Mark A. Ragan

发表

A hybrid clustering approach to recognition of protein families in 114 microbial genomes

Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan, 2004, BMC Bioinformatics.

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats

Xavier Messeguer, Mark A. Ragan, Todd J. Treangen, 2008, ISBRA.

Information Integration in Molecular Bioscience

Yi-Ping Phoebe Chen, Mark A. Ragan, Alexander Garcia Castro, 2005, Applied bioinformatics.

Bioinformatic workflows: G-PIPE as an implementation

Yi-Ping Phoebe Chen, Mark A. Ragan, Alexander Garcia, 2005 .

Cognitive support for an argumentative structure during the ontology development process

Mark A. Ragan, Alexander Garcia Castro, Angela Norena, 2006 .

A two-phase strategy for detecting recombination in nucleotide sequences

Mark A. Ragan, Robert G. Beiko, Cheong Xin Chan, 2007, South Afr. Comput. J..

Visualization of image data from cells to

Anne E Carpenter, Mark A. Ragan, Anne E. Carpenter, 2010 .

Faculty Opinions recommendation of Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.

Mark A. Ragan, 2012 .

Breast cancer classification: linking molecular mechanisms to disease prognosis

Mark A. Ragan, Atefeh Taherian-Fard, Sriganesh Srihari, 2015, Briefings Bioinform..

Automated computational genomics: a case study

Mark A. Ragan, 2003 .

Advanced computing for systems biology

Mark A. Ragan, Kevin Burrage, Lindsay Hood, 2006, Briefings Bioinform..

mCOPA: analysis of heterogeneous features in cancer expression data

Mark A. Ragan, Chenwei Wang, Stefan Maetschke, 2012, Journal of Clinical Bioinformatics.

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

Xavier Messeguer, Mark A. Ragan, Todd J. Treangen, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

An efficient parallel implementation of Markov clustering algorithm for large-scale protein-protein interaction networks that uses MPI

Mark A. Ragan, Nicholas A. Hamilton, Kevin Burrage, 2009 .

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

Mark A. Ragan, Lars K. Nielsen, Liam G. Fearnley, 2014, BIOINFORMATICS.

Quadratic Kernelization for Convex Recoloring of Trees

Michael R. Fellows, Michael A. Langston, Mark A. Ragan, 2010, Algorithmica.

Freeing phylogenies from alignments

Mark A. Ragan, Isidore Rigoutsos, Michael Höhl, 2003, ISMB 2003.

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

Mark A. Ragan, Brad J. Marsh, 2008, 2008 International Symposium on Parallel Architectures, Algorithms, and Networks (i-span 2008).

Evaluation and expression of “drug-likeness” of small molecules using Semantic Web technologies.

Mark A. Ragan, Melissa J. Davis, JooYoung Choi, 2008, APBC 2009.

JPIPE, a pipeline module for JEMBOSS

Yi-Ping Phoebe Chen, Mark A. Ragan, Alexander Garcia, 2003, ISMB 2003.

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction

Mark A. Ragan, Isidore Rigoutsos, Michael Höhl, 2006, Evolutionary bioinformatics online.

Detecting recombination in evolving nucleotide sequences

Mark A. Ragan, Robert G. Beiko, Cheong Xin Chan, 2006, BMC Bioinformatics.

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

Mark A. Ragan, Michael Zuker, Chikako Ragan, 2011, PLoS Comput. Biol..

Automatic, context-specific generation of Gene Ontology slims

Mark A. Ragan, Muhammad Shoaib B. Sehgal, Melissa J. Davis, 2010, BMC Bioinformatics.

Automating the Search for Lateral Gene Transfer

Mark A. Ragan, 2006, APBC.

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

Mark A. Ragan, Stefan Maetschke, Melissa J. Davis, 2013, Briefings Bioinform..

Faculty Opinions recommendation of How difficult is inference of mammalian causal gene regulatory networks

Mark A. Ragan, 2015 .

A Semantic Web Ontology for Small Molecules and Their Biological Targets

Mark A. Ragan, Joo-Young Choi, Melissa J. Davis, 2010, J. Chem. Inf. Model..

