Mark A. Ragan, PhD - Publications

Affiliations: 
Institute for Molecular Bioscience University of Queensland, Saint Lucia, Queensland, Australia 
Area:
Computational Biology, Bioinformatics

166 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA. Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings in Bioinformatics. PMID 28673025 DOI: 10.1093/bib/bbx067  0.64
2016 Fard AT, Srihari S, Mar JC, Ragan MA. Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. Npj Systems Biology and Applications. 2: 16001. PMID 28725466 DOI: 10.1038/npjsba.2016.1  0.72
2016 Cong Y, Chan YB, Ragan MA. A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF. Scientific Reports. 6: 30308. PMID 27453035 DOI: 10.1038/srep30308  0.92
2016 Cong Y, Chan YB, Ragan MA. Exploring lateral genetic transfer among microbial genomes using TF-IDF. Scientific Reports. 6: 29319. PMID 27452976 DOI: 10.1038/srep29319  0.92
2016 Bernard G, Chan CX, Ragan MA. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer. Scientific Reports. 6: 28970. PMID 27363362 DOI: 10.1038/srep28970  0.92
2016 Stephens TG, Bhattacharya D, Ragan MA, Chan CX. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. Peerj. 4: e2038. PMID 27190724 DOI: 10.7717/peerj.2038  0.92
2016 Srihari S, Kalimutho M, Lal S, Singla J, Patel D, Simpson PT, Khanna KK, Ragan MA. Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach. Molecular Biosystems. PMID 26805938 DOI: 10.1039/c5mb00655d  0.92
2015 Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Molecular Oncology. PMID 26456802 DOI: 10.1016/j.molonc.2015.09.007  0.92
2015 Srihari S, Singla J, Wong L, Ragan MA. Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct. 10: 57. PMID 26427375 DOI: 10.1186/s13062-015-0086-1  0.92
2015 Yeoh YK, Paungfoo-Lonhienne C, Dennis PG, Robinson N, Ragan MA, Schmidt S, Hugenholtz P. The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application. Environmental Microbiology. PMID 26032777 DOI: 10.1111/1462-2920.12925  0.92
2015 Paungfoo-Lonhienne C, Yeoh YK, Kasinadhuni NR, Lonhienne TG, Robinson N, Hugenholtz P, Ragan MA, Schmidt S. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Scientific Reports. 5: 8678. PMID 25728892 DOI: 10.1038/srep08678  0.92
2015 Taherian-Fard A, Srihari S, Ragan MA. Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings in Bioinformatics. 16: 461-74. PMID 24950687 DOI: 10.1093/bib/bbu020  0.92
2014 Srihari S, Raman V, Hon Wai Leong, Ragan MA. Evolution and Controllability of Cancer Networks: A Boolean Perspective. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 11: 83-94. PMID 26355510 DOI: 10.1109/TCBB.2013.128  0.72
2014 Srihari S, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA. Complex-based analysis of dysregulated cellular processes in cancer. Bmc Systems Biology. 8: S1. PMID 25521701 DOI: 10.1186/1752-0509-8-S4-S1  0.92
2014 Chan CX, Bernard G, Poirion O, Hogan JM, Ragan MA. Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports. 4: 6504. PMID 25266120 DOI: 10.1038/srep06504  0.92
2014 Liu C, Srihari S, Cao KA, Chenevix-Trench G, Simpson PT, Ragan MA, Khanna KK. A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Research. 42: 6106-27. PMID 24792170 DOI: 10.1093/nar/gku284  0.92
2014 Madhamshettiwar PB, Maetschke SR, Davis MJ, Reverter A, Ragan MA. INsPeCT: INtegrative Platform for Cancer Transcriptomics. Cancer Informatics. 13: 59-66. PMID 24653643 DOI: 10.4137/CIN.S13630  0.92
2014 Ragan MA, Bernard G, Chan CX. Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra. Rna Biology. 11: 176-85. PMID 24572375 DOI: 10.4161/rna.27505  0.92
2014 Maetschke SR, Ragan MA. Characterizing cancer subtypes as attractors of Hopfield networks. Bioinformatics (Oxford, England). 30: 1273-9. PMID 24407221 DOI: 10.1093/bioinformatics/btt773  0.92
2014 Paungfoo-Lonhienne C, Lonhienne TG, Yeoh YK, Webb RI, Lakshmanan P, Chan CX, Lim PE, Ragan MA, Schmidt S, Hugenholtz P. A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology. 7: 142-54. PMID 24350979 DOI: 10.1111/1751-7915.12105  0.92
2014 Fearnley LG, Davis MJ, Ragan MA, Nielsen LK. Extracting reaction networks from databases-opening Pandora's box. Briefings in Bioinformatics. 15: 973-83. PMID 23946492 DOI: 10.1093/bib/bbt058  0.92
