Institute for Molecular Bioscience

Emeritus Professor Mark Ragan

Emeritus Professor
Institute for Molecular Bioscience
+61 7 334 62616

Highlights

Mark Ragan is an Emeritus Professor at the Institute for Molecular Bioscience, The University of Queensland in Brisbane, Australia.

He was founding Head of IMB's former Division of Genomics & Computational Biology (2000-2014), founding Director of the Australian Research Council (ARC) Centre of Excellence in Bioinformatics (2003-2015), and co-founder of QFAB Bioinformatics.

Mark is a graduate of the University of Chicago (Biochemistry) and Dalhousie University (Biology). His 200+ peer-reviewed research publications in biochemistry, molecular biology, evolutionary biology, genomics, algorithmics, bioinformatics and computational biology have attracted more than 13500 citations.

Core technologies in his research group (integration of large bioscience data, scalable algorithms on trees and networks, bioinformatic workflows, high-performance and data-centric computing) were applied to problems of genome sequencing and de novo assembly, comparative evolutionary genomics, and inference of biomolecular networks particularly in the coral reef symbiont Symbiodinium, and in targeting therapies against DNA damage repair networks in familial breast cancer.

Mark was also involved in national and international infrastructure initiatives in genomics, computing, data and bioinformatics services.

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  Ragan Research Group: Computational genomics

Publications

Books (2)
Book Chapters (11)
Journal Articles (220)
Conference Papers (49)
Preprint (1)
Data Collections (4)

Books

Ragan, Mark A. (2023). Kingdoms, empires, and domains: The history of high-level biological classification. New York, NY United States: Oxford University Press. doi: 10.1093/oso/9780197643037.001.0001
Ragan, Mark A. and Chapman, David J. (1978). A biochemical phylogeny of the protists. New York , NY, U.S.A.: Academic Press. doi: 10.1016/B978-0-12-575550-4.50005-6

Book Chapters

Taherian Fard, Atefeh and Ragan, Mark A. (2019). Quantitative modelling of the Waddington epigenetic landscape. Computational stem cell biology: methods and protocols. (pp. 157-171) edited by Patrick Cahan. New York, United States: Humana Press. doi: 10.1007/978-1-4939-9224-9_7
Ragan, Mark A. (2018). Bioinformatics. Encyclopedia of information science and technology. (pp. 419-430) edited by Mehdi Khosrow-Pour. Hersey, PA, United States: IGI Global. doi: 10.4018/978-1-5225-2255-3.ch037
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2017). Scaling up the phylogenetic detection of lateral gene transfer events. In Keith, JM (Ed.), Bioinformatics (pp. 421-432) New York, United States: Humana Press. doi:10.1007/978-1-4939-6622-6_16
Ragan, Mark A. (2014). Bioinformatics. Encyclopedia of Information Science and Technology. (pp. 393-401) edited by Mehdi Khosrow-Pour. United Kingdom: Sweet and Maxwell. doi: 10.4018/978-1-4666-5888-2
Skippington, Elizabeth and Ragan, Mark A. (2013). Lateral genetic transfer and cellular networks. Lateral gene transfer in evolution. (pp. 123-135) edited by Uri Gophna. New York, United States: Springer. doi: 10.1007/978-1-4614-7780-8_6
Beiko, Robert G. and Ragan, Mark A. (2008). Detecting lateral genetic transfer: A phylogenetic approach. Bioinformatics: Data, Sequence Analysis and Evolution. (pp. 457-469) edited by Jonathan M. Keith. Totow, NJ, United States: Humana Press. doi: 10.1007/978-1-60327-159-2-21
Charlebois, R.L., Beiko, R.G. and Ragan, M. A. (2004). Genome Phylogenies. Organelles, Genomics and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. (pp. 189-206) edited by Hirt, R.P.; Horner and D.S.. Boca Raton Florida, USA: CRC Press:.
Baum, B. and Ragan, M. A. (2004). The MRP Method. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. (pp. 17-34) edited by Bininda-Emonds, Olaf and R. P.. Netherlands: Dordrecht: Kluwer Academic.
Sensen, Christopher W, Charlebois, Robert L., Singh, Rama K., Klenk, Hans-Peter, Ragan, Maark A. and Doolittle, W. Ford (1998). Sequencing the genome of Sulfolobus solfataricus P2.. Bacterial genomes: physical structure and analysis. (pp. 552-558) edited by F. J. de Bruijn, James R. Lupski and George M. Weinstock. New York , NY, United States: Chapman and Hall.
Ragan, M. A. (1981). Chemical constituents of seaweeds. The Biology of Seaweeds. (pp. 589-626) edited by Christopher S. Lobban and Michael J. Wynne. Berkeley, CA, U.S.A.: University of California Press.
Ragan, Mark A. and Craigie, J. S. (1978). Phenolic compounds in brown and red algae. Physiological and Biochemical Methods. (pp. 157-179) edited by Johan A. Hellebust and J. S. Craigie. Cambridge UK: Cambridge University Press.