SEMA, a semantic literature annotator

Yi-Ping Phoebe Chen, Mark A. Ragan, Alexander Garcia, 2003, ISMB 2003.

Position Paper for Semantic Web Life Sciences Workshop

Jane Hunter, Mark A. Ragan, Suzanne Little, 2004 .

Quadratic Kernelization for Convex Recoloring of Trees

Michael R. Fellows, Michael A. Langston, Mark A. Ragan, 2007, Algorithmica.

A two-phase approach for detecting recombination in nucleotide sequences

Mark A. Ragan, Robert G. Beiko, Cheong Xin Chan, 2007, 0709.1874.

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case

Chris F. Taylor, Alexander García Castro, Mark A. Ragan, 2006, BMC Bioinformatics.

RMaNI: Regulatory Module Network Inference framework

Mark A. Ragan, Stefan Maetschke, Melissa J. Davis, 2013, BMC Bioinformatics.

IllouraTM: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data

Mark A. Ragan, Tim McComb, Brad J. Marsh, 2009, Bioinform..

MACHOS: Markov clusters of homologous subsequences

Mark A. Ragan, Simon Wong, M. Ragan, 2008, ISMB.

Characterizing cancer subtypes as attractors of Hopfield networks

Mark A. Ragan, Stefan Maetschke, S. Maetschke, 2014, Bioinform..

Seevolution: visualizing chromosome evolution

Mark A. Ragan, Aaron E. Darling, Andrés Esteban-Marcos, 2009, Bioinform..

Genome-Scale Computational Biology and Bioinformatics in Australia

Mark A. Ragan, Tim Littlejohn, Bruce Ross, 2008, PLoS Comput. Biol..

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

Mark A. Ragan, Stefan Maetschke, Martin Simonsen, 2012, Bioinform..

A visual framework for sequence analysis using n-grams and spectral rearrangement

Mark A. Ragan, Stefan Maetschke, Karin S. Kassahn, 2010, Bioinform..

The MRP Method

Mark A. Ragan, Bernard R. Baum, M. Ragan, 2004 .

A word-oriented approach to alignment validation

Mark A. Ragan, Robert G. Beiko, Cheong Xin Chan, 2005, Bioinform..

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

Mark A. Ragan, Stefan Maetschke, Martin Simonsen, 2011 .

Clustering evolving proteins into homologous families

Mark A. Ragan, Cheong Xin Chan, Maisarah Mahbob, 2013, BMC Bioinformatics.

Eleventh International Seaweed Symposium

Mark A. Ragan, Carolyn J. Bird, 1984, Developments in Hydrobiology.

A hybrid clustering approach to genome-scale recognition of protein families

Timothy J. Harlow, Mark A. Ragan, J. P. Gogarten, 2003, ISMB 2003.

Extracting reaction networks from databases–opening Pandora’s box

Mark A. Ragan, Lars K. Nielsen, Melissa J. Davis, 2013, Briefings Bioinform..

Twelfth International Seaweed Symposium

Mark A. Ragan, Carolyn J. Bird, M. Ragan, 1987, Developments in Hydrobiology.

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

Mark A. Ragan, Sriganesh Srihari, M. Ragan, 2013, ArXiv.

Automatic, context-specific generation of Gene

Mark A. Ragan, Melissa J. Davis, Muhammad Shoaib, 2010 .

Faculty Opinions recommendation of Panorama of ancient metazoan macromolecular complexes.

Mark A. Ragan, 2015 .

The use of conceptual maps for two ontology developments: nutrigenomics, and a management system for genealogies.

Mark A. Ragan, Susanna-Assunta Sansone, Philippe Rocca-Serra, 2005 .

Kernelization for Convex Recoloring

Michael R. Fellows, Michael A. Langston, Mark A. Ragan, 2006, ACiD.

BMC Systems Biology BioMed Central Research article Protein-protein interaction as a predictor of subcellular location

Mark A. Ragan, Melissa J. Davis, Simon Wong, 2008 .

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

Alexander García Castro, Mark A. Ragan, Leyla J. García, 2004, BMC Bioinformatics.

