Mark A. Ragan

According to our database, Mark A. Ragan authored at least 40 papers between 1990 and 2019.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2019

Alignment-free inference of hierarchical and reticulate phylogenomic relationships.

Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M. Hogan, Stefan R. Maetschke, Mark A. Ragan

Briefings Bioinform., 2019

2015

Breast cancer classification: linking molecular mechanisms to disease prognosis.

Atefeh Taherian Fard, Sriganesh Srihari, Mark A. Ragan

Briefings Bioinform., 2015

2014

Evolution and Controllability of CancerNetworks: A Boolean Perspective.

Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong, Mark A. Ragan

IEEE ACM Trans. Comput. Biol. 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

Characterizing cancer subtypes as attractors of Hopfield networks.

Stefan Maetschke, Mark A. Ragan

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

Extracting reaction networks from databases-opening Pandora's box.

Liam G. Fearnley, Melissa J. Davis, Mark A. Ragan, Lars Keld Nielsen

Briefings Bioinform., 2014

Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells.

Liam G. Fearnley, Mark A. Ragan, Lars Keld Nielsen

Proceedings of the BIOINFORMATICS 2014, 2014

2013

Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification

Sriganesh Srihari, Mark A. Ragan

CoRR, 2013

RMaNI: Regulatory Module Network Inference framework.

Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan

BMC Bioinform., 2013

Clustering evolving proteins into homologous families.

Cheong Xin Chan, Maisarah Mahbob, Mark A. Ragan

BMC Bioinform., 2013

Systematic tracking of dysregulated modules identifies novel genes in cancer.

Sriganesh Srihari, Mark A. Ragan

Bioinform., 2013

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

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling.

Martin Simonsen, Stefan Maetschke, Mark A. Ragan

Bioinform., 2012

Gene Ontology-driven inference of protein-protein interactions using inducers.

Stefan Maetschke, Martin Simonsen, Melissa J. Davis, Mark A. Ragan

Bioinform., 2012

2011

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations.

Chikako Ragan, Michael Zuker, Mark A. Ragan

PLoS Comput. Biol., 2011

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

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

Automatic, context-specific generation of Gene Ontology slims.

Melissa J. Davis, Muhammad Shoaib B. Sehgal, Mark A. Ragan

BMC Bioinform., 2010

A visual framework for sequence analysis using <i>n</i>-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

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

Protein-protein interaction as a predictor of subcellular location.

Chang Shin, Simon Wong, Melissa J. Davis, Mark A. Ragan

BMC Syst. Biol., 2009

Illoura^TM: 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

Seevolution: visualizing chromosome evolution.

Andrés Esteban-Marcos, Aaron E. Darling, Mark A. Ragan

Bioinform., 2009

2008

Genome-Scale Computational Biology and Bioinformatics in Australia.

Mark A. Ragan, Tim Littlejohn, Bruce Ross

PLoS Comput. Biol., 2008

The Visible Cell Project: Changing the Way We Think about Cells.

Mark A. Ragan, Brad J. Marsh

Proceedings of the 9th International Symposium on Parallel Architectures, 2008

MACHOS: Markov clusters of homologous subsequences.

Simon Wong, Mark A. Ragan

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats.

Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer

Proceedings of the Bioinformatics Research and Applications, 2008

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, Mark A. Ragan

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

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

Connected Coloring Completion for General Graphs: Algorithms and Complexity.

Benny Chor, Michael R. Fellows, Mark A. Ragan, Igor Razgon, Frances A. Rosamond, Sagi Snir

Proceedings of the Computing and Combinatorics, 13th Annual International Conference, 2007

2006

Detecting recombination in evolving nucleotide sequences.

Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan

BMC 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, Chris F. Taylor, Karim Nashar, Mark A. Ragan, Susanna-Assunta Sansone

BMC Bioinform., 2006

Advanced computing for systems biology.

Kevin Burrage, Lindsay Hood, Mark A. Ragan

Briefings Bioinform., 2006

Automating the Search for Lateral Gene Transfer.

Mark A. Ragan

Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

Kernelization for Convex Recoloring.

Hans L. Bodlaender, Michael R. Fellows, Michael A. Langston, Mark A. Ragan, Frances A. Rosamond, Mark Weyer

Proceedings of the Algorithms and Complexity in Durham 2006, 2006

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

A word-oriented approach to alignment validation.

Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan

Bioinform., 2005

2004

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

1990

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