Journal Articles

Dougan, Katherine E., González-Pech, Raúl A., Stephens, Timothy G., Shah, Sarah, Chen, Yibi, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30 (9), 831-840. doi: 10.1016/j.tim.2022.02.001
Gonzalez-Pech, Raul A., Stephens, Timothy G., Chen, Yibi, Mohamed, Amin R., Cheng, Yuanyuan, Shah, Sarah, Dougan, Katherine E., Fortuin, Michael D. A., Lagorce, Remi, Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2021). Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 19 (1) 73, 73. doi: 10.1186/s12915-021-00994-6
Bongaerts, Pim, Cooke, Ira R., Ying, Hua, Wels, Dagmar, den Haan, Stijn , Hernandez-Agreda, Alejandra, Brunner, Christopher A., Dove, Sophie, Englebert, Norbert, Eyal, Gal, Forêt, Sylvain, Grinblat, Mila, Hay, Kyra B., Harii, Saki, Hayward, David C., Lin, Yu, Mihaljević, Morana, Moya, Aurelie, Muir, Paul, Sinniger, Frederic, Smallhorn-West, Patrick, Torda, Gergely, Ragan, Mark A., van Oppen, Madeleine J.H. and Hoegh-Guldberg, Ove (2021). Morphological stasis masks ecologically divergent coral species on tropical reefs. Current Biology, 31 (11), 1-13+. doi: 10.1016/j.cub.2021.03.028
Cooke, Ira, Ying, Hua, Forêt, Sylvain, Bongaerts, Pim, Strugnell, Jan M., Simakov, Oleg, Zhang, Jia, Field, Matt A., Rodriguez-Lanetty, Mauricio, Bell, Sara C., Bourne, David G., van Oppen, Madeleine J.H., Ragan, Mark A. and Miller, David J. (2020). Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. Science Advances, 6 (48) eabc6318, 1-13. doi: 10.1126/sciadv.abc6318
Mohamed, Amin R., Chan, Cheong Xin, Ragan, Mark A., Zhang, Jia, Cooke, Ira, Ball, Eldon E. and Miller, David J. (2020). Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports, 12 (4), 435-443. doi: 10.1111/1758-2229.12859
Stephens, Timothy G., González-Pech, Raúl A., Cheng, Yuanyuan, Mohamed, Amin R., Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2020). Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18 (1) 56, 56. doi: 10.1186/s12915-020-00782-8
Robbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019). A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 (12), 2090-2100. doi: 10.1038/s41564-019-0532-4
González-Pech, Raúl A., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2019). Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution, 34 (9), 799-806. doi: 10.1016/j.tree.2019.04.010
Nones, K., Johnson, J., Newell, F., Patch, A. M., Thorne, H., Kazakoff, S. H., de Luca, X. M., Parsons, M. T., Ferguson, K., Reid, L. E., McCart Reed, A. E., Srihari, S., Lakis, V., Davidson, A. L., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., The Kathleen Cuningham Foundation Consortium for Research into Familial Aspects of Breast Cancer (kConFab), The Australian Breast Cancer Tissue Bank (ABCTB), The Brisbane Breast Bank (BBB), Beesley, J., Harris, J. M., Barnes, D., Degasperi, A., Ragan, M. A., Spurdle, A. B., Khanna, K. K. ... Simpson, P. T. (2019). Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Annals of Oncology, 30 (7) mdz132, 1071-1079. doi: 10.1093/annonc/mdz132
Jaspers, Cornelia, Fraune, Sebastian, Arnold, A. Elizabeth, Miller, David J., Bosch, Thomas C. G., Voolstra, Christian R., Consortium of Australian Academy of Science Boden Research Conference Participants, Adamska, Maja, Ainsworth, Tracy, Ball, Eldon, Boote, Chloe, Bourne, David, Butterfield, Nicholas J., Chan, Cheong Xin, Cooke, Ira, Cowman, Peter F., Darling, Aaron, Davy, Simon K., Mohamed, Amin, Fabricius, Katharina, Fortunato, Sofia, Hernandez, Alejandra, Hoogenboom, Mia, Moya, Aurelie, Pita, Lucia, Ragan, Mark A., Robbins, Steven J., Andrade, Natalia R., Sakamaki, Kazuhiro ... Ying, Hua (2019). Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology, 133, 81-87. doi: 10.1016/j.zool.2019.02.007
Bernard, Guillaume, Chan, Cheong Xin, Chan, Yao-ban, Chua, Xin-Yi, Cong, Yingnan, Hogan, James M., Maetschke, Stefan R. and Ragan, Mark A. (2019). Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings in Bioinformatics, 20 (2), 426-435. doi: 10.1093/bib/bbx067
Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D., Korhonen, Pasi K., Gobert, Geoffrey N., Nawaratna, Sujeevi, Hasan, Shihab, Martínez, David M., You, Hong, Lavin, Martin, Jones, Malcolm K., Ragan, Mark A., Stoye, Jens, Oleaga, Ana, Emery, Aidan M., Webster, Bonnie, Rollinson, David, Gasser, Robin B., McManus, Donald P. and Krause, Lutz (2019). Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLOS Pathogens, 15 (1) e1007513, e1007513. doi: 10.1371/journal.ppat.1007513
Oey, Harald, Zakrzewski, Martha, Narain, Kanwar, Devi, K Rekha, Agatsuma, Takeshi, Nawaratna, Sujeevi, Gobart, Geoffrey, Jones, Malcolm, Ragan, Mark A, McManus, Donald P and Krause, Lutz (2018). Whole-genome sequence of the oriental lung fluke Paragonimus westermani. GigaScience, 8 (1). doi: 10.1093/gigascience/giy146
Stephens, Timothy G., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2018). Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8 (1) 17175, 17175. doi: 10.1038/s41598-018-35620-z
Bernard, Guillaume, Greenfield, Paul, Ragan, Mark A. and Chan, Cheong Xin (2018). k-mer similarity, networks of microbial genomes, and taxonomic rank. mSystems, 3 (6) e00257-18, 1-16. doi: 10.1128/msystems.00257-18
Liu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J. H., Voolstra, Christian R., Ragan, Mark A. and Chan, Cheong Xin (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1 (1) 95, 95. doi: 10.1038/s42003-018-0098-3
Mohamed, Amin R., Cumbo, Vivian R., Harii, Saki, Shinzato, Chuya, Chan, Cheong Xin, Ragan, Mark A., Satoh, Nori, Ball, Eldon E. and Miller, David J. (2018). Deciphering the nature of the coral-Chromera association. The ISME Journal, 12 (3), 776-790. doi: 10.1038/s41396-017-0005-9
Yeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8
González-Pech, Raúl A., Ragan, Mark A. and Chan, Cheong Xin (2017). Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports, 7 (15021) 15021, 15021. doi: 10.1038/s41598-017-15029-w
Bissett, Andrew, Fitzgerald, Anna, Court, Leon, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I. ... Young, Andrew (2017). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016). Gigascience, 6 (5) gix021, 1-1. doi: 10.1093/gigascience/gix021
Taherian Fard, Atefeh and Ragan, Mark A. (2017). Modeling the attractor landscape of disease progression: a network-based approach. Frontiers in Genetics, 8 (APR) 48, 48. doi: 10.3389/fgene.2017.00048
Cong, Yingnan, Chan, Yao-ban, Phillips, Charles A., Langston, Michael A. and Ragan, Mark A. (2017). Robust inference of genetic exchange communities from microbial genomes using TF-IDF. Frontiers in Microbiology, 8 (JAN) 21, 1-11. doi: 10.3389/fmicb.2017.00021
Anderson, Alison M., Kalimutho, Murugan, Harten, Sarah, Nanayakkara, Devathri M., Khanna, Kum Kum and Ragan, Mark A. (2017). The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells. Scientific Reports, 7 (1) 39873. doi: 10.1038/srep39873
Bernard, Guillaume, Ragan, Mark A. and Chan, Cheong Xin (2016). Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]. F1000Research, 5 (2789) 2789, 2789. doi: 10.12688/f1000research.10225.2
Anderson, Alison M. and Ragan, Mark A. (2016). Palmitoylation: a protein s-acylation with implications for breast cancer. npj Breast Cancer, 2 (1) 16028, 16028. doi: 10.1038/npjbcancer.2016.28
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016). Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 (1) 37389, 37389. doi: 10.1038/srep37389
Liu, Chao, Rohart, Florian, Simpson, Peter T., Khanna, Kum Kum, Ragan, Mark A. and Le Cao, Kim-Anh (2016). Integrating multi-omics data to dissect mechanisms of DNA repair dysregulation in breast cancer. Scientific Reports, 6 (1) 34000, 34000.1-34000.11. doi: 10.1038/srep34000
Cong, Yingnan, Chan, Yao-ban and Ragan, Mark A. (2016). Exploring lateral genetic transfer among microbial genomes using TF-IDF. Scientific Reports, 6 (1) 29319, 29319. doi: 10.1038/srep29319
Cong, Yingnan, Chan, Yao-ban and Ragan, Mark A. (2016). A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF. Scientific Reports, 6 (1) 30308, 30308. doi: 10.1038/srep30308
Mohamed, A. R., Cumbo, V., Harii, S., Shinzato,C., Chan, C. X., Ragan, M. A., Bourne, D. G., Willis, B. L., Ball, E. E., Satoh, N. and Miller, D. J. (2016). The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology, 25 (13), 3127-3141. doi: 10.1111/mec.13659
Bernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer. Scientific Reports, 6 (1) 28970, 28970.1-28970.12. doi: 10.1038/srep28970
Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat ... Young, Andrew (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 (1) 21, 21.1-21.11. doi: 10.1186/s13742-016-0126-5
Stephens, Timothy, Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2016). PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4 (5) e2038, e2038.1-e2038.13. doi: 10.7717/peerj.2038
Srihari, Sriganesh, Kalimutho, Murugan, Lal, Samir, Singla, Jitin, Patel, Dhaval, Simpson, Peter T., Khanna, Kum Kum and Ragan, Mark A. (2016). Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach. Molecular Biosystems, 12 (3), 963-972. doi: 10.1039/C5MB00655D
Taherian Fard, Atefeh, Srihari, Sriganesh, Mar, Jessica C. and Ragan, Mark A. (2016). Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. NPJ Systems Biology and Applications, 2 (1) 16001, 16001. doi: 10.1038/npjsba.2016.1
Srihari, Sriganesh, Singla, Jitin, Wong, Limsoon and Ragan, Mark A. (2015). Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct, 10 (57) 57, 57. doi: 10.1186/s13062-015-0086-1
ReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015). The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 (Art No.: 68) 68. doi: 10.3389/fmars.2015.00068
Liu, Chao, Srihari, Sriganesh, Lal, Samir, Gautier, Benoit, Simpson, Peter T., Khanna, Kum Kum, Ragan, Mark A. and LeCao, Kim-Anh (2015). Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Molecular Oncology, 10 (1), 179-193. doi: 10.1016/j.molonc.2015.09.007
Yeoh, Yun Kit, Paungfoo-Lonhienne, Chanyarat, Dennis, Paul G., Robinson, Nicole, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2015). The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.. Environmental Microbiology, 18 (5), 1338-1351. doi: 10.1111/1462-2920.12925
Paungfoo-Lonhienne, Chanyarat, Yeoh, Yun Kit, Kasinadhuni, Naga Rup Pinaki, Lonhienne, Thierry G. A., Robinson, Nicole, Hugenholtz, Philip, Ragan, Mark A. and Schmidt, Susanne (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.. Scientific Reports, 5 (8678) 8678, 1-6. doi: 10.1038/srep08678
Srihari, Sriganesh, Madhamshettiwar, Piyush B., Song, Sarah, Liu, Chao, Simpson, Peter T., Khanna, Kumkum and Ragan, Mark A. (2014). Complex-based analysis of dysregulated cellular processes in cancer. BMC Systems Biology, 8 (Supplement 4) S1. doi: 10.1186/1752-0509-8-S4-S1
Chan, Cheong Xin, Bernard, Guillaume, Poirion, Olivier, Hogan, James M. and Ragan, Mark A. (2014). Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports, 4 (3) 6504, e6504.1-e6504.9. doi: 10.1038/srep06504
Taherian-Fard, Atefeh, Srihari, Sriganesh and Ragan, Mark A. (2014). Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings in Bioinformatics, 16 (3) bbu020, 461-474. doi: 10.1093/bib/bbu020
Liu, Chao, Srihari, Sriganesh, Le Cao, Kim-Anh, Chenevix-Trench, Georgia, Simpson, Peter T., Ragan, Mark A. and Khanna, Kum Kum (2014). A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Research, 42 (10), 6106-6127. doi: 10.1093/nar/gku284
Maetschke, Stefan R. and Ragan, Mark A. (2014). Characterizing cancer subtypes as attractors of Hopfield networks. Bioinformatics, 30 (9), 1273-1279. doi: 10.1093/bioinformatics/btt773
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J., Reverter, Antonio and Ragan, Mark A. (2014). INsPeCT: INtegrative Platform for Cancer Transcriptomics. Cancer Informatics, 13, 59-66. doi: 10.4137/CIN.S13630
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105
Ragan, Mark A., Bernard, Guillaume and Chan, Cheong Xin (2014). Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra. RNA Biology, 11 (3), 176-185. doi: 10.4161/rna.27505
Maetschke, Stefan R., Madhamshettiwar, Piyush B., Davis, Melissa J. and Ragan, Mark A. (2014). Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Briefings in Bioinformatics, 15 (2) bbt034, 195-211. doi: 10.1093/bib/bbt034
Lonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014). Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 (2), 785-790. doi: 10.2135/cropsci2013.07.0488
Srihari, Sriganesh, Raman, Venkatesh, Leong, Hon Wai and Ragan, Mark A. (2013). Evolution and controllability of cancer networks: a boolean perspective. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11 (1), 83-94. doi: 10.1109/TCBB.2013.128
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J. and Ragan, Mark A. (2013). RMaNI: Regulatory module network inference framework. BMC Bioinformatics, 14 (Suppl. 16) S14, S14.1-S14.10. doi: 10.1186/1471-2105-14-S16-S14
Fearnley, Liam, Davis, Melissa, Ragan, Mark A. and Nielsen, Lars K. (2013). Extracting reaction networks from databases-opening Pandora's box. Briefings in Bioinformatics, 15 (6), 973-983. doi: 10.1093/bib/bbt058
Ragan, Mark A. and Chan, Cheong Xin (2013). Biological intuition in alignment-free methods: response to Posada. Journal of Molecular Evolution, 77 (1-2), 1-2. doi: 10.1007/s00239-013-9573-0
Davis, Melissa J. and Ragan, Mark A. (2013). Understanding cellular function and disease with comparative pathway analysis. Genome Medicine, 5 (7) 64, 64.1-64.2. doi: 10.1186/gm468
Ragan, Mark A. (2013). Yeast rises to the occasion. Elife, 2 (2) e00933, e00933.1-e00933.2. doi: 10.7554/elife.00933
Srihari, Sriganesh and Ragan, Mark A. (2013). Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics, 29 (12), 1553-1561. doi: 10.1093/bioinformatics/btt191
Primmer, C. R., Papakostas, S., Leder, E. H., Davis, M. J. and Ragan, M. A. (2013). Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology, 22 (12), 3216-3241. doi: 10.1111/mec.12309
Chan, Cheong Xin, Mahbob, Maisarah and Ragan, Mark A. (2013). Clustering evolving proteins into homologous families. BMC Bioinformatics, 14 (1) 120, 120.1-120.11. doi: 10.1186/1471-2105-14-120
Muscat, George E. O., Eriksson, Natalie A., Byth, Karen, Loi, Sherene, Graham, Dinny, Jindal, Shalini, Davis, Melissa J., Clyne, Colin, Funder, John W., Simpson, Evan R., Ragan, Mark A., Kuczek, Elizabeth, Fuller, Peter J., Tilley, Wayne D., Leedman, Peter J. and Clarke, Christine L. (2013). Research resource: nuclear receptors as transcriptome: discriminant and prognostic value in breast cancer. Molecular Endocrinology, 27 (2), 350-365. doi: 10.1210/me.2012-1265
Chan, Cheong Xin and Ragan, Mark A. (2013). Next-generation phylogenomics. Biology Direct, 8 (1) 3, 3.1-3.14. doi: 10.1186/1745-6150-8-3
Wang, Chenwei, Taciroglu, Alperen, Maetschke, Stefan R., Nelson, Colleen C., Ragan, Mark A. and Davis, Melissa J. (2012). mCOPA: analysis of heterogeneous features in cancer expression data. Journal of Clinical Bioinformatics, 2 (1) 22, 22.1-22.11. doi: 10.1186/2043-9113-2-22
Skippington, Elizabeth and Ragan, Mark A. (2012). Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities. Open Biology, 2 (SEP) 120112, 120112. doi: 10.1098/rsob.120112
Cridland, Jasmyn A., Curley, Eva Z., Wykes, Michelle N ., Schroder, Kate, Sweet, Matthew J., Roberts, Tara L., Ragan, Mark A., Kassahn, Karin S. and Stacey, Katryn J. (2012). The mammalian PYHIN gene family: Phylogeny, evolution and expression. BMC Evolutionary Biology, 12 (1) 140, 140.1-140.33. doi: 10.1186/1471-2148-12-140
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J., Reverter, Antonio and Ragan, Mark A. (2012). Gene regulatory network inference: Evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Medicine, 4 (5) 41, 41.1-41.15. doi: 10.1186/gm340
Simonsen, Martin, Maetschke, Stefan R. and Ragan, Mark A. (2012). Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics, 28 (6) btr720, 851-857. doi: 10.1093/bioinformatics/btr720
Maetschke, Stefan R., Simonsen, Martin, Davis, Melissa J. and Ragan, Mark A. (2012). Gene Ontology-driven inference of protein-protein interaction using inducers. Bioinformatics, 28 (1) btr610, 69-75. doi: 10.1093/bioinformatics/btr610
Davis, Melissa J., Shin, Chang Jin, Jing, Ning and Ragan, Mark A. (2012). Rewiring the dynamic interactome. Molecular Biosystems, 8 (8), 2054-2066. doi: 10.1039/c2mb25050k
