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ORCIDMark A. Ragan
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- affiliation: University of Queensland, Brisbane, Australia
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2010 – 2019
- 2019
[j31]Guillaume Bernard
, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M. Hogan, Stefan R. Maetschke, Mark A. Ragan:
Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings Bioinform. 20(2): 426-435 (2019)- 2015
- [j30]Atefeh Taherian Fard, Sriganesh Srihari, Mark A. Ragan:
Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings Bioinform. 16(3): 461-474 (2015) - 2014
- [j29]Stefan Maetschke, Piyush B. Madhamshettiwar, Melissa J. Davis, Mark A. Ragan:
Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Briefings Bioinform. 15(2): 195-211 (2014) - [j28]Liam G. Fearnley, Melissa J. Davis, Mark A. Ragan, Lars Keld Nielsen:
Extracting reaction networks from databases-opening Pandora's box. Briefings Bioinform. 15(6): 973-983 (2014) - [j27]Stefan Maetschke, Mark A. Ragan:
Characterizing cancer subtypes as attractors of Hopfield networks. Bioinform. 30(9): 1273-1279 (2014) - [j26]Sriganesh Srihari, Piyush B. Madhamshettiwar, Sarah Song, Chao Liu, Peter T. Simpson, Kum Khanna, Mark A. Ragan:
Complex-based analysis of dysregulated cellular processes in cancer. BMC Syst. Biol. 8(S-4): S1 (2014) - [j25]Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong, Mark A. Ragan:
Evolution and Controllability of CancerNetworks: A Boolean Perspective. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 83-94 (2014) - [c9]Liam G. Fearnley, Mark A. Ragan, Lars Keld Nielsen:
Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells. BIOINFORMATICS 2014: 117-122 - 2013
- [j24]Sriganesh Srihari, Mark A. Ragan:
Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinform. 29(12): 1553-1561 (2013) - [j23]Cheong Xin Chan, Maisarah Mahbob, Mark A. Ragan:
Clustering evolving proteins into homologous families. BMC Bioinform. 14: 120 (2013) - [j22]Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan:
RMaNI: Regulatory Module Network Inference framework. BMC Bioinform. 14(S-16): S14 (2013) - [i1]Sriganesh Srihari, Mark A. Ragan:
Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification. CoRR abs/1304.5565 (2013) - 2012
- [j21]Stefan Maetschke, Martin Simonsen, Melissa J. Davis, Mark A. Ragan:
Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinform. 28(1): 69-75 (2012) - [j20]Martin Simonsen, Stefan Maetschke, Mark A. Ragan:
Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinform. 28(6): 851-857 (2012) - [j19]Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis:
mCOPA: analysis of heterogeneous features in cancer expression data. J. Clin. Bioinform. 2: 22 (2012) - 2011
- [j18]Hans L. Bodlaender, Michael R. Fellows, Michael A. Langston, Mark A. Ragan, Frances A. Rosamond, Mark Weyer:
Quadratic Kernelization for Convex Recoloring of Trees. Algorithmica 61(2): 362-388 (2011) - [j17]Chikako Ragan, Michael Zuker, Mark A. Ragan:
Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations. PLoS Comput. Biol. 7(2) (2011) - 2010
- [j16]Stefan Maetschke, Karin S. Kassahn, Jasmyn A. Dunn, Siew-Ping Han, Eva Z. Curley, Katryn J. Stacey, Mark A. Ragan:
A visual framework for sequence analysis using n-grams and spectral rearrangement. Bioinform. 26(6): 737-744 (2010) - [j15]Melissa J. Davis, Muhammad Shoaib B. Sehgal, Mark A. Ragan:
Automatic, context-specific generation of Gene Ontology slims. BMC Bioinform. 11: 498 (2010) - [j14]Joo-Young Choi, Melissa J. Davis, Andrew F. Newman, Mark A. Ragan:
A Semantic Web Ontology for Small Molecules and Their Biological Targets. J. Chem. Inf. Model. 50(5): 732-741 (2010)
2000 – 2009
- 2009
- [j13]Andrés Esteban-Marcos, Aaron E. Darling, Mark A. Ragan:
Seevolution: visualizing chromosome evolution. Bioinform. 25(7): 960-961 (2009) - [j12]Tim McComb, Oliver Cairncross, Andrew B. Noske, David L. A. Wood, Brad J. Marsh, Mark A. Ragan:
IllouraTM: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinform. 25(9): 1208-1210 (2009) - [j11]Chang Shin, Simon Wong, Melissa J. Davis, Mark A. Ragan:
Protein-protein interaction as a predictor of subcellular location. BMC Syst. Biol. 3: 28 (2009) - [j10]Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha:
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 180-189 (2009) - 2008
- [j9]Mark A. Ragan, Tim Littlejohn, Bruce Ross:
Genome-Scale Computational Biology and Bioinformatics in Australia. PLoS Comput. Biol. 4(8) (2008) - [c8]Melissa J. Davis, Andrew F. Newman, Imran Khan, Jane Hunter, Mark A. Ragan:
Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions. APBC 2008: 145-154 - [c7]Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer:
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. ISBRA 2008: 74-86 - [c6]Simon Wong, Mark A. Ragan:
MACHOS: Markov clusters of homologous subsequences. ISMB 2008: 77-85 - [c5]Mark A. Ragan, Brad J. Marsh:
The Visible Cell Project: Changing the Way We Think about Cells. ISPAN 2008: 10 - 2007
- [j8]Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan:
A two-phase strategy for detecting recombination in nucleotide sequences. South Afr. Comput. J. 38: 20-27 (2007) - [c4]Benny Chor, Michael R. Fellows, Mark A. Ragan, Igor Razgon, Frances A. Rosamond, Sagi Snir:
Connected Coloring Completion for General Graphs: Algorithms and Complexity. COCOON 2007: 75-85 - [c3]Hans L. Bodlaender, Michael R. Fellows, Michael A. Langston, Mark A. Ragan, Frances A. Rosamond, Mark Weyer:
Quadratic Kernelization for Convex Recoloring of Trees. COCOON 2007: 86-96 - 2006
- [j7]Kevin Burrage, Lindsay Hood, Mark A. Ragan:
Advanced computing for systems biology. Briefings Bioinform. 7(4): 390-398 (2006) - [j6]Alexander García Castro, Philippe Rocca-Serra, Robert Stevens, Chris F. Taylor, Karim Nashar, Mark A. Ragan, Susanna-Assunta Sansone:
The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. BMC Bioinform. 7: 267 (2006) - [j5]Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan:
Detecting recombination in evolving nucleotide sequences. BMC Bioinform. 7: 412 (2006) - [c2]Hans L. Bodlaender, Michael R. Fellows, Michael A. Langston, Mark A. Ragan, Frances A. Rosamond, Mark Weyer:
Kernelization for Convex Recoloring. ACiD 2006: 23-35 - [c1]Mark A. Ragan:
Automating the Search for Lateral Gene Transfer. APBC 2006: 3 - 2005
- [j4]Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan:
A word-oriented approach to alignment validation. Bioinform. 21(10): 2230-2239 (2005) - [j3]Alexander García Castro, Samuel Thoraval, Leyla J. García, Mark A. Ragan:
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. BMC Bioinform. 6: 87 (2005) - 2004
- [j2]Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan:
A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinform. 5: 45 (2004)
1990 – 1999
- 1990
- [j1]Carolyn J. Bird, Ellen L. Rice, Colleen A. Murphy, Qing Yan Liu, Mark A. Ragan:
Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp. Nucleic Acids Res. 18(13): 4023-4024 (1990)
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