2014 Maetschke SR, Madhamshettiwar PB, Davis MJ, Ragan MA. Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Briefings in Bioinformatics. 15: 195-211. PMID 23698722 DOI: 10.1093/bib/bbt034  0.92
2014 Lonhienne T, Mason MG, Ragan MA, Hugenholtzc P, Schmidt S, Paungfoo-Lonhienne C. Yeast as a biofertilizer alters plant growth and morphology Crop Science. 54: 785-790. DOI: 10.2135/cropsci2013.07.0488  0.92
2014 Srihari S, Raman V, Wai Leong H, Ragan MA. Evolution and controllability of cancernetworks: A boolean perspective Ieee/Acm Transactions On Computational Biology and Bioinformatics. 11: 83-94. DOI: 10.1109/TCBB.2013.128  0.92
2014 Fearnley LG, Ragan MA, Nielsen LK. Towards a large integrated model of signal transduction and gene regulation events in mammalian cells Bioinformatics 2014 - 5th Int. Conf. On Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference On Biomedical Engineering Systems and Technologies, Biostec 2014. 117-122.  0.92
2013 Madhamshettiwar PB, Maetschke SR, Davis MJ, Ragan MA. RMaNI: Regulatory Module Network Inference framework. Bmc Bioinformatics. 14: S14. PMID 24564496 DOI: 10.1186/1471-2105-14-S16-S14  0.92
2013 Srihari S, Raman V, Leong HW, Ragan MA. Evolution and Controllability of Cancer Networks: A Boolean Perspective. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 24166654  0.72
2013 Davis MJ, Ragan MA. Understanding cellular function and disease with comparative pathway analysis. Genome Medicine. 5: 64. PMID 23889971 DOI: 10.1186/gm468  0.92
2013 Ragan MA, Chan CX. Biological intuition in alignment-free methods: response to Posada. Journal of Molecular Evolution. 77: 1-2. PMID 23877343 DOI: 10.1007/s00239-013-9573-0  0.92
2013 Ragan MA. Yeast rises to the occasion. Elife. 2: e00933. PMID 23795300 DOI: 10.7554/eLife.00933  0.92
2013 Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA. Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology. 22: 3216-41. PMID 23763602 DOI: 10.1111/mec.12309  0.92
2013 Srihari S, Ragan MA. Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics (Oxford, England). 29: 1553-61. PMID 23613489 DOI: 10.1093/bioinformatics/btt191  0.92
2013 Chan CX, Mahbob M, Ragan MA. Clustering evolving proteins into homologous families. Bmc Bioinformatics. 14: 120. PMID 23566217 DOI: 10.1186/1471-2105-14-120  0.92
2013 Chan CX, Ragan MA. Next-generation phylogenomics. Biology Direct. 8: 3. PMID 23339707 DOI: 10.1186/1745-6150-8-3  0.92
2013 Muscat GE, Eriksson NA, Byth K, Loi S, Graham D, Jindal S, Davis MJ, Clyne C, Funder JW, Simpson ER, Ragan MA, Kuczek E, Fuller PJ, Tilley WD, Leedman PJ, et al. Research resource: nuclear receptors as transcriptome: discriminant and prognostic value in breast cancer. Molecular Endocrinology (Baltimore, Md.). 27: 350-65. PMID 23292282 DOI: 10.1210/me.2012-1265  0.92
2013 Skippington E, Ragan MA. Lateral genetic transfer and cellular networks Lateral Gene Transfer in Evolution. 123-135. DOI: 10.1007/978-1-4614-7780-8-6  0.92
2012 Wang C, Taciroglu A, Maetschke SR, Nelson CC, Ragan MA, Davis MJ. mCOPA: analysis of heterogeneous features in cancer expression data. Journal of Clinical Bioinformatics. 2: 22. PMID 23216803 DOI: 10.1186/2043-9113-2-22  0.92
2012 Skippington E, Ragan MA. Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities. Open Biology. 2: 120112. PMID 23091700 DOI: 10.1098/rsob.120112  0.92
2012 Cridland JA, Curley EZ, Wykes MN, Schroder K, Sweet MJ, Roberts TL, Ragan MA, Kassahn KS, Stacey KJ. The mammalian PYHIN gene family: phylogeny, evolution and expression. Bmc Evolutionary Biology. 12: 140. PMID 22871040 DOI: 10.1186/1471-2148-12-140  0.92
2012 Davis MJ, Shin CJ, Jing N, Ragan MA. Rewiring the dynamic interactome. Molecular Biosystems. 8: 2054-66, 2013. PMID 22729145 DOI: 10.1039/c2mb25050k  0.92
2012 Madhamshettiwar PB, Maetschke SR, Davis MJ, Reverter A, Ragan MA. Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Medicine. 4: 41. PMID 22548828 DOI: 10.1186/gm340  0.92
2012 Skippington E, Ragan MA. Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes. Genome Biology and Evolution. 4: 330-45. PMID 22223756 DOI: 10.1093/gbe/evs001  0.92
2012 Simonsen M, Maetschke SR, Ragan MA. Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics (Oxford, England). 28: 851-7. PMID 22219205 DOI: 10.1093/bioinformatics/btr720  0.92
