List of works by Mark A. Ragan

A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy

scientific article

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

2007 thesis

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

scientific article published on 23 September 2019

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

scientific article

A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene.

scientific article published on July 1994

A new species of Burkholderia isolated from sugarcane roots promotes plant growth

scientific article

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.

scientific article published on 25 July 2016

A novel heuristic for local multiple alignment of interspersed DNA repeats

scientific article

A semantic web ontology for small molecules and their biological targets

scientific article

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

scientific article

A word-oriented approach to alignment validation

scientific article published on 22 February 2005

Advanced computing for systems biology.

scientific article published on 25 September 2006

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

scientific article published on July 2016

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

scientific article published on June 2013

Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1α of Ichthyophonus irregularis

article

Are protein domains modules of lateral genetic transfer?

scientific article

Are rRNA sequence comparisons the Rosetta stone of phylogenetics?

scientific article published on 01 December 1986

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

scientific article published on 4 January 2012

Automatic, context-specific generation of Gene Ontology slims

scientific article

Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation

scientific article

Biological Intuition in Alignment-Free Methods: Response to Posada

article

Breast cancer classification: linking molecular mechanisms to disease prognosis

scientific article

Characterization of a galactose-1-phosphate uridylyltransferase gene from the marine red alga Gracilaria gracilis

scientific article

Characterization of the nuclear gene encoding mitochondrial aconitase in the marine red alga Gracilaria verrucosa.

scientific article published on July 1995

Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa

scientific article

Characterizing cancer subtypes as attractors of Hopfield networks

scientific article published on 8 January 2014

Chelation of divalent metal ions by brown algal polyphenols

article published in 1979

Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America

scientific article

Cloning and characterization of a nuclear gene encoding a starch-branching enzyme from the marine red alga Gracilaria gracilis

scientific article published in August 1998

Cloning and characterization of the nuclear gene and cDNAs for triosephosphate isomerase of the marine red alga Gracilaria verrucosa

scientific article

Cloning and characterization of the nuclear gene encoding plastid glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa

scientific article published in July 1994

Clustering evolving proteins into homologous families

scientific article

Completing the sequence of the Sulfolobus solfataricus P2 genome

scientific article published in August 1998

Complex-based analysis of dysregulated cellular processes in cancer

scientific article

Constructing multigenome views of whole microbial genomes.

scientific article

Crosstalk between sugarcane and a plant-growth promoting Burkholderia species

scientific article (publication date: 21 November 2016)

Detecting lateral genetic transfer : a phylogenetic approach.

scientific article published on January 2008

Detecting recombination in evolving nucleotide sequences

scientific article

Detection of lateral gene transfer among microbial genomes.

scientific article

Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission

scientific article published in May 2002

Do different surrogate methods detect lateral genetic transfer events of different relative ages?

scientific article

Dynamics of genome rearrangement in bacterial populations

scientific article published in 2008

Erratum: Visualization of image data from cells to organisms

scholarly article by Thomas Walter et al published June 2010 in Nature Methods

Evolution and Controllability of Cancer Networks: A Boolean Perspective

scientific article published on January 2014

Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.

scientific article published on 13 May 2009

Exploring lateral genetic transfer among microbial genomes using TF-IDF.

scientific article published on 25 July 2016

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

scientific article

Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts

scientific article

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

scientific article

Genome-scale computational biology and bioinformatics in Australia

scientific article

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

scientific article published on 27 November 2020

INsPeCT: INtegrative Platform for Cancer Transcriptomics.

scientific article published on 12 March 2014

Identification of human haploinsufficient genes and their genomic proximity to segmental duplications

scientific article

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

scientific article

Inferring phylogenies of evolving sequences without multiple sequence alignment.

scientific article

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

scientific article

Information Integration in Molecular Bioscience

Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer

scientific article

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

scientific article published in 2016

Is multiple-sequence alignment required for accurate inference of phylogeny?

scientific article

Lateral genetic transfer and the construction of genetic exchange communities

scientific article published on 21 January 2011

Lateral genetic transfer: open issues

scientific article published on August 2009

Lateral transfer of genes and gene fragments in prokaryotes

scientific article

MACHOS: Markov clusters of homologous subsequences

scientific article

Matrix representation in reconstructing phylogenetic relationships among the eukaryotes

scientific article published on 01 January 1992

Microbial phylogenomics: Branching out

scientific article published in Nature

Mineralocorticoid receptors: evolutionary and pathophysiological considerations.

scientific article published on 22 February 2011

Molecular epidemiology of clinical Cryptococcus neoformans strains from India

scientific article

Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra

scientific article (publication date: 2014)

Morphological stasis masks ecologically divergent coral species on tropical reefs

scientific article published on 02 April 2021

Next-generation phylogenomics

scientific article (publication date: 22 January 2013)

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

scientific article

Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp

scientific article published in July 1990

Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2.

scientific article published on October 1996

Paired-ion reversed-phase high-performance liquid chromatography of phenol sulfates in synthetic mixtures, algas extracts and urine

scientific article published on 01 October 1979

Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer.

scientific article published on 26 September 2015

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

scientific article

Phylogenetic inference based on matrix representation of trees

scientific article published on 01 March 1992

Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.

scientific article

Protein contact prediction using patterns of correlation

scientific article

Protein-protein interaction as a predictor of subcellular location

scientific article

Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota

scientific article published in September 2000

Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations

scientific article

RMaNI: Regulatory Module Network Inference framework

scientific article published on 22 October 2013

Recapitulating phylogenies using k-mers: from trees to networks

scientific article published on 29 November 2016

Research resource: nuclear receptors as transcriptome: discriminant and prognostic value in breast cancer

scientific article

Rewiring the dynamic interactome

scientific article published on 22 June 2012

Ribosomal RNA and the major lines of evolution: a perspective

scientific article published on January 1988

Sampling phylogenetic tree space with the generalized Gibbs sampler

scientific article published on 8 January 2005

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

scientific article published on January 2017

Searching for convergence in phylogenetic Markov chain Monte Carlo

scientific article published in August 2006

Seevolution: visualizing chromosome evolution

scientific article published on 20 February 2009

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

scientific article

Systematic tracking of dysregulated modules identifies novel genes in cancer

scientific article published on 23 April 2013

The Sulfolobus solfataricus P2 genome project.

scientific article published on June 1996

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application

scientific article

The lobster parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): nuclear 18S rDNA sequence, phylogeny and detection using oligonucleotide primers

scientific article published in July 1996

The mammalian PYHIN gene family: phylogeny, evolution and expression

scientific article (publication date: 7 August 2012)

The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells

scientific article published on 04 January 2017

The nuclear gene and cDNAs encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa: cloning, characterization and phylogenetic analysis

scientific article published on September 1995

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.

scientific article

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

scientific article (publication date: 25 May 2006)

Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse

scientific article published on December 2009

Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH.

scientific article

Trees and networks before and after Darwin

scientific article

Understanding cellular function and disease with comparative pathway analysis

scientific article

Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach

scientific article published on 01 March 2016

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction

scientific article

Visualization of image data from cells to organisms

scientific article

Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium

scientific article published on 23 January 2019

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.

scientific article

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

scientific article

Yeast rises to the occasion

scientific article published on 18 June 2013

cDNA cloning and characterization of the nuclear gene encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa

scientific article published in May 1993

k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank

scientific article published on 20 November 2018

mCOPA: analysis of heterogeneous features in cancer expression data

scientific article

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