Bird, C. J., Garbary, D. J., Lewis, N., Ragan, M. A. and von Aderkas, P. (2012). In memoriam: Jack Lamont McLachlan. Phycologia, 51 (1), 118-118.
Skippington, Elizabeth and Ragan, Mark A. (2012). Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella Genomes. Genome Biology and Evolution, 4 (3), 330-345. doi: 10.1093/gbe/evs001
Bodlaender, Hans L., Fellows, Michael R., Langston, Michael A., Ragan, Mark A., Rosamond, Frances A. and Weyer, Mark (2011). Quadratic kernelization for convex recoloring of trees. Algorithmica, 61 (2), 362-388. doi: 10.1007/s00453-010-9404-2
Skippington, Elizabeth and Ragan, Mark A. (2011). Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. BMC Genomics, 12 (1) 532, 532.1-532.16. doi: 10.1186/1471-2164-12-532
Skippington, Elizabeth and Ragan, Mark A. (2011). Lateral genetic transfer and the construction of genetic exchange communities. Fems Microbiology Reviews, 35 (5), 707-735. doi: 10.1111/j.1574-6976.2010.00261.x
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2011). Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology, 193 (15), 3964-3977. doi: 10.1128/JB.01524-10
Bird, Carolyn J., Garbary, David J., Lewis, Nancy I., Ragan, Mark A. and von Aderkas, Patrick (2011). In Memoriam : Jack Lamont McLachlan (1 April 1930-13 December 2010). Phycologia, 50 (4), 329-339.
Ragan, Mark A. (2011). Review of Darwin’s Pictures. Views of Evolutionary Theory, 1837-1874, by Julia Voss. Systematic Biology, 60 (3), 388-390. doi: 10.1093/sysbio/syr001
Kassahn, Karin S., Ragan, Mark A. and Funder, John W. (2011). Mineralocorticoid receptors: evolutionary and pathophysiological considerations. Endocrinology, 152 (5), 1883-1890. doi: 10.1210/en.2010-1444
Ragan, Chikako, Zuker, Michael and Ragan, Mark A. (2011). Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLoS Computational Biology, 7 (2) e1001090, e1001090-1-e1001090-11. doi: 10.1371/journal.pcbi.1001090
Davis, Melissa J., Sehgal, Muhammad Shoaib B. and Ragan, Mark A. (2010). Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics, 11 (1) 498, 498-1-498-13. doi: 10.1186/1471-2105-11-498
Han, Siew Ping, Kassahn, Karin S., Skarshewski, Adam, Ragan, Mark A., Rothnagel, Joseph A. and Smith, Ross (2010). Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts. RNA, 16 (9), 1760-1768. doi: 10.1261/rna.2142810
Choi, JooYoung, Davis, Melissa J., Newman, Andrew F. and Ragan, Mark A. (2010). A semantic web ontology for small molecules and their biological targets. Journal of Chemical Information and Modeling, 50 (5), 732-741. doi: 10.1021/ci900461j
Maetschke, Stefan R., Kassahn, Karin S., Dunn, Jasmyn A., Han, Siew-Ping, Curley, Eva Z., Stacey, Katryn J. and Ragan, Mark A. (2010). A visual framework for sequence analysis using n-grams and spectral rearrangement. Bioinformatics, 26 (6) btq042, 737-744. doi: 10.1093/bioinformatics/btq042
Walter, Thomas, Shattuck, David W., Baldock, Richard, Bastin, Mark E., Carpenter, Anne E., Duce, Suzanne, Ellenburg, Jan, Fraser, Adam, Hamilton, Nicholas, Pieper, Steve, Ragan, Mark A., Schneider, Jurgen E., Tomancak, Pavel and Heriche, Jean-Karim (2010). Visualization of image data from cells to organisms. Nature Methods, 7 (3s), S26-S41. doi: 10.1038/NMETH.1431
Shin, C. J., Davis, M. J. and Ragan, M. A. (2009). Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics, 9 (23), 5256-5266. doi: 10.1002/pmic.200900262
Chan, Cheong Xin, Beiko, Robert G., Darling, Aaron E. and Ragan, Mark A. (2009). Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution, 1, 429-438. doi: 10.1093/gbe/evp044
Ragan, M. A. (2009). Trees and networks before and after Darwin. Biology Direct, 4 (1) 43, 43 - 1-43 - 38. doi: 10.1186/1745-6150-4-43
Ragan, M. A. and Beiko, R. G. (2009). Lateral genetic transfer: open issues. Philosophical Transactions of The Royal Society B: Biological Sciences, 364 (1527), 2241-2251. doi: 10.1098/rstb.2009.0031
Ragan, M. A., McInerney, J. O. and Lake, J. A. (2009). The network of life: genome beginnings and evolution. Philosophical Transactions of The Royal Society B-Biological Sciences, 364 (1527), 2169-2175. doi: 10.1098/rstb.2009.0046
Kassahn, K. S., Dang, V. T., Wilkins, S. J., Perkins, A. C. and Ragan, M. A. (2009). Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome Research, 19 (8), 1404-1418. doi: 10.1101/gr.086827.108
Ragan, Chikako, Cloonan, Nicole, Grimmond, Sean M., Zuker, Michael and Ragan, Mark A. (2009). Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. PLoS One, 4 (5) e5745, e5745.1-e5745.22. doi: 10.1371/journal.pone.0005745
McComb, Tim, Cairncross, Oliver, Noske, Andrew B., Wood, David L. A., Marsh, Brad J. and Ragan, Mark A. (2009). Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinformatics, 25 (9), 1208-1210. doi: 10.1093/bioinformatics/btp125
Esteban-Marcos, A, Darling, A. E. and Ragan, M. A. (2009). Seevolution: visualizing chromosome evolution. Bioinformatics, 25 (7), 960-961. doi: 10.1093/bioinformatics/btp096
Chan, Cheong Xin, Darling, Aaron E., Beiko, Robert G. and Ragan, Mark A. (2009). Are protein domains modules of lateral genetic transfer?. PLoS One, 4 (2) e4524, e4524.1-e4524.8. doi: 10.1371/journal.pone.0004524
Treangen, T. J., Darling, A. E., Achaz. G., Ragan, M. A., Messequer, X. and Rocha, E. P. (2009). A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (2) 4770094, 180-189. doi: 10.1109/TCBB.2009.9
Shin, Chang Jin, Wong, Simon, Davis, Melissa J. and Ragan, Mark A. (2009). Protein-protein interaction as a predictor of subcellular location. BMC Systems Biology, 3 (1) 28, x-x. doi: 10.1186/1752-0509-3-28
Beiko, Robert G. and Ragan, Mark A. (2009). Untangling hybrid phylogenetic signals: Horizontal gene transfer and artifacts of phylogenetic reconstruction. Methods in Molecular Biology, 532, 241-256. doi: 10.1007/978-1-60327-853-9
Ragan, Mark A. (2009). Thinking laterally about genomes. Genome informatics. International Conference on Genome Informatics, 23 (1), 221-222. doi: 10.1142/9781848165632_0023
Dang, Vinh T., Kassahn, Karin S., Marcos, Andres Esteban and Ragan, Mark A. (2008). Identification of human haploinsufficient genes and their genomic proximity to segmental duplications. European Journal of Human Genetics, 16 (11), 1350-1357. doi: 10.1038/ejhg.2008.111
Ragan, Mark A., Littlejohn, Tim and Ross, Bruce (2008). Genome-scale computational biology and bioinformatics in Australia. PLoS Computational Biology, 4 (8) e1000068, x-x. doi: 10.1371/journal.pcbi.1000068
Beiko, Robert G and Ragan, Mark A (2008). Detecting lateral genetic transfer : a phylogenetic approach. Methods in molecular biology (Clifton, N.J.), 452, 457-469. doi: 10.1007/978-1-60327-159-2_21
Wong, Simon and Ragan, Mark A. (2008). MACHOS: Markov clusters of homologous subsequences. Bioinformatics, 24 (13), i77-i85. doi: 10.1093/bioinformatics/btn144
Darling, Aaron E., Miklos, Istvan and Ragan, Mark A. (2008). Dynamics of genome rearrangement in bacterial populations. PLoS Genetics, 4 (7) e1000128, e1000128 - 1-e1000128 - 16. doi: 10.1371/journal.pgen.1000128
Ragan, Mark (2008). Genomics and evolution of microbial eukaryotes. Botanica Marina, 51 (1), 71-72. doi: 10.1515/BOT.2008.008
Hoehl, Michael and Ragan, Mark A. (2007). Is multiple-sequence alignment required for accurate inference of phylogeny?. Systematic Biology, 56 (2), 206-221. doi: 10.1080/10635150701294741
Andersson, Jan O., Sjogren, Asa M., Horner, David S., Murphy, Colleen A., Dyal, Patricia L., Svard, Staffan G., Logsdon, John M., Ragan, Mark A., Hirt, Robert P. and Roger, Andrew J. (2007). 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 (1) 51, 51-1-51-25. doi: 10.1186/1471-2164-8-51
Ragan, Mark A. (2006). ARC Centre in Bioinformatics. Asia Pacific Biotech News, 10 (24), 1391-1394. doi: 10.1142/S0219030306002060
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2006). Detecting Recombination in Evolving Nucleotide Sequences. BMC Bioinformatics, 7 (Article 412) 412, 1-15. doi: 10.1186/1471-2105-7-412
Beiko, R. G., Keith, J. M., Harlow, T. J. and Ragan, M. A. (2006). Searching for convergence in phylogenetic Markov chain Monte Carlo. Systematic Biology, 55 (4), 553-565. doi: 10.1080/10635150600812544