2012 Maetschke SR, Simonsen M, Davis MJ, Ragan MA. Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinformatics (Oxford, England). 28: 69-75. PMID 22057159 DOI: 10.1093/bioinformatics/btr610  0.92
2011 Skippington E, Ragan MA. Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. Bmc Genomics. 12: 532. PMID 22035052 DOI: 10.1186/1471-2164-12-532  0.92
2011 Chan CX, Beiko RG, Ragan MA. Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology. 193: 3964-77. PMID 21622749 DOI: 10.1128/JB.01524-10  0.92
2011 Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. Plos Computational Biology. 7: e1001090. PMID 21390282 DOI: 10.1371/journal.pcbi.1001090  0.92
2011 Kassahn KS, Ragan MA, Funder JW. Mineralocorticoid receptors: evolutionary and pathophysiological considerations. Endocrinology. 152: 1883-90. PMID 21343255 DOI: 10.1210/en.2010-1444  0.92
2011 Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. Fems Microbiology Reviews. 35: 707-35. PMID 21223321 DOI: 10.1111/j.1574-6976.2010.00261.x  0.92
2011 Bodlaender HL, Fellows MR, Langston MA, Ragan MA, Rosamond FA, Weyer M. Quadratic kernelization for convex recoloring of trees Algorithmica (New York). 61: 362-388. DOI: 10.1007/s00453-010-9404-2  0.92
2010 Davis MJ, Sehgal MS, Ragan MA. Automatic, context-specific generation of Gene Ontology slims. Bmc Bioinformatics. 11: 498. PMID 20929524 DOI: 10.1186/1471-2105-11-498  0.92
2010 Han SP, Kassahn KS, Skarshewski A, Ragan MA, Rothnagel JA, Smith R. Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts. Rna (New York, N.Y.). 16: 1760-8. PMID 20651029 DOI: 10.1261/rna.2142810  0.92
2010 Choi J, Davis MJ, Newman AF, Ragan MA. A semantic web ontology for small molecules and their biological targets. Journal of Chemical Information and Modeling. 50: 732-41. PMID 20405959 DOI: 10.1021/ci900461j  0.92
2010 Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK. Visualization of image data from cells to organisms. Nature Methods. 7: S26-41. PMID 20195255 DOI: 10.1038/nmeth.1431  0.92
2010 Maetschke SR, Kassahn KS, Dunn JA, Han SP, Curley EZ, Stacey KJ, Ragan MA. A visual framework for sequence analysis using n-grams and spectral rearrangement. Bioinformatics (Oxford, England). 26: 737-44. PMID 20130028 DOI: 10.1093/bioinformatics/btq042  0.92
2009 Ragan MA. Thinking laterally about genomes. Genome Informatics. International Conference On Genome Informatics. 23: 221-2. PMID 20180279  0.92
2009 Ragan MA. Trees and networks before and after Darwin. Biology Direct. 4: 43; discussion 43. PMID 19917100 DOI: 10.1186/1745-6150-4-43  0.92
2009 Shin CJ, Davis MJ, Ragan MA. Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics. 9: 5256-66. PMID 19834899 DOI: 10.1002/pmic.200900262  0.92
2009 Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364: 2241-51. PMID 19571244 DOI: 10.1098/rstb.2009.0031  0.92
2009 Ragan MA, McInerney JO, Lake JA. The network of life: genome beginnings and evolution. Introduction. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364: 2169-75. PMID 19571237 DOI: 10.1098/rstb.2009.0046  0.92
2009 Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA. Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. Plos One. 4: e5745. PMID 19478946 DOI: 10.1371/journal.pone.0005745  0.92
2009 Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Research. 19: 1404-18. PMID 19439512 DOI: 10.1101/gr.086827.108  0.92
2009 Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP. A novel heuristic for local multiple alignment of interspersed DNA repeats. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 180-9. PMID 19407343 DOI: 10.1109/TCBB.2009.9  0.92
2009 Beiko RG, Ragan MA. Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction. Methods in Molecular Biology (Clifton, N.J.). 532: 241-56. PMID 19271189 DOI: 10.1007/978-1-60327-853-9_14  0.92
2009 McComb T, Cairncross O, Noske AB, Wood DL, Marsh BJ, Ragan MA. Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinformatics (Oxford, England). 25: 1208-10. PMID 19258351 DOI: 10.1093/bioinformatics/btp125  0.92
2009 Shin CJ, Wong S, Davis MJ, Ragan MA. Protein-protein interaction as a predictor of subcellular location. Bmc Systems Biology. 3: 28. PMID 19243629 DOI: 10.1186/1752-0509-3-28  0.92