Complex-based analysis of dysregulated cellular processes in cancer

Chao Liu, Mark A. Ragan, Sriganesh Srihari, 2014, BMC Systems Biology.

Advanced computing for systems

Mark A. Ragan, Kevin Burrage, Lindsay Hood, 2006 .

Systematic tracking of dysregulated modules identifies novel genes in cancer

Mark A. Ragan, Sriganesh Srihari, M. Ragan, 2013, Bioinform..

Connected Coloring Completion for General Graphs: Algorithms and Complexity

Michael R. Fellows, Sagi Snir, Mark A. Ragan, 2007, COCOON.

Benchmarking the Detection and Analysis of Recombination

Mark A. Ragan, Robert G. Beiko, Cheong Xin Chan, 2004, ISMB 2004.

Faculty Opinions recommendation of Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Mark A. Ragan, 2013 .

Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions

Jane Hunter, Imran Khan, Mark A. Ragan, 2008, APBC.

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

James M. Hogan, Mark A. Ragan, Yao-ban Chan, 2017, Briefings Bioinform..

Sampling phylogenetic tree space with the generalized Gibbs sampler

Peter Adams, Darryn Bryant, Mark A. Ragan, 2005 .

Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer

Limsoon Wong, Mark A. Ragan, Sriganesh Srihari, 2015, Biology Direct.

Breast cancer classification: linking molecular mechanisms to disease prognosis

Mark A. Ragan, Sriganesh Srihari, M. Ragan, 2015, Briefings Bioinform..

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF

Michael A. Langston, Mark A. Ragan, Yao-ban Chan, 2017, Front. Microbiol..

Exploring lateral genetic transfer among microbial genomes using TF-IDF

Mark A. Ragan, Yao-ban Chan, Yingnan Cong, 2016, Scientific Reports.

Paul Greenfield, Mark A. Ragan, Cheong Xin Chan, 2017, mSystems.

Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach

Mark A. Ragan, Atefeh Taherian Fard, M. Ragan, 2017, Front. Genet..

Identification of domoic acid, a neuroexcitatory amino acid, in toxic mussels from eastern Prince Edward Island

Mark A. Ragan, Maurice V. Laycock, Michael Falk, 1989 .

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

Mark A. Ragan, M. Ragan, Elizabeth Skippington, 2012, Genome biology and evolution.

Phylogenetic Supertrees

Charles Semple, Mark A. Ragan, David Bryant, 2004, Computational Biology.

INsPeCT: INtegrative Platform for Cancer Transcriptomics

Mark A. Ragan, Antonio Reverter, Stefan R. Maetschke, 2014, Cancer informatics.

Evolution and Controllability of Cancer Networks: A Boolean Perspective

Venkatesh Raman, Hon Wai Leong, Mark A. Ragan, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction

Mark A. Ragan, Isidore Rigoutsos, Michael Höhl, 2006 .

mCOPA : analysis of heterogeneous features in cancer expression data

Mark A. Ragan, Colleen C. Nelson, Alperen Taciroglu, 2013 .

Transcriptome-Wide Prediction of miRNA Targets in Human and Mouse Using FASTH

Mark A. Ragan, Michael Zuker, Chikako Ragan, 2009, PloS one.

Kernelization for convex recoloring of trees

Michael R. Fellows, Michael A. Langston, Mark A. Ragan, 2006 .

The network of life: genome beginnings and evolution

James O. McInerney, Mark A. Ragan, James A. Lake, 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

Microbial phylogenomics: Branching out

Mark A. Ragan, Robert G. Beiko, Robert L. Charlebois, 2003, Nature.

Are rRNA sequence comparisons the Rosetta stone of phylogenetics?

Mark A. Ragan, Lynn J. Rothschild, Susan A. Gerbi, 1986, Cell.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

Mark A. Ragan, Cheong Xin Chan, M. Ragan, 2016, Scientific Reports.

The complete genome of the crenarchaeon Sulfolobus solfataricus P2

Mark A. Ragan, Xu Peng, Terry Gaasterland, 2001, Proceedings of the National Academy of Sciences of the United States of America.