Garcia Castro, Alexander, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A. and Sansone, Susanna-Assunta (2006). The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. BMC Bioinformatics, 7 (1) 267, 267 - 1-267 - 14. doi: 10.1186/1471-2105-7-267
Ragan, Mark A., Harlow, Timothy J. and Beiko, Robert G. (2006). Do different surrogate methods detect lateral genetic transfer events of different relative ages?. Trends In Microbiology, 14 (1), 4-8. doi: 10.1016/j.tim.2005.11.004
Hoehl, Michael, Rigoutsos, Isidore and Ragan, Mark A. (2006). Pattern-based phylogenetic distance estimation and tree reconstruction. Evolutionary Bioinformatics, 2, 359-375. doi: 10.1177/117693430600200016
Burrage, Kevin, Hood, Lindsay and Ragan, Mark A. (2006). Advanced computing for systems biology. Briefings in Bioinformatics, 7 (4), 390-398. doi: 10.1093/bib/bbl033
Garcia, Alexander Garcia, Thoraval, Samuel, Garcia, Leyla J. and Ragan, Mark A. (2005). Workflows in bioinformatics: Meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics, 6 (1) 87, 87.1-87.10. doi: 10.1186/1471-2105-6-87
Keith, J. M., Adams, P., Ragan, M. A. and Bryant, D. E. (2005). Sampling phylogenetic tree space with the generalized Gibbs sampler. Molecular Phylogenetics and Evolution, 34 (3), 459-468. doi: 10.1016/j.ympev.2004.11.016
Beiko, Robert G., Chan, Cheong Xin and Ragan, Mark A. (2005). A Word-Oriented Approach to Alignment Validation. Bioinformatics, 21 (10), 2230-2239. doi: 10.1093/bioinformatics/bti335
Jain, N., Wickes, B. L., Keller, S. A., Fu, J., Casadevall, A., Jain, P., Ragan, M. A., Banerjee, U. and Fries, B. C. (2005). Molecular epidemiology of clinical Cryptococcus neoformans strains from India. Journal of Clinical Microbiology, 43 (11), 5733-5742. doi: 10.1128/JCM.43.11.5733-5742.2005
Mar, Jessica C., Harlow, Timothy J . and Ragan, Mark A. (2005). Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. BMC Evolutionary Biology, 5 (1), 8.1-8.20. doi: 10.1186/1471-2148-5-8
Beiko, R. G., Harlow, T. J. and Ragan, M. A. (2005). Highways of gene sharing in prokaryotes. Proceedings of The National Academy of Sciences of The United States of America, 102 (40), 14332-14337. doi: 10.1073/pnas.0504068102
Garcia Castro, Alexander, Chen, Yi-Ping Phoebe and Ragan, Mark A. (2005). Information integration in molecular bioscience. Applied Bioinformatics, 4 (3), 157-173. doi: 10.2165/00822942-200594030-00001
Harlow, Timothy J., Gogarten, J. Peter and Ragan, Mark A. (2004). A hybrid clustering approach to recognition of protein families in 114 microbial genomes. Bmc Bioinformatics, 5 (1) 45, Article 45. doi: 10.1186/1471-2105-5-45
Hamilton, Nicholas, Burrage, Kevin, Ragan, Mark A. and Huber, Thomas (2004). Protein contact prediction using patterns of correlation. Proteins-structure Function And Bioinformatics, 56 (4), 679-684. doi: 10.1002/prot.20160
Charlebois, R. L., Beiko, R. G. and Ragan, M. A. (2003). Microbial Phylogenomics: Branching out. Nature, 421 (6920), 217-217. doi: 10.1038/421217a
Ragan, M.A. (2003). Bioinformatics: a glimpse of the future. BIOSILICO, 1 (4), 119-120.
Ragan, Mark A., Murphy, Colleen A. and Rand, Thomas G. (2003). Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1α of Ichthyophonus irregularis. Molecular Phylogenetics And Evolution, 29 (3), 550-562. doi: 10.1016/S1055-7903(03)00134-9
Pekkarinen, Marketta, Lom, Jiri, Murphy, Colleen A., Ragan, Mark A. and Dykova, Iva (2003). Phylogenetic position and ultrastructure of two Dermocystidium species (Ichthyosporea) from the common perch (Perca fluviatilis). Acta Protozoologica, 42 (4), 287-307.
Clarke, G. D. P., Beiko, R. G., Ragan, M. A. and Charlebois, R. L. (2002). 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 (8), 2072-2080. doi: 10.1128/JB.184.8.2072-2080.2002
Ragan, M. A. and Charlebois, R. L. (2002). Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission. International Journal of Systematic And Evolutionary Microbiology, 52, 777-787. doi: 10.1099/ijs.0.02026-0
Ragan, MA (2002). Reconciling the many faces of lateral gene transfer - Response from Ragan. Trends In Microbiology, 10 (1), 4-4. doi: 10.1016/S0966-842X(01)02283-1
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., Chan-Weiher, Christina C.-Y., Clausen, Ib Groth, Curtis, Bruce A., De Moors, Anick, Erauso, Gael, Fletcher, Cynthia, Gordon, Paul M. K., Heikamp-de Jong, Ineke, Jeffries, Alex C., Kozera, Catherine J., Medina, Nadine, Peng, Xu, Thi-Ngoc, Hoa Phan, Redder, Peter, Schenk, Margaret E., Theriault, Cynthia, Tolstrup, Niels, Charlebois, Robert L., Doolittle, W. Ford, Duguet, Michel, Gaasterland, Terry, Garrett, Roger A., Ragan, Mark A. ... Van der Oost, John (2001). The complete genome of the crenarchaeon sulfolobus solfataricus P2. Proceedings of the National Academy of Sciences, 98 (14), 7835-7840. doi: 10.1073/pnas.141222098
Ragan, Mark A. (2001). On surrogate methods for detecting lateral gene transfer. FEMS Microbiology Letters, 201 (2), 187-191. doi: 10.1111/j.1574-6968.2001.tb10755.x
Ragan, M. A. (2001). Detection of lateral gene transfer among microbial genomes. Current Opinion In Genetics & Development, 11 (6), 620-626. doi: 10.1016/S0959-437X(00)00244-6
Ragan, Mark A., MacCallum, Greg S., Murphy, Colleen A., Cannone, Jamie J., Gutell, Robin R. and McGladdery, Sharon E. (2000). Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota. Diseases of Aquatic Organisms, 42 (3), 185-190. doi: 10.3354/dao042185
Rand, Thomas G., White, Kelly, Cannone, Jamie J., Gutell, Robin R., Murphy, Colleen A. and Ragan, Mark A. (2000). Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea from the Nova Scotia shelf. Diseases of Aquatic Organisms, 41 (1), 31-36. doi: 10.3354/dao041031
Charlebois, RL, Singh, RK, Chan-Weiher, CCY, Allard, G, Chow, C, Confalonieri, F, Curtis, B, Duguet, M, Erauso, G, Faguy, D, Gaasterland, T, Garrett, RA, Gordon, P, Jeffries, AC, Kozera, C, Kushwaha, N, Lafleur, E, Medina, N, Peng, X, Penny, SL, She, QX, St Jean, A, van der Oost, J, Young, F, Zivanovic, Y, Doolittle, WF, Ragan, MA and Sensen, CW (2000). Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome, 43 (1), 116-136. doi: 10.1139/gen-43-1-116
Baker, GC, Beebee, TJC and Ragan, MA (1999). Prototheca richardsi, a pathogen of anuran larvae, is related to a clade of protistan parasites near the animal-fungal divergence. Microbiology-Uk, 145 (7), 1777-1784. doi: 10.1099/13500872-145-7-1777
Lluisma A.O. and Ragan M.A. (1999). Occurrence of closely spaced genes in the nuclear genome of the agarophyte Gracilaria gracilis. Journal of Applied Phycology, 11 (1), 99-104. doi: 10.1023/A:1008008906649
Ragan, MA (1998). On the delineation and higher-level classification of algae. European Journal of Phycology, 33 (1), 1-15.
Ragan M.A. and Gaasterland T. (1998). Microbial genescapes: a prokaryotic view of the yeast genome.. Microbial & comparative genomics, 3 (4), 219-235.
Ragan, M. A. and Gaasterland, T. (1998). Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microbial and Comparative Genomics, 3 (4), 199-217.
Ragan, Mark (1998). On the delineation and higher-level classification of algae. European Journal of Phycology, 33 (1), 1-15. doi: 10.1017/S0967026298001577
Lluisma A.O. and Ragan M.A. (1998). Characterization of a galactose-1-phosphate uridylyltransferase gene from the marine red alga Graeilaria gracilis. Current Genetics, 34 (2), 112-119. doi: 10.1007/s002940050374
Lluisma A.O. and Ragan M.A. (1998). Characterization of the UDP-glucose pyrophosphorylase gene from the marine red alga Gracilaria gracilis. Journal of Applied Phycology, 10 (6), 581-588. doi: 10.1023/A:1008050421875
Lluisma A.O. and Ragan M.A. (1998). Cloning and characterization of a nuclear gene encoding a starch branching enzyme from the marine red alga Gracilaria gracilis. Current Genetics, 34 (2), 105-111. doi: 10.1007/s002940050373
Gaasterland T. and Ragan M.A. (1998). Constructing multigenome views of whole microbial genomes.. Microbial & comparative genomics, 3 (3), 177-192.
Sensen C.W., Charlebois R.L., Chow C., Clausen I.G., Curtis B., Doolittle W.F., Duguet M., Erauso G., Gaasterland T., Garrett R.A., Gordon P., De Jong I.H., Jeffries A.C., Kozera C., Medina N., De Moors A., Van Der Oost J., Phan H., Ragan M.A., Schenk M.E., She Q., Singh R.K. and Tolstrup N. (1998). Completing the sequence of the Sulfolobus solfataricus P2 genome. Extremophiles, 2 (3), 305-312. doi: 10.1007/s007920050073