2009 Esteban-Marcos A, Darling AE, Ragan MA. Seevolution: visualizing chromosome evolution. Bioinformatics (Oxford, England). 25: 960-1. PMID 19233896 DOI: 10.1093/bioinformatics/btp096  0.92
2009 Chan CX, Darling AE, Beiko RG, Ragan MA. Are protein domains modules of lateral genetic transfer? Plos One. 4: e4524. PMID 19229333 DOI: 10.1371/journal.pone.0004524  0.92
2009 Burrage PM, Burrage K, Kurowski K, Lorenc M, Nicolau DV, Swain M, Ragan MA. A parallel plasma membrane simulation Hibi09 - 2009 International Workshop On High Performance Computational Systems Biology. 105-112. DOI: 10.1109/HiBi.2009.18  0.92
2008 Ragan MA, Littlejohn T, Ross B. Genome-scale computational biology and bioinformatics in Australia. Plos Computational Biology. 4: e1000068. PMID 18769502 DOI: 10.1371/journal.pcbi.1000068  0.92
2008 Darling AE, Miklós I, Ragan MA. Dynamics of genome rearrangement in bacterial populations. Plos Genetics. 4: e1000128. PMID 18650965 DOI: 10.1371/journal.pgen.1000128  0.92
2008 Wong S, Ragan MA. MACHOS: Markov clusters of homologous subsequences. Bioinformatics (Oxford, England). 24: i77-85. PMID 18586748 DOI: 10.1093/bioinformatics/btn144  0.92
2008 Beiko RG, Ragan MA. Detecting lateral genetic transfer : a phylogenetic approach. Methods in Molecular Biology (Clifton, N.J.). 452: 457-69. PMID 18566777 DOI: 10.1007/978-1-60327-159-2_21  0.92
2008 Dang VT, Kassahn KS, Marcos AE, Ragan MA. Identification of human haploinsufficient genes and their genomic proximity to segmental duplications. European Journal of Human Genetics : Ejhg. 16: 1350-7. PMID 18523451 DOI: 10.1038/ejhg.2008.111  0.92
2008 Ragan M, Marsh B. The Visible Cell™ project: Changing the way we think about cells Proceedings of the International Symposium On Parallel Architectures, Algorithms and Networks, I-Span. 10. DOI: 10.1109/I-SPAN.2008.53  0.92
2008 Treangen TJ, Darling AE, Ragan MA, Messeguer X. Gapped extension for local multiple alignment of interspersed DNA repeats Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4983: 74-86. DOI: 10.1007/978-3-540-79450-9_8  0.92
2008 Davis MJ, Newman A, Khan I, Hunter J, Ragan MA. Integrating hierarchical controlled vocabularies with owl ontology: A case study from the domain of molecular interactions Series On Advances in Bioinformatics and Computational Biology. 6: 145-154.  0.92
2007 Höhl M, Ragan MA. Is multiple-sequence alignment required for accurate inference of phylogeny? Systematic Biology. 56: 206-21. PMID 17454975 DOI: 10.1080/10635150701294741  0.92
2007 Andersson JO, Sjögren AM, Horner DS, Murphy CA, Dyal PL, Svärd SG, Logsdon JM, Ragan MA, Hirt RP, Roger AJ. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. Bmc Genomics. 8: 51. PMID 17298675 DOI: 10.1186/1471-2164-8-51  0.92
2007 Chan CX, Beiko RG, Ragan MA. Large-scale detection of recombination in nucleotide sequences Aip Conference Proceedings. 971: 101-104. DOI: 10.1063/1.2883829  0.92
2007 Chor B, Fellows M, Ragan MA, Razgon I, Rosamond F, Snir S. Connected coloring completion for general graphs: Algorithms and complexity Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4598: 75-85.  0.92
2006 Burrage K, Hood L, Ragan MA. Advanced computing for systems biology. Briefings in Bioinformatics. 7: 390-8. PMID 17000735 DOI: 10.1093/bib/bbl033  0.92
2006 Chan CX, Beiko RG, Ragan MA. Detecting recombination in evolving nucleotide sequences. Bmc Bioinformatics. 7: 412. PMID 16978423 DOI: 10.1186/1471-2105-7-412  0.92
2006 Beiko RG, Keith JM, Harlow TJ, Ragan MA. Searching for convergence in phylogenetic Markov chain Monte Carlo. Systematic Biology. 55: 553-65. PMID 16857650 DOI: 10.1080/10635150600812544  0.92
2006 Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA. The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case. Bmc Bioinformatics. 7: 267. PMID 16725019 DOI: 10.1186/1471-2105-7-267  0.92
2006 Ragan MA, Harlow TJ, Beiko RG. Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends in Microbiology. 14: 4-8. PMID 16356716 DOI: 10.1016/j.tim.2005.11.004  0.92
2005 Jain N, Wickes BL, Keller SM, Fu J, Casadevall A, Jain P, Ragan MA, Banerjee U, Fries BC. Molecular epidemiology of clinical Cryptococcus neoformans strains from India. Journal of Clinical Microbiology. 43: 5733-42. PMID 16272511 DOI: 10.1128/JCM.43.11.5733-5742.2005  0.92
