Mark A. Ragan

Publication Activity (10 Years)

Years Active: 1990-2019
Publications (10 Years): 1

Top Topics

Protein Interaction

Automatic Selection

Gene Regulatory Networks

Computational Methods

Top Venues

Briefings Bioinform.

Publications

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) (2019)
Atefeh Taherian-Fard, Sriganesh Srihari, Mark A. Ragan
Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings Bioinform. 16 (3) (2015)
Stefan Maetschke, Mark A. Ragan
Characterizing cancer subtypes as attractors of Hopfield networks. Bioinform. 30 (9) (2014)
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) (2014)
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) (2014)
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)
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) (2014)
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) (2014)
Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan
RMaNI: Regulatory Module Network Inference framework. BMC Bioinform. 14 (S-16) (2013)
Sriganesh Srihari, Mark A. Ragan
Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinform. 29 (12) (2013)
Cheong Xin Chan, Maisarah Mahbob, Mark A. Ragan
Clustering evolving proteins into homologous families. BMC Bioinform. 14 (2013)
Sriganesh Srihari, Mark A. Ragan
Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification CoRR (2013)
Stefan Maetschke, Martin Simonsen, Melissa J. Davis, Mark A. Ragan
Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinform. 28 (1) (2012)
Martin Simonsen, Stefan Maetschke, Mark A. Ragan
Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinform. 28 (6) (2012)
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 (2012)
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) (2011)
Chikako Ragan, Michael Zuker, Mark A. Ragan
Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations. PLoS Comput. Biol. 7 (2) (2011)
Melissa J. Davis, Muhammad Shoaib B. Sehgal, Mark A. Ragan
Automatic, context-specific generation of Gene Ontology slims. BMC Bioinform. 11 (2010)
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) (2010)
Stefan Maetschke, Karin S. Kassahn, Jasmyn A. Dunn, Siew-Ping Han, Eva Z. Curley, Katryn J. Stacey, Mark A. Ragan
-grams and spectral rearrangement. Bioinform. 26 (6) (2010)
Tim McComb, Oliver Cairncross, Andrew B. Noske, David L. A. Wood, Brad J. Marsh, Mark A. Ragan
: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinform. 25 (9) (2009)
Andrés Esteban-Marcos, Aaron E. Darling, Mark A. Ragan
Seevolution: visualizing chromosome evolution. Bioinform. 25 (7) (2009)
Chang Shin, Simon Wong, Melissa J. Davis, Mark A. Ragan
Protein-protein interaction as a predictor of subcellular location. BMC Syst. Biol. 3 (2009)
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) (2009)
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)
Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. ISBRA (2008)
Simon Wong, Mark A. Ragan
MACHOS: Markov clusters of homologous subsequences. ISMB (2008)
Mark A. Ragan, Tim Littlejohn, Bruce Ross
Genome-Scale Computational Biology and Bioinformatics in Australia. PLoS Comput. Biol. 4 (8) (2008)
Mark A. Ragan, Brad J. Marsh
The Visible Cell Project: Changing the Way We Think about Cells. ISPAN (2008)
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)
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)
Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
A two-phase strategy for detecting recombination in nucleotide sequences. South Afr. Comput. J. 38 (2007)
Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
Detecting recombination in evolving nucleotide sequences. BMC Bioinform. 7 (2006)
Hans L. Bodlaender, Michael R. Fellows, Michael A. Langston, Mark A. Ragan, Frances A. Rosamond, Mark Weyer
Kernelization for Convex Recoloring. ACiD (2006)
Mark A. Ragan
Automating the Search for Lateral Gene Transfer. APBC (2006)
Kevin Burrage, Lindsay Hood, Mark A. Ragan
Advanced computing for systems biology. Briefings Bioinform. 7 (4) (2006)
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 (2006)
Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan
A word-oriented approach to alignment validation. Bioinform. 21 (10) (2005)
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 (2005)
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 (2004)
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) (1990)