Ragan, MA (1997). A third kingdom of eukaryotic life: History of an idea - ISEP president's address. Archiv Fur Protistenkunde, 148 (3), 225-243.
Lang, BF, McFadden, GI, Moestrup, O and Ragan, MA (1997). Selected papers from the Eleventh Biennial Meeting of the International Society for Evolutionary Protistology (ISEP) - 8th-13th August 1996, Universitat Koln, Koln, Germany - Preface. Archiv Fur Protistenkunde, 148 (3), 218-218.
Lluisma A.O. and Ragan M.A. (1997). Expressed sequence tags (ESTs) from the marine red alga Gracilaria gracilis. Journal of Applied Phycology, 9 (3), 287-293. doi: 10.1023/A:1007920607900
Charlebois, R. L., Gaasterland, T., Ragan, M. A., Doolittle, W. F. and Sensen, C. W. (1996). The Sulfolobus solfataricus P2 genome project (vol 389, pg 88, 1996). Febs Letters, 398 (2-3), 343-343.
Ragan, MA, Logsdon, JM, Sensen, CW, Charlebois, RL and Doolittle, WF (1996). An archaebacterial homolog of pelota, a meiotic cell division protein in eukaryotes. Fems Microbiology Letters, 144 (2-3), 151-155. doi: 10.1111/j.1574-6968.1996.tb08522.x
Ragan M.A., Goggin C.L., Cawthorn R.J., Cerenius L., Jamieson A.V.C., Plourde S.M., Rand T.G., Soderhall K. and Gutell R.R. (1996). 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 (21), 11907-11912. doi: 10.1073/pnas.93.21.11907
Ragan, MA (1996). Opening address by ISA president. Hydrobiologia, 327, R41-R42.
Zhou, YH and Ragan, MA (1996). Nuclear-encoded protein-coding genes of the agarophyte Gracilaria verrucosa (Gracilariales, Rhodophyta). Hydrobiologia, 327, 429-436.
Ragan, MA, Cawthorn, RJ, Despres, B, Murphy, CA, Singh, RK, Loughlin, MB and Bayer, RC (1996). The lobster parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): Nuclear 18S rDNA sequence, phylogeny and detection using oligonucleotide primers. Journal of Eukaryotic Microbiology, 43 (4), 341-346. doi: 10.1111/j.1550-7408.1996.tb03998.x
Charlebois, RL, Gaasterland, T, Ragan, MA, Doolittle, WF and Sensen, CW (1996). The Sulfolobus solfataricus P2 genome project. Febs Letters, 389 (1), 88-91. doi: 10.1016/0014-5793(96)00525-X
Sensen C.W., Klenk H.-P., Singh R.K., Allard G., Chan C.C.-Y., Liu Q.Y., Penny S.L., Young F., Schenk M.E., Gaasterland T., Doolittle W.F., Ragan M.A. and Charlebois R.L. (1996). Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Molecular Microbiology, 22 (1), 175-191. doi: 10.1111/j.1365-2958.1996.tb02666.x
Charlebois, R. L., Gaasterland, T., Ragan, M. A., Doolittle, W. F. and Sensen, C. W. (1996). Erratum: The Sulfolobus solfataricus P2 genome project (FEBS letters 389 (1996) (88-91)) (PII S001457939600525X). FEBS Letters, 398 (2-3)
Lluisma, AO and Ragan, MA (1995). Relationships Among Eucheuma-Denticulatum, Eucheuma-Isiforme and Kappaphycus-Alvarezii (Gigartinales, Rhodophyta) Based On Nuclear Ssu-Ribosomal-Rna Gene-Sequences. Journal of Applied Phycology, 7 (5), 471-477. doi: 10.1007/BF00003931
Saunders, GW, Bird, CJ, Ragan, MA and Rice, EL (1995). Phylogenetic-Relationships of Species of Uncertain Taxonomic Position Within the Acrochaetiales-Palmariales Complex (Rhodophyta) - Inferences From Phenotypic and 18S Rdna Sequence Data. Journal of Phycology, 31 (4), 601-611. doi: 10.1111/j.1529-8817.1995.tb02556.x
Fan, M, Chen, LC, Ragan, MA, Gutell, RR, Warner, JR, Currie, BP and Casadevall, A (1995). The 5S Ribosomal-Rna and the Ribosomal-Rna Intergenic Spacer of the 2 Varieties of Cryptococcus-Neoformans. Journal of Medical and Veterinary Mycology, 33 (4), 215-221.
Zhou, YH and Ragan, MA (1995). Characterization of the Nuclear Gene Encoding Mitochondrial Aconitase in the Marine Red Alga Gracilaria-Verrucosa. Plant Molecular Biology, 28 (4), 635-646. doi: 10.1007/BF00021189
Ragan, MA and Gutell, RR (1995). Are Red Algae Plants. Botanical Journal of the Linnean Society, 118 (2), 81-105. doi: 10.1111/j.1095-8339.1995.tb00463.x
Zhou, YH and Ragan, MA (1995). Characterization of the Polyubiquitin Gene in the Marine Red Alga Gracilaria-Verrucosa. Biochimica Et Biophysica Acta-Gene Structure and Expression, 1261 (2), 215-222. doi: 10.1016/0167-4781(95)00006-3
Oliveira, Mariana C., Kurniawan, Joelius, Bird, Carolyn J., Rice, Ellen L., Murphy, Colleen A., Singh, Rama K., Gutell, Robin R. and Ragan, Mark A. (1995). A preliminary investigation of the order Bangiales (Bangiophycidae, Rhodophyta) based on nuclear small-subunit ribosomal RNA gene sequences.. Phycological Research, 43 (2), 71-79. doi: 10.1111/j.1440-1835.1995.tb00007.x
Zhou Y.-H. and Ragan M.A. (1995). Cloning and characterization of the nuclear gene and cDNAs for triosephosphate isomerase of the marine red alga Gracilaria verrucosa. Current Genetics, 28 (4), 317-323. doi: 10.1007/BF00326429
Zhou Y.-H. and Ragan M.A. (1995). 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 (4), 324-332. doi: 10.1007/BF00326430
Bird, CJ, Ragan, MA, Critchley, AT, Rice, EL and Gutell, RR (1994). Molecular Relationships Among the Gracilariaceae (Rhodophyta) - Further Observations On Some Undetermined Species. European Journal of Phycology, 29 (3), 195-202. doi: 10.1080/09670269400650641
Trust, T. J, Logan, S. M., Gustafson, C. E., Romaniuk, P. J., Kim, N. W., Chan, V. L., Ragan, M. A., Guerry, P. and Gutell, R. R. (1994). Phylogenetic and Molecular Characterization of a 23S Ribosomal-Rna 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 (15), 4597-4609. doi: 10.1128/jb.176.15.4597-4609.1994
Ragan M.A., Bird C.J., Rice E.L., Gutell R.R., Murphy C.A. and Singh R.K. (1994). 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 (15), 7276-7280. doi: 10.1073/pnas.91.15.7276
Zhou, Yi-Hong and Ragan, Mark A. (1994). Cloning and characterization of the nuclear gene encoding plastid glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa. Current Genetics, 26 (1), 79-86. doi: 10.1007/BF00326308
Cerff, Rüdiger, Bohnert, Hans J., Ragan, Mark and Sachs, Martin M. (1994). Plant-wide nomenclature of nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases. Plant Molecular Biology Reporter, 12 (2), S36-S38. doi: 10.1007/BF02671565
Ragan, MA, Parsons, TJ, Sawa, T and Straus, NA (1994). 18S Ribosomal Dna-Sequences Indicate a Monophyletic Origin of Charophyceae. Journal of Phycology, 30 (3), 490-500. doi: 10.1111/j.0022-3646.1994.00490.x
Oliveira, MC and Ragan, MA (1994). Variant Forms of a Group-I Intron in Nuclear Small-Subunit Ribosomal-Rna Genes of the Marine Red Alga Porphyra-Spiralis Var Amplifolia. Molecular Biology and Evolution, 11 (2), 195-207.
Fan, M, Currie, BP, Gutell, RR, Ragan, MA and Casadevall, A (1994). The 16S-Like, 5.8S-Like and 23S-Like Ribosomal-Rnas of the 2 Varieties of Cryptococcus-Neoformans - Sequence, Secondary Structure, Phylogenetic Analysis and Restriction Fragment Polymorphisms. Journal of Medical and Veterinary Mycology, 32 (3), 163-180.
Baum, Bernard R. and Ragan, Mark A. (1993). Reply to A. G. Rodrigo's "A Comment on Baum's Method for Combining Phylogenetic Trees". Taxon, 42 (3), 637-640. doi: 10.2307/1222541
Ragan, MA, Bird, CJ, Rice, EL and Singh, RK (1993). The Nuclear 18S Ribosomal-Rna Gene of the Red Alga Hildenbrandia-Rubra Contains a Group-I Intron. Nucleic Acids Research, 21 (16), 3898-3898. doi: 10.1093/nar/21.16.3898
Zhou, Yi-Hong and Ragan, Mark A. (1993). cDNA cloning and characterization of the nuclear gene encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa. Current Genetics, 23 (5-6), 483-489. doi: 10.1007/BF00312639
Bird, C. J., Rice, E. L., Murphy, C. A. and Ragan, M. A. (1992). Phylogenetic relationships in the Gracilariales (Rhodophyta) as determined by 18S rDNA sequences. Phycologia, 31 (6), 510-522. doi: 10.2216/i0031-8884-31-6-510.1
Ragan, Mark A. (1992). Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution, 1 (1), 53-58. doi: 10.1016/1055-7903(92)90035-F
Ragan, Mark A. (1992). Phylogenetic Inference Based on Matrix Representation of Trees. Molecular Phylogenetics and Evolution, 1 (1), 53-58. doi: 10.1016/1055-7903(92)90035-F
Destombe, C., Cembella, A. D., Murphy, C. A. and Ragan, M.A. (1992). Nucleotide sequence of the 18S ribosomal RNA genes from the marine dinoflagellate Alexandrium tamarense (Gonyaulacales, Dinophyta). Phycologia, 31 (1), 121-124. doi: 10.2216/i0031-8884-31-1-121.1