2005 Garcia Castro A, Chen YP, Ragan MA. Information integration in molecular bioscience. Applied Bioinformatics. 4: 157-73. PMID 16231958 DOI: 10.2165/00822942-200594030-00001  0.92
2005 Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America. 102: 14332-7. PMID 16176988 DOI: 10.1073/pnas.0504068102  0.92
2005 Garcia Castro A, Thoraval S, Garcia LJ, Ragan MA. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. Bmc Bioinformatics. 6: 87. PMID 15813976 DOI: 10.1186/1471-2105-6-87  0.92
2005 Beiko RG, Chan CX, Ragan MA. A word-oriented approach to alignment validation. Bioinformatics (Oxford, England). 21: 2230-9. PMID 15728118 DOI: 10.1093/bioinformatics/bti335  0.92
2005 Keith JM, Adams P, Ragan MA, Bryant D. Sampling phylogenetic tree space with the generalized Gibbs sampler. Molecular Phylogenetics and Evolution. 34: 459-68. PMID 15683921 DOI: 10.1016/j.ympev.2004.11.016  0.92
2005 Mar JC, Harlow TJ, Ragan MA. Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. Bmc Evolutionary Biology. 5: 8. PMID 15676079 DOI: 10.1186/1471-2148-5-8  0.92
2004 Hamilton N, Burrage K, Ragan MA, Huber T. Protein contact prediction using patterns of correlation. Proteins. 56: 679-84. PMID 15281121 DOI: 10.1002/prot.20160  0.92
2004 Harlow TJ, Gogarten JP, Ragan MA. A hybrid clustering approach to recognition of protein families in 114 microbial genomes. Bmc Bioinformatics. 5: 45. PMID 15115543 DOI: 10.1186/1471-2105-5-45  0.92
2003 Ragan MA, Murphy CA, Rand TG. Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1alpha of Ichthyophonus irregularis. Molecular Phylogenetics and Evolution. 29: 550-62. PMID 14615193 DOI: 10.1016/S1055-7903(03)00134-9  0.92
2003 Charlebois RL, Beiko RG, Ragan MA. Microbial phylogenomics: Branching out. Nature. 421: 217. PMID 12529621 DOI: 10.1038/421217a  0.92
2003 Pekkarinen M, Lom J, Murphy CA, Ragan MA, Dyková I. Phylogenetic Position and Ultrastructure of Two Dermocystidium Species (Ichthyosporea) from the Common Perch (Perca fluviatilis) Acta Protozoologica. 42: 287-307.  0.92
2003 Ragan M. Bioinformatics: A glimpse of the future Drug Discovery Today: Biosilico. 1: 119-120.  0.92
2002 Ragan MA, Charlebois RL. Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission. International Journal of Systematic and Evolutionary Microbiology. 52: 777-87. PMID 12054238 DOI: 10.1099/ijs.0.02026-0  0.92
2002 Clarke GD, Beiko RG, Ragan MA, Charlebois RL. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. Journal of Bacteriology. 184: 2072-80. PMID 11914337 DOI: 10.1128/JB.184.8.2072-2080.2002  0.92
2002 Lawrence JG, Ochman H. Reconciling the many faces of lateral gene transfer. Trends in Microbiology. 10: 1-4. PMID 11755071 DOI: 10.1016/S0966-842X(01)02282-X  0.92
2001 Ragan MA. Detection of lateral gene transfer among microbial genomes. Current Opinion in Genetics & Development. 11: 620-6. PMID 11682304 DOI: 10.1016/S0959-437X(00)00244-6  0.92
2001 Ragan MA. On surrogate methods for detecting lateral gene transfer. Fems Microbiology Letters. 201: 187-91. PMID 11470360 DOI: 10.1016/S0378-1097(01)00262-2  0.92
2001 She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, ... ... Ragan MA, et al. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proceedings of the National Academy of Sciences of the United States of America. 98: 7835-40. PMID 11427726 DOI: 10.1073/pnas.141222098  0.92
2000 Ragan MA, MacCallum GS, Murphy CA, Cannone JJ, Gutell RR, McGladdery SE. Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota. Diseases of Aquatic Organisms. 42: 185-90. PMID 11104069 DOI: 10.3354/dao042185  0.92
2000 Rand TG, White K, Cannone JJ, Gutell RR, Murphy CA, Ragan MA. Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea from the Nova Scotia shelf. Diseases of Aquatic Organisms. 41: 31-6. PMID 10907136 DOI: 10.3354/dao041031  0.92
2000 Charlebois RL, Singh RK, Chan-Weiher CC, Allard G, Chow C, Confalonieri F, Curtis B, Duguet M, Erauso G, Faguy D, Gaasterland T, Garrett RA, Gordon P, Jeffries AC, Kozera C, ... ... Ragan MA, et al. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 43: 116-36. PMID 10701121  0.92
