; Mark A. Ragan (Bioinform., 2005)

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. - Alexander García Castro; Samuel Thoraval; Leyla J. García; Mark A. Ragan (BMC Bioinform., 2005)

Kernelization for Convex Recoloring. - Hans L. Bodlaender; Michael R. Fellows; Michael A. Langston; Mark A. Ragan; Frances A. Rosamond; Mark Weyer (ACiD, 2006)

Automating the Search for Lateral Gene Transfer. - Mark A. Ragan (APBC, 2006)

Advanced computing for systems biology. - Kevin Burrage; Lindsay Hood; Mark A. Ragan (Briefings Bioinform., 2006)

The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. - Alexander García Castro; Philippe Rocca-Serra; Robert Stevens 001; Chris F. Taylor; Karim Nashar; Mark A. Ragan; Susanna-Assunta Sansone (BMC Bioinform., 2006)

Detecting recombination in evolving nucleotide sequences. - Cheong Xin Chan; Robert G. Beiko; Mark A. Ragan (BMC Bioinform., 2006)

Connected Coloring Completion for General Graphs: Algorithms and Complexity. - Benny Chor; Michael R. Fellows; Mark A. Ragan; Igor Razgon; Frances A. Rosamond; Sagi Snir (COCOON, 2007)

A two-phase strategy for detecting recombination in nucleotide sequences. - Cheong Xin Chan; Robert G. Beiko; Mark A. Ragan (South Afr. Comput. J., 2007)

Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions. - Melissa J. Davis; Andrew F. Newman; Imran Khan; Jane Hunter 001; Mark A. Ragan (APBC, 2008)

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Mark A. Ragan; Xavier Messeguer (ISBRA, 2008)

MACHOS: Markov clusters of homologous subsequences. - Simon Wong; Mark A. Ragan (ISMB, 2008)

The Visible Cell Project: Changing the Way We Think about Cells. - Mark A. Ragan; Brad J. Marsh (ISPAN, 2008)

Genome-Scale Computational Biology and Bioinformatics in Australia. - Mark A. Ragan; Tim Littlejohn; Bruce Ross (PLoS Comput. Biol., 2008)

Seevolution: visualizing chromosome evolution. - Andrés Esteban-Marcos; Aaron E. Darling; Mark A. Ragan (Bioinform., 2009)

IllouraTM: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. - Tim McComb; Oliver Cairncross; Andrew B. Noske; David L. A. Wood; Brad J. Marsh; Mark A. Ragan (Bioinform., 2009)

Protein-protein interaction as a predictor of subcellular location. - Chang Shin; Simon Wong; Melissa J. Davis; Mark A. Ragan (BMC Syst. Biol., 2009)

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Guillaume Achaz; Mark A. Ragan; Xavier Messeguer; Eduardo P. C. Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

A visual framework for sequence analysis using n-grams and spectral rearrangement. - Stefan Maetschke; Karin S. Kassahn; Jasmyn A. Dunn; Siew-Ping Han; Eva Z. Curley; Katryn J. Stacey; Mark A. Ragan (Bioinform., 2010)

Automatic, context-specific generation of Gene Ontology slims. - Melissa J. Davis; Muhammad Shoaib B. Sehgal; Mark A. Ragan (BMC Bioinform., 2010)

A Semantic Web Ontology for Small Molecules and Their Biological Targets. - Joo-Young Choi; Melissa J. Davis; Andrew F. Newman; Mark A. Ragan (J. Chem. Inf. Model., 2010)

Quadratic Kernelization for Convex Recoloring of Trees. - Hans L. Bodlaender; Michael R. Fellows; Michael A. Langston; Mark A. Ragan; Frances A. Rosamond; Mark Weyer (Algorithmica, 2011)

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations. - Chikako Ragan; Michael Zuker; Mark A. Ragan (PLoS Comput. Biol., 2011)

Gene Ontology-driven inference of protein-protein interactions using inducers. - Stefan Maetschke; Martin Simonsen; Melissa J. Davis; Mark A. Ragan (Bioinform., 2012)

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. - Martin Simonsen; Stefan Maetschke; Mark A. Ragan (Bioinform., 2012)

mCOPA: analysis of heterogeneous features in cancer expression data. - Chenwei Wang; Alperen Taciroglu; Stefan Maetschke; Colleen C. Nelson; Mark A. Ragan; Melissa J. Davis (J. Clin. Bioinform., 2012)

Systematic tracking of dysregulated modules identifies novel genes in cancer. - Sriganesh Srihari; Mark A. Ragan (Bioinform., 2013)

Clustering evolving proteins into homologous families. - Cheong Xin Chan; Maisarah Mahbob; Mark A. Ragan (BMC Bioinform., 2013)

RMaNI: Regulatory Module Network Inference framework. - Piyush B. Madhamshettiwar; Stefan Maetschke; Melissa J. Davis; Mark A. Ragan (BMC Bioinform., 2013)

Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification - Sriganesh Srihari; Mark A. Ragan (CoRR, 2013)

Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells. - Liam G. Fearnley; Mark A. Ragan; Lars Keld Nielsen (BIOINFORMATICS, 2014)

Extracting reaction networks from databases-opening Pandora's box. - Liam G. Fearnley; Melissa J. Davis; Mark A. Ragan; Lars Keld Nielsen (Briefings Bioinform., 2014)

Supervised, semi-supervised and unsupervised inference of gene regulatory networks. - Stefan Maetschke; Piyush B. Madhamshettiwar; Melissa J. Davis; Mark A. Ragan (Briefings Bioinform., 2014)

Characterizing cancer subtypes as attractors of Hopfield networks. - Stefan Maetschke; Mark A. Ragan (Bioinform., 2014)

Complex-based analysis of dysregulated cellular processes in cancer. - Sriganesh Srihari; Piyush B. Madhamshettiwar; Sarah Song; Chao Liu; Peter T. Simpson; Kum Khanna; Mark A. Ragan (BMC Syst. Biol., 2014)

Evolution and Controllability of CancerNetworks: A Boolean Perspective. - Sriganesh Srihari; Venkatesh Raman 001; Hon Wai Leong; Mark A. Ragan (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Breast cancer classification: linking molecular mechanisms to disease prognosis. - Atefeh Taherian Fard; Sriganesh Srihari; Mark A. Ragan (Briefings Bioinform., 2015)

Alignment-free inference of hierarchical and reticulate phylogenomic relationships. - Guillaume Bernard 003; Cheong Xin Chan; Yao-ban Chan; Xin-Yi Chua; Yingnan Cong; James M. Hogan; Stefan R. Maetschke; Mark A. Ragan (Briefings Bioinform., 2019)