Ragan, MA (1992). Matrix Representation in Reconstructing Phylogenetic-Relationships Among the Eukaryotes. Biosystems, 28 (1-3), 47-55. doi: 10.1016/0303-2647(92)90007-L
Bird C.J., Murphy C.A., Rice E.L. and Ragan M.A. (1992). The 18S rRNA gene sequences of four commercially important seaweeds. Journal of Applied Phycology, 4 (4), 379-384. doi: 10.1007/BF02185796
Ragan, Mark A. (1992). Matrix representation in reconstructing phylogenetic relationships among the eukaryotes. BioSystems, 28 (1-3), 47-55. doi: 10.1016/0303-2647(92)90007-L
Ragan, Mark A. (1990). Evaluation of dye-based assay for mannuronan 5'-epimerase. Hydrobiologia, 204-205 (1), 415-417. doi: 10.1007/BF00040265
Bird, Carolyn J., Rice, Ellen L., Murphy, Colleen A., Liu, Qing Yan and Ragan, Mark A. (1990). 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 (13), 4023-4024. doi: 10.1093/nar/18.13.4023
Chen, L. C.-M., McCracken, I. and Ragan, M. A. (1990). Biotechnology potential for hoshi-nori production. World Aquaculture, 21 (3), 106-107.
Chen, L.-C. M., McCracken, I., Ragan, M. A. and Reith, M. (1990). 海苔生産におけるバイオテクノロジー導入の可能性. 海苔と海藻, 35, 10-12.
Ragan M.A. (1990). Evaluation of dye-based assay for mannuronan 5′-epimerase. Hydrobiologia, 204-205 (1), 415-417. doi: 10.1007/BF00040265
Wright, J. L. C., Boyd, R. K., Defreitas, A. S. W., Falk, M., Foxall, R. A., Jamieson, W. D., Laycock, M. V., McCulloch, A. W., McInnes, A. G., Odense, P., Pathak, V. P., Quilliam, M. A., Ragan, M. A., Sim, P. G., Thibault, P., Walter, J. A., Gilgan, M., Richard, D. J. A. and Dewar, D. (1989). Identification of domoic acid, a neuroexcitatory amino acid, in toxic mussels from eastern Prince Edward Island. Canadian Journal of Chemistry-Revue Canadienne De Chimie, 67 (3), 481-490. doi: 10.1139/v89-075
Ragan, M. A. (1989). 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.
Ragan, Mark A. (1988). Ribosomal RNA and the major lines of evolution: a perspective. Biosystems, 21 (3-4), 177-187. doi: 10.1016/0303-2647(88)90011-1
Rothschild, LJ, Ragan, MA, Coleman, AW, Heywood, P and Gerbi, SA (1986). Are Ribosomal-Rna Sequence Comparisons the Rosetta Stone of Phylogenetics. Cell, 47 (5), 640-640. doi: 10.1016/0092-8674(86)90505-2
Ragan, Mark A. and Glombitza, Karl-Werner (1986). Phlorotannins, brown algal polyphenols. Progress in Phycological Research, 4, 129-241.
Ragan, Mark A. (1985). Brown algal polyphenols: synthesis of "fucophlorethol A" octamethyl ether (2,2',4,6,6'-pentamethoxy-4'-(2,4,6-trimethoxyphenoxy)biphenyl). Canadian Journal of Chemistry, 63 (2), 291-293. doi: 10.1139/v85-049
McInnes, A. Gavin, Ragan, Mark A., Smith, Donald G. and Walter, John A. (1985). The high molecular weight polyphloroglucinols of the marine brown alga Fucusvesiculosus L. H-1 and C-13 nuclear magnetic resonance spectroscopy. Canadian Journal of Chemistry, 63 (2), 304-313. doi: 10.1139/v85-051
Ragan, MA (1985). Brown Algal Polyphenols - Synthesis of Fucophlorethol-A Octamethyl Ether (2,2',4,6,6'-Pentamethoxy-4'-(2,4,6-Trimethoxyphenoxy)Biphenyl). Canadian Journal of Chemistry-Revue Canadienne De Chimie, 63 (2), 291-293. doi: 10.1139/v85-049
Nishizawa, Makoto, Yamagishi, Takashi, Nonaka, Gen-Ichiro, Nishioka, Itsuo and Ragan, Mark A. (1985). Tannins and Related Compounds 34. Gallotannins of the freshwater green alga Spirogyra sp.. Phytochemistry, 24 (10), 2411-2413. doi: 10.1016/S0031-9422(00)83053-8
Ragan, Mark A. (1985). Physodes and the Phenolic Compounds of Brown-Algae 4. the High Molecular Weight Polyphloroglucinols of the Marine Brown Alga Fucus vesiculosus L. - Degradative Analysis. Canadian Journal of Chemistry-Revue Canadienne De Chimie, 63 (2), 294-303. doi: 10.1139/v85-050
Ragan MA (1984). Fucus 'lignin': a reassessment. Phytochemistry, 23 (9), 2029-2032.
Ragan, Mark A. (1984). Bioactivities in marine genera of Atlantic Canada: the unexplored potential. Proceedings of the Nova Scotia Institute of Science, 34 (2), 83-132.
Ragan, MA (1984). Fucus Lignin - a Reassessment. Phytochemistry, 23 (9), 2029-2032. doi: 10.1016/S0031-9422(00)84964-X
Laycock, Maurice V. and Ragan, Mark A. (1984). L-3,4-Dihydroxyphenylalanine-3-Sulfate From the Brown Alga, Ascophyllum nodosum. Journal of Natural Products, 47 (6), 1033-1035. doi: 10.1021/np50036a025
McInnes A.G., Ragan M.A., Smith D.G. and Walter J.A. (1984). High-molecular-weight phloroglucinol-based tannins from brown algae: Structural variants. Hydrobiologia, 116-117 (1), 597-602. doi: 10.1007/BF00027755
Ragan, Mark A. and Jamieson, W. D. (1982). Physodes and the Phenolic Compounds of Brown Algae 4. Oligomeric Polyphloroglucinols From Fucus vesiculosus: Photoplate Mass Spectrometric Investigation. Phytochemistry, 21 (11), 2709-2711. doi: 10.1016/0031-9422(82)83103-8
Ragan, MA, Ragan, CM and Jensen, A (1980). Natural Chelators in Sea-Water - Detoxification of Zn2+ by Brown Algal Polyphenols. Journal of Experimental Marine Biology and Ecology, 44 (2-3), 261-267. doi: 10.1016/0022-0981(80)90157-4
Ragan, Mark A. and Craigie, JS (1980). Quantitative Studies On Brown Algal Phenols 4. Ultraviolet Spectrophotometry of Extracted Polyphenols and Implications for Measuring Dissolved Organic-Matter in sea water. Journal of Experimental Marine Biology and Ecology, 46 (2-3), 231-239. doi: 10.1016/0022-0981(80)90033-7
Chapman, DJ and Ragan, MA (1980). Evolution of Biochemical Pathways - Evidence From Comparative Biochemistry. Annual Review of Plant Physiology and Plant Molecular Biology, 31 (1), 639-678. doi: 10.1146/annurev.pp.31.060180.003231
Ragan, Mark A., Smidsrød, Olav and Larsen, Bjørn (1979). Chelation of divalent metal ions by brown algal polyphenols. Marine Chemistry, 7 (3), 265-271. doi: 10.1016/0304-4203(79)90043-4
Ragan, Mark A. and Jensen, Arne (1979). Quantitative studies on brown algal phenols. 3. Light-mediated exudation of polyphenols from Ascophyllum nodosum (L.) Le Jol. Journal of Experimental Marine Biology and Ecology, 36 (1), 91-101. doi: 10.1016/0022-0981(79)90102-3
Ragan, Mark A. and Jensen, Arne (1979). Widespread Distribution of Sulfated Polyphenols in Brown Algae. Phytochemistry, 18 (2), 261-262. doi: 10.1016/0031-9422(79)80066-7
Ragan, Mark A. and Mackinnon, M. D. (1979). Paired-Ion Reversed-Phase High-Performance Liquid Chromatography of Phenol Sulfates in Synthetic Mixtures, Algal Extracts and Urine. Journal of Chromatography, 178 (2), 505-513. doi: 10.1016/S0021-9673(00)92509-3
Ragan, Mark A. (1978). Phenol sulfate esters: ultraviolet, infrared, 1H- and 13C-nuclear magnetic resonance spectroscopic investigation.. Canadian Journal of Chemistry, 56 (50), 2681-2685. doi: 10.1139/v78-441
Ragan, M. A. and Jensen, A. (1978). Quantitative studies on brown algal phenols. 2. Seasonal variation in polyphenol content of Ascophyllum nodosum (L.) Le Jol. and Fucus vesiculosus (L.). Journal of Experimental Marine Biology and Ecology, 34 (3), 245-258. doi: 10.1016/S0022-0981(78)80006-9
Ragan, MA (1978). Phenol Sulfate Esters - Ultraviolet, Infrared, H-1 and C-13 Nuclear Magnetic-Resonance Spectroscopic Investigation. Canadian Journal of Chemistry-Revue Canadienne De Chimie, 56 (20), 2681-2685. doi: 10.1139/v78-441
Jensen, Arne and Ragan, Mark A. (1978). 1,2,3,5-Tetrahydroxybenzene 2,5-Disulfate Ester - Phenolic Precursor in Gelbstoff-Forming Exudates From Marine Brown Alga Ascophyllum nodosum (L.) LeJol. Tetrahedron Letters, 19 (9), 847-850. doi: 10.1016/S0040-4039(01)85415-0
Craigie, James S., McInnes, A. Gavin, Ragan, Mark A. and Walter, John A. (1977). 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-Revue Canadienne De Chimie, 55 (9), 1575-1582. doi: 10.1139/v77-219
Ragan, Mark A. and Jensen, Arne (1977). 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 (2), 209-221. doi: 10.1016/0022-0981(77)90013-2
Ragan, Mark A. and Craigie, J. S. (1976). Physodes and the phenolic compounds of brown algae. Isolation and characterization of phloroglucinol polymers from Fucus vesiculosus (I,.). Canadian Journal of Biochemistry, 54 (1), 66-73. doi: 10.1139/o76-011
Ragan, M. A. (1976). Physodes and the phenolic compounds of brown algae. Composition and significance of physodes in vivo. Botanica Marina, 19 (3), 145-154. doi: 10.1515/botm.1976.19.3.145