1999 Baker GC, Beebee TJ, Ragan MA. Prototheca richardsi, a pathogen of anuran larvae, is related to a clade of protistan parasites near the animal-fungal divergence. Microbiology (Reading, England). 145: 1777-84. PMID 10439417  0.92
1999 Lluisma AO, Ragan MA. Occurrence of closely spaced genes in the nuclear genome of the agarophyte Gracilaria gracilis Journal of Applied Phycology. 11: 99-104. DOI: 10.1023/A:1008008906649  0.92
1998 Ragan MA, Gaasterland T. Microbial genescapes: a prokaryotic view of the yeast genome. Microbial & Comparative Genomics. 3: 219-35. PMID 10027191  0.92
1998 Gaasterland T, Ragan MA. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microbial & Comparative Genomics. 3: 199-217. PMID 10027190  0.92
1998 Sensen CW, Charlebois RL, Chow C, Clausen IG, Curtis B, Doolittle WF, Duguet M, Erauso G, Gaasterland T, Garrett RA, Gordon P, de Jong IH, Jeffries AC, Kozera C, Medina N, ... ... Ragan MA, et al. Completing the sequence of the Sulfolobus solfataricus P2 genome. Extremophiles : Life Under Extreme Conditions. 2: 305-12. PMID 9783178 DOI: 10.1007/s007920050073  0.92
1998 Gaasterland T, Ragan MA. Constructing multigenome views of whole microbial genomes. Microbial & Comparative Genomics. 3: 177-92. PMID 9775388  0.92
1998 Lluisma AO, Ragan MA. Characterization of a galactose-1-phosphate uridylyltransferase gene from the marine red alga Gracilaria gracilis. Current Genetics. 34: 112-9. PMID 9724413 DOI: 10.1007/s002940050374  0.92
1998 Lluisma AO, Ragan MA. Cloning and characterization of a nuclear gene encoding a starch-branching enzyme from the marine red alga Gracilaria gracilis. Current Genetics. 34: 105-11. PMID 9724412 DOI: 10.1007/s002940050373  0.92
1998 Berger L, Speare R, Daszak P, Green DE, Cunningham AA, Goggin CL, Slocombe R, Ragan MA, Hyatt AD, McDonald KR, Hines HB, Lips KR, Marantelli G, Parkes H. Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America. Proceedings of the National Academy of Sciences of the United States of America. 95: 9031-6. PMID 9671799 DOI: 10.1073/pnas.95.15.9031  0.92
1998 Lluisma AO, Ragan MA. Characterization of the UDP-glucose pyrophosphorylase gene from the marine red alga Gracilaria gracilis Journal of Applied Phycology. 10: 581-588. DOI: 10.1023/A:1008050421875  0.92
1998 Ragan MA. On the delineation and higher-level classification of algae European Journal of Phycology. 33: 1-15. DOI: 10.1017/S0967026298001577  0.92
1997 Lluisma AO, Ragan MA. Expressed sequence tags (ESTs) from the marine red alga Gracilaria gracilis Journal of Applied Phycology. 9: 287-293. DOI: 10.1023/A:1007920607900  0.92
1996 Ragan MA, Logsdon JM, Sensen CW, Charlebois RL, Doolittle WF. An archaebacterial homolog of pelota, a meiotic cell division protein in eukaryotes. Fems Microbiology Letters. 144: 151-5. PMID 8900058 DOI: 10.1016/0378-1097(96)00351-5  0.92
1996 Sensen CW, Klenk HP, Singh RK, Allard G, Chan CC, Liu QY, Penny SL, Young F, Schenk ME, Gaasterland T, Doolittle WF, Ragan MA, Charlebois RL. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Molecular Microbiology. 22: 175-91. PMID 8899719 DOI: 10.1111/j.1365-2958.1996.tb02666.x  0.92
1996 Ragan MA, Goggin CL, Cawthorn RJ, Cerenius L, Jamieson AV, Plourde SM, Rand TG, Söderhäll K, Gutell RR. A novel clade of protistan parasites near the animal-fungal divergence. Proceedings of the National Academy of Sciences of the United States of America. 93: 11907-12. PMID 8876236 DOI: 10.1073/pnas.93.21.11907  0.92
1996 Ragan MA, Cawthorn RJ, Despres B, Murphy CA, Singh RK, Loughlin MB, Bayer RC. The lobster parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): nuclear 18S rDNA sequence, phylogeny and detection using oligonucleotide primers. The Journal of Eukaryotic Microbiology. 43: 341-6. PMID 8768439  0.92
1996 Charlebois RL, Gaasterland T, Ragan MA, Doolittle WF, Sensen CW. The Sulfolobus solfataricus P2 genome project. Febs Letters. 389: 88-91. PMID 8682213 DOI: 10.1016/0014-5793(96)00525-X  0.92
1996 Zhou YH, Ragan MA. Nuclear-encoded protein-coding genes of the agarophyte Gracilaria verrucosa (Gracilariales, Rhodophyta) Hydrobiologia. 326: 429-436.  0.92
1995 Zhou YH, Ragan MA. The nuclear gene and cDNAs encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa: cloning, characterization and phylogenetic analysis. Current Genetics. 28: 324-32. PMID 8590478 DOI: 10.1007/BF00326430  0.92
1995 Zhou YH, Ragan MA. Cloning and characterization of the nuclear gene and cDNAs for triosephosphate isomerase of the marine red alga Gracilaria verrucosa. Current Genetics. 28: 317-23. PMID 8590477 DOI: 10.1007/BF00326429  0.92
1995 Fan M, Chen LC, Ragan MA, Gutell RR, Warner JR, Currie BP, Casadevall A. The 5S rRNA and the rRNA intergenic spacer of the two varieties of Cryptococcus neoformans. Journal of Medical and Veterinary Mycology : Bi-Monthly Publication of the International Society For Human and Animal Mycology. 33: 215-21. PMID 8531018 DOI: 10.1080/02681219580000451  0.92
1995 Zhou YH, Ragan MA. Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa. Biochimica Et Biophysica Acta. 1261: 215-22. PMID 7711065 DOI: 10.1016/0167-4781(95)00006-3  0.92
1995 Zhou YH, Ragan MA. Characterization of the nuclear gene encoding mitochondrial aconitase in the marine red alga Gracilaria verrucosa. Plant Molecular Biology. 28: 635-46. PMID 7647296 DOI: 10.1007/BF00021189  0.92
1995 Ragan MA, Gutell RR. Are red algae plants? Botanical Journal of the Linnean Society. 118: 81-105. DOI: 10.1016/S0024-4074(95)80010-7  0.92
1995 Lluisma AO, Ragan MA. Relationships among Eucheuma denticulatum, Eucheuma isiforme and Kappaphycus alvarezii (Gigartinales, Rhodophyta) based on nuclear ssu-rRNA gene sequences Journal of Applied Phycology. 7: 471-477. DOI: 10.1007/BF00003931  0.92
1994 Oliveira MC, Ragan MA. Variant forms of a group I intron in nuclear small-subunit rRNA genes of the marine red alga Porphyra spiralis var. amplifolia. Molecular Biology and Evolution. 11: 195-207. PMID 8170361  0.92
1994 Trust TJ, Logan SM, Gustafson CE, Romaniuk PJ, Kim NW, Chan VL, Ragan MA, Guerry P, Gutell RR. Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp. Journal of Bacteriology. 176: 4597-609. PMID 8045890  0.92
1994 Ragan MA, Bird CJ, Rice EL, Gutell RR, Murphy CA, Singh RK. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proceedings of the National Academy of Sciences of the United States of America. 91: 7276-80. PMID 8041780 DOI: 10.1073/pnas.91.15.7276  0.92
1994 Zhou YH, Ragan MA. Cloning and characterization of the nuclear gene encoding plastid glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa. Current Genetics. 26: 79-86. PMID 7954900 DOI: 10.1007/BF00326308  0.92
1994 Fan M, Currie BP, Gutell RR, Ragan MA, Casadevall A. The 16S-like, 5.8S and 23S-like rRNAs of the two varieties of Cryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms. Journal of Medical and Veterinary Mycology : Bi-Monthly Publication of the International Society For Human and Animal Mycology. 32: 163-80. PMID 7525916 DOI: 10.1080/02681219480000231  0.92
1994 Bird CJ, Ragan MA, Critchley AT, Rice EL, Gutell RR. Molecular relationships among the gracilariaceae (Rhodophyta): Further observations on some undetermined species European Journal of Phycology. 29: 195-202. DOI: 10.1080/09670269400650641  0.92
1994 Ragan MA, Parsons TJ, Sawa T, Straus NA. 18s ribosomal DNA sequences indicate a monophyletic origin of Charophyceae Journal of Phycology. 30: 490-499.  0.92
1993 Ragan MA, Bird CJ, Rice EL, Singh RK. The nuclear 18S ribosomal RNA gene of the red alga Hildenbrandia rubra contains a group I intron. Nucleic Acids Research. 21: 3898. PMID 8367310  0.92
1993 Zhou YH, Ragan MA. cDNA cloning and characterization of the nuclear gene encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa. Current Genetics. 23: 483-9. PMID 7916671 DOI: 10.1007/BF00312639  0.92
1992 Ragan MA. Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution. 1: 53-8. PMID 1342924 DOI: 10.1016/1055-7903(92)90035-F  0.92
1992 Ragan MA. Matrix representation in reconstructing phylogenetic relationships among the eukaryotes. Bio Systems. 28: 47-55. PMID 1292666 DOI: 10.1016/0303-2647(92)90007-L  0.92
1992 Bird CJ, Murphy CA, Rice EL, Ragan MA. The 18S rRNA gene sequences of four commercially important seaweeds Journal of Applied Phycology. 4: 379-384. DOI: 10.1007/BF02185796  0.92
1990 Bird CJ, Rice EL, Murphy CA, Liu QY, Ragan MA. Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp. Nucleic Acids Research. 18: 4023-4. PMID 2374738 DOI: 10.1093/nar/18.13.4023  0.92