Conference Papers

Simpson, P., Nones, K., Johnson, J., Newell, F., Patch, A-M, Thorne, H., Kazakoff, S., De Luca, X., Parsons, M., Ferguson, K., Reid, L., Reed, A. McCart, Srihari, S., Lakis, V., Davidson, A., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., Beasley, J., Degasperi, A., Nik-Zainal, S., Ragan, M., Spurdle, A., Khanna, K. K., Lakhani, S., Pearson, J., Chenevix-Trench, G. and Waddell, N. (2019). Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 4-8 December 2018. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS18-P5-10-01
Srihari, S., Singla, J., Wong, L., Simpson, P. T., Khanna, K. K. and Ragan, M. A. (2016). Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. 38th Annual CTRC-AACR San Antonio Breast Cancer Symposium, San Antonio, Texas, 8-12 December 2015. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS15-PD6-05
Robinson, N., Brackin, R., Paungfoo-Lonhienne, C., Lonhienne, T., Westermann, M., Salazar, M., Yeoh, Y. K ., Hugenholtz, P., Ragan, M. A., Redding, M., Pratt, C., Wang, W. J., Royle, A., DiBella, L., Lakshmanan, P. and Schmidt, S. (2016). Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef. International Nitrogen Initiative Conference, Melbourne, Australia, 4-8 December 2016. Melbourne, Australia: International Nitrogen Initiative.
Chan, Cheong Xin, Stephens, Timothy G., Ling, Edmund Y. S., Foret, Sylvain, Morrow, Kathleen, Bourne, David G., Voolstra, Christian R., Leggat, William, Miller, David J. and Ragan, Mark A. (2015). Genome Analysis of Two Symbiodinium Isolates. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069489
Chan, Cheong Xin, Bernard, Guillaume, Chalmers, Benjamin D. B. and Ragan, Mark A. (2015). Scalable phylogenomic approaches to study algal evolution. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069493
Fangrath, S, Mudge, S., Deng, Y, Robinson, N, Schmidt, S, Hugenholtz, P, Ragan, M and Paungfoo-Lonhienne, C (2014). Plant growth promoting rhizobacteria (PGPR) for use in horticulture.. The 29th International Horticultural Congress, Brisbane Convention Centre, Brisbane Qld, Australia, 17 - 22 August 2014.
Fearnley, Liam G., Ragan, Mark A. and Nielsen, Lars K. (2014). Towards a large integrated model of signal transduction and gene regulation events in mammalian cells. BIOINFORMATICS 2014: 5th International Conference on Bioinformatics Models, Methods and Algorithms, Angers, Loire Valley, France, 3-6 March 2014. London, UK: SciTePress. doi: 10.5220/0004739601170122
Wang, Chenwei, Taciroglu, Alperen, Maetschke, Stefan, Nelson, Colleen, Ragan, Mark and Davis, Melissa (2013). mCOPA : analysis of heterogeneous features in cancer expression data. The Prostate Cancer World Congress and 14th Australasian Prostate Cancer Conference, Melbourne, VIC Australia, 6-10 August 2013. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing Ltd.. doi: 10.1111/bju.12293
Skippington, Elizabeth and Ragan, Mark A. (2010). Lateral genetic transfer and the evolution of cellular networks in Escherichia coli.. Systems Biology of Microorganisms 2010, Paris, France, 22-24 March 2010.
Ragan, Mark A. (2009). Trees and networks before and after Darwin.. International Society for the History, Philosophy and Social Studies of Biology 2009 Meeting, Brisbane, Australia, 12-16 July 2009.
Kassahn, K. S., Dang, V. T. and Ragan, M. A. (2009). The significance of whole-genome duplications for vertebrate evolution. 56th annual conference of the Genetics Society of Australasia, Brisbane, Australia, 7-10 July 2009. Kensington, N.S.W.: Genetics Society of Australasia.
Choi, JooYoung, Davis, Melissa J. and Ragan, Mark A. (2009). Evaluation and expression of “drug-likeness” of small molecules using Semantic Web technologies.. Seventh Asia-Pacific Bioinformatics Conference, Beijing, China, 13-16 January 2009.
Bustamam, A., Sehgal, M. S., Hamilton, N. A., Wong, S., Ragan, M. A. and Burrage, K (2009). An efficient parallel implementation of Markov clustering algorithm for large-scale protein-protein interaction networks that uses MPI. 5th IMT-GT international conference on mathematics, statistics and their applications, Bukittinggi, Indonesia, 9 -11 June 2009. Indonesia: Department of Mathematics, Andalas University.
Burrage, P. M., Burrage, K., Kurowski, K., Lorenc, M., Nicolau Jr., D. V., Swain, M. and Ragan, M. A. (2009). A parallel plasma membrane simulation. HiBi 09: 1st International Workshop on High Performance Computational Systems Biology, Trento, Italy, 14-16 October, 2009. Piscataway, NJ, U.S.A.: I E E E. doi: 10.1109/HiBi.2009.18
Ragan, Mark and Marsh, Brad (2008). The Visible Cell™ project: Changing the way we think about cells. 9th International Symposium on Parallel Architectures, Algorithms and Networks, I-SPAN 2008, , , May 7, 2008-May 9, 2008. doi: 10.1109/I-SPAN.2008.53
Choi, JooYoung, Davis, Melissa J. and Ragan, Mark A. (2008). Evaluation and expression of “drug-likeness” of small molecules using Semantic Web technologies.. 19th International Conference on Genome Informatics (GIW-2008), Gold Coast , Australia, 1-3 December 2008.
Treangen, Todd J., Darling, Aaron E., Ragan, Mark A. and Messeguer, Xavier (2008). Gapped extension for local multiple alignment of interspersed DNA repeats. 4th International Symposium on Bioinformatics Research and Applications ISBRA 2008, Atlanta, GA, 6-9 May 2008. Berlin, Germany: Springer-Verlag. doi: 10.1007/978-3-540-79450-9_8
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2008). Large-scale detection of recombination in nucleotide sequences. International Conference on Mathematical Biology 2007, Putrajaya, Malaysia, 4-6 September 2007. Melville, NY, USA: American Institute of Physics. doi: 10.1063/1.2883829
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, 28-30 January 2007. Johannesburg, South Africa: University of the Witwatersrand.
Davis, M., Newman, A., Khan, I., Hunter, J. and Ragan, M. A. (2007). Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions. 6th Asia Pacific Bioinformatics Conference (APBC'08), Kyoto, Japan, 14-17 January 2008. London, U.K.: Imperial College Press. doi: 10.1142/9781848161092_0017
Chor, Benny, Fellows, Michael, Ragan, Mark, Razgon, Igor, Rosamond, Frances and Snir, Sagi (2007). Connected coloring completion for general graphs: Algorithms and complexity. 13th Annual International Computing and Combinatorics Conference (COCOON 2007), Banff, Alberta, Canada, 16-19 July 2007. Berlin, Germany: Springer. doi: 10.1007/978-3-540-73545-8_10
Bodlaender, Hans L., Fellows, Michael R., Langston, Michael A., Ragan, Mark A., Rosamond, Frances A. and Weyer, Mark (2007). Quadratic kernelization for convex recoloring of trees. 13th Annual International Conference on Computing and Combinatorics (COCOON 2007), Banff, Alberta, Canada, 16-19 July 2007. Berlin, Germany: Springer. doi: 10.1007/978-3-540-73545-8_11
Ragan, M. A. (2007). The Visible Cell™: changing the way we think about cells. South Pacific User Services Conference SPUSC-007, Gold Coast, Australia, 26-30 November 2007.
Darling, Aaron, Miklós, Istvan and Ragan, Mark A. (2007). Selection on genome arrangement in a recently emerged bacterial pathogen. Fifth Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'07), San Diego, CA, USA, 16-18 September 2007.
Garcia Castro, Alexander, Norena, Angela, Betancourt, Andres and Ragan, Mark A. (2006). Cognitive support for an argumentative structure during the ontology development process. 9th International Protégé Conference, Stanford, California, July 24-26, 2006.
Bodlaender, H. L., Fellows, M. R., Langston, M. A., Ragan, M. A. and Rosamond, R. A. (2006). Kernelization for convex recoloring of trees. Algorithms and Complexity in Durham 2006, Durham University, Durham UK, 18-20 September, 2006. London: College Publications.
Ragan, MA (2006). Automating the search for lateral gene transfer. 4th Asia-Pacific Bioinformatics Conference, Taipei Taiwan, Feb 13-16, 2006. COVENT GARDEN: IMPERIAL COLLEGE PRESS. doi: 10.1142/9781860947292_0002
Garcia, Alexander, Thoraval, Samuel, Garcia, Leyla J., Chen, Yi-Ping Phoebe and Ragan, Mark A. (2005). Bioinformatic workflows: G-PIPE as an implementation. NETTAB 2005: Workflows management: new abilities for the biological information overflow, Second University of Naples, Naples, 5-7 October 2005.
Garcia, Alexander, Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Taylor, Chris and Ragan, Mark A. (2005). The use of conceptual maps for two ontology developments: nutrigenomics, and a management system for genealogies.. 8th International Protégé Conference, Madrid, Spain, July 18-21, 2005.
Hunter, Jane, Ragan, Mark A. and Little, Suzanne (2004). Position Paper for Semantic Web Life Sciences Workshop. W3C's Semantic Web Life Sciences Workshop, Cambridge, Massachusetts, 27-28 October, 2004.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Benchmarking the Detection and Analysis of Recombination. 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB), Glasgow, UK, 31 July - 4 August 2004.
Ragan, M. A. (2004). Postgraduate bioinformatics education initiatives in Australia. Workshop on Education in Bioinformatics WEB-04, Glasgow, Scotland, 30 July 2004.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events. First ARC Centre in Bioinformatics Annual All Hands Meeting, The University of Queensland, 10-11 May, 2004.
Hamilton, N., Burrage, K., Ragan, M. A. and Huber, T. (2004). Protein contact prediction using patterns of correlation. 29th Annual Lorne Conference on Protein Structure and Function, Lorne, Victoria, 8-12 February 2004.
Garcia, A., Ward, P., Appleby, N., Basford, K. E. and Ragan, M. A. (2004). From genotype to phenotype: modeling knowledge in functional plant genomics. Summer Symposium in Bioinformatics, Australian National University, Canberra, 6-10 December, 2004. Canberra: Australian mathematical Sciences Institute.
Ragan, M.A. (2003). Automated inference pipeline for assessment of lateral genetic transfer among microbial genomes. Genome Informatics 2003, Yokohama Pacifico/Yokohama, Japan, 14-17 December 2003. Tokyo, Japan: Universal Academy Press, Inc..
Garcia, A., Garcia, L. J., Ragan, M. .A. and Chen, Y.-P. P. (2003). JPIPE, a pipeline module for JEMBOSS. 11th International Conference on Intelligent Systems in Molecular Biology (ISBM 2003), Brisbane, Australia, 29 June - 3 July 2003.
Harlow, T.J., Gogarten, J. P. and Ragan, M. .A. (2003). A hybrid clustering approach to genome-scale recognition of protein families. 11th International Conference on Intelligent Systems in Molecular Biology (ISBM 2003), Brisbane, Australia, 29 June - 3 July 2003.
Beiko, R.G., Charlebois, R. L. and Ragan, M. A. (2003). Genome phylogenies based on the mean normalized BLAST score. 11th International Conference on Intelligent Systems in Molecular Biology, Brisbane, Australia, 29 June - 3 July 2003.
Hohl, M., Rigoutsos, I. and Ragan, M. A. (2003). Freeing phylogenies from alignments. 11th International Conference on Intelligent Systems in Molecular Biology, Brisbane, Australia, 29 June - 3 July 2003.
Garcia, A., Cleary, J., Ragan, M. .A. and Chen, Y.-P. P. (2003). SEMA, a semantic literature annotator. 11th International Conference on Intelligent Systems in Molecular Biology (ISBM 2003), Brisbane, Australia, 29 June - 3 July 2003.
Ragan, M. A. (2003). Automated computational genomics: a case study. Australian Partnership in Advanced Computing APAC03, Queensland, Australia, 2003.
Sensen, C. W., Dalton, T. E., Brousseau, R., Clark, F., Crosby, W., Foxall, R. A., Liu, Q. Y., Hemmingsen, S., Nash, J., Ragan, M. A., Thomas, D. Y., Wood, G. and van der Meer, J. P. (2000). The Canadian Bioinformatics Resource: new opportunities for bioinformatics in Canada.. TERENA Networking 2000 Conference, Lisbon Portugal, 22-25 May 2000. Amsterdam, The Netherlands: Elsevier BV * North-Holland.
Berger L., Speare R., Daszak P., Green D.E., Cunningham A.A., Goggin C.L., Slocombe R., Ragan M.A., Hyatt A.D., McDonald K.R., Hines H.B., Lips K.R., Marantelli G. and Parkes H. (1998). Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America. doi: 10.1073/pnas.95.15.9031
Zhou, Yi-Hong and Ragan, Mark A. (1996). Nuclear-encoded protein-coding genes of the agarophyte Gracilaria verrucosa (Gracilariales, Rhodophyta). Kluwer Academic Publishers. doi: 10.1007/BF00047842
Ragan, MA and Lee, AR (1991). Making Phylogenetic Sense of Biochemical and Morphological Diversity Among the Protists. 4Th International Congress of Systematic and Evolutionary Biology ( Icseb-4 ), College Pk Md, Jul , 1990. PORTLAND: DIOSCORIDES PRESS.
Ragan, Mark A. (1989). Biochemical pathways and the phylogeny of the eukaryotes.. 1988 Nobel Symposium "The Hierarchy of Life", Karlskoge, Sweden, 29 August-2 September 1988. Amsterdam , Netherlands: Elsevier.
Chapman, D. J. and Ragan, M. A. (1980). Chemotaxonomy in the algae: a viewpoint. International Symposium on Taxonomy of Algae, Madras, India, 9-16 December, 1974. Madras, India: University of Madras Press.
Jamieson, W. D., Ragan, M. A., Craigie, J. S., Embree, D. J. and Mandy, M. E. (1977). Photoplate high resolution mass spectrometry of high molecular weight algal tannin derivatives. 25th Annual Conference on Mass Spectrometry and Allied Topics, Washington, DC, USA, 29 May-3 June 1977. Washington, DC, USA: American Society for Mass Spectrometry.

Preprint

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase strategy for detecting recombination in nucleotide sequences.

Data Collections

González-Pech, Raúl A., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2021). Genome assemblies and the associated annotations for seven Symbiodinium isolates. The University of Queensland. (Dataset) doi: 10.14264/f1b3a11
Stephens, Timothy, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088. The University of Queensland. (Dataset) doi: 10.14264/uql.2020.222
Bernard, Guillaume , Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free network of 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.952
Bernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.908