1990 Ragan MA. Evaluation of dye-based assay for mannuronan 5′-epimerase Hydrobiologia. 204: 415-417. DOI: 10.1007/BF00040265  0.92
1989 Ragan MA. Biochemical pathways and the phylogency of the eukaryotes The Hierarchy of Life. Molecules and Morphology in Phylogenetic Analysis: Proceedings From Nobel Symposium 70. Ics824. 145-160.  0.92
1988 Ragan MA. Ribosomal RNA and the major lines of evolution: a perspective. Bio Systems. 21: 177-87. PMID 3293666 DOI: 10.1016/0303-2647(88)90011-1  0.92
1986 Rothschild LJ, Ragan MA, Coleman AW, Heywood P, Gerbi SA. Are rRNA sequence comparisons the Rosetta stone of phylogenetics? Cell. 47: 640. PMID 3779840  0.92
1984 Ragan MA. Fucus 'lignin': A reassessment Phytochemistry. 23: 2029-2032. DOI: 10.1016/S0031-9422(00)84964-X  0.92
1984 McInnes AG, Ragan MA, Smith DG, Walter JA. High-molecular-weight phloroglucinol-based tannins from brown algae: Structural variants Hydrobiologia. 116: 597-602. DOI: 10.1007/BF00027755  0.92
1984 Laycock MV, Ragan MA. L-3,4-dihydroxyphenylalanine-3-sulfate from the brown alga, Ascophyllum nodosum Journal of Natural Products. 47: 1033-1035.  0.92
1982 Ragan MA, Jamieson WD. Oligomeric polyphloroglucinols from Fucus vesiculosus: Photoplate mass spectrometric investigation Phytochemistry. 21: 2709-2711. DOI: 10.1016/0031-9422(82)83103-8  0.92
1980 Ragan MA, Ragan CM, Jensen A. Natural chelators in sea water: Detoxification of Zn2+ by brown algal polyphenols Journal of Experimental Marine Biology and Ecology. 44: 261-267. DOI: 10.1016/0022-0981(80)90157-4  0.92
1980 Ragan MA, Craigie JS. Quantitative studies on brown algal phenols IV. Ultraviolet spectrophotometry of extracted polyphenols and implications for measuring dissolved organic matter in sea water Journal of Experimental Marine Biology and Ecology. 46: 231-239. DOI: 10.1016/0022-0981(80)90033-7  0.92
1979 Ragan MA, Mackinnon MD. Paired-ion reversed-phase high-performance liquid chromatography of phenol sulfates in synthetic mixtures, algal extracts and urine. Journal of Chromatography. 178: 505-13. PMID 528658 DOI: 10.1016/S0021-9673(00)92509-3  0.92
1979 Ragan MA, Smidsrød O, Larsen B. Chelation of divalent metal ions by brown algal polyphenols Marine Chemistry. 7: 265-271. DOI: 10.1016/0304-4203(79)90043-4  0.92
1979 Ragan MA, Jensen A. Widespread distribution of sulfated polyphenols in brown algae Phytochemistry. 18: 261-262. DOI: 10.1016/0031-9422(79)80066-7  0.92
1979 Ragan MA, Jensen A. Quantitative studies on brown algal phenols. III. Light-mediated exudation of polyphenols from Ascophyllum nodosum (L.) Le Jol Journal of Experimental Marine Biology and Ecology. 36: 91-101. DOI: 10.1016/0022-0981(79)90102-3  0.92
1978 Jensen A, Ragan MA. 1,2,3,5-tetrahydroxybenzene 2,5-disulfate ester: The "phenolic precursor" in gelbstoff-forming exudates from the marine brown alga Ascophyllum nodosum (L.) Lejol Tetrahedron Letters. 19: 847-850. DOI: 10.1016/S0040-4039(01)85415-0  0.92
1978 Ragan MA, Jensen A. Quantitative studies on brown algal phenols. II. Seasonal variation in polyphenol content of Ascophyllum nodosum (L.) Le Jol. and Fucus vesiculosus (L.) Journal of Experimental Marine Biology and Ecology. 34: 245-258. DOI: 10.1016/S0022-0981(78)80006-9  0.92
1977 Ragan MA, Jensen A. Quantitative studies on brown algal phenols. I. Estimation of absolute polyphenol content of Ascophyllum nodosum (L.) Le Jol. and Fucus vesiculosus (L.) Journal of Experimental Marine Biology and Ecology. 30: 209-221. DOI: 10.1016/0022-0981(77)90013-2  0.92
1977 Craigie JS, McInnes AG, Ragan MA, Walter JA. Chemical constituents of the physodes of brown algae. Characterization by 1H and 13C nuclear magnetic resonance spectroscopy of oligomers of phloroglucinol from Fucus vesiculosus (L.) Canadian Journal of Chemistry. 55: 1575-1582.  0.92
1976 Ragan MA, Craigie JS. Physodes and the phenolic compounds of brown algae. Isolation and characterization of phloroglucinol polymers from Fucus vesiculosus (L.) Canadian Journal of Biochemistry. 54: 66-73. PMID 1252984  0.92
1976 Ragan MA. Physodes and the Phenolic Compounds of Brown Algae. Composition and Significance of Physodes in vivo Botanica Marina. 19: 145-154. DOI: 10.1515/botm.1976.19.3.145  0.92
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