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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. 23 6
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, 9: 847-850. 45   10
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 33   16 0
Ragan, Mark A. and Chapman, David J. A biochemical phylogeny of the protists. New York , NY, U.S.A.: Academic Press, 1978. doi:10.1016/B978-0-12-575550-4.50005-6 18   0
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 87   20 Cited 20 times in Scopus20 0
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 57   6 Cited 5 times in Scopus5 5
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 51-1-51-25. doi:10.1186/1471-2164-8-51 75   51 Cited 49 times in Scopus49 0
Harlow, T.J., Gogarten, J. P. and Ragan, M. .A. (2003). A hybrid clustering approach to genome-scale recognition of protein families. In: Program, 11th International Conference on Intelligent Systems in Molecular Biology (ISBM 2003). 11th International Conference on Intelligent Systems in Molecular Biology (ISBM 2003), Brisbane, Australia, (115-115). 29 June - 3 July 2003. 37  
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 Article 45. doi:10.1186/1471-2105-5-45 74   27 Cited 34 times in Scopus34 0
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 26   151 Cited 134 times in Scopus134 0
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 22   16 0
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. In: I. M. Arnawa, M. Muhafzan and S. Bahri, Proceedings of the 5th IMT-GT international conference on mathematics, statistics and their applications 2009 (ICMSA 2009). 5th IMT-GT international conference on mathematics, statistics and their applications, Bukittinggi, Indonesia, (94-101). 9 -11 June 2009. 423  
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 100   3 Cited 3 times in Scopus3 46
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 31   12 Cited 12 times in Scopus12 12
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 27   121 Cited 117 times in Scopus117 3
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: 180-189. doi:10.1109/TCBB.2009.9 46   6 Cited 6 times in Scopus6 0
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. In: 2009 International Workshop on High Performance Computational Systems Biology (HiBi 2009). Proceedings. HiBi 09: 1st International Workshop on High Performance Computational Systems Biology, Trento, Italy, (105-112). 14-16 October, 2009. doi:10.1109/HiBi.2009.18 47   0 Cited 0 times in Scopus0 0
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 28   0
Ragan, Mark A. (2006) ARC Centre in Bioinformatics. Asia Pacific Biotech News, 10 24: 1391-1394. doi:10.1142/S0219030306002060 66   0
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 74   20 Cited 21 times in Scopus21 0
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: e4524.1-e4524.8. doi:10.1371/journal.pone.0004524 105   30 Cited 29 times in Scopus29 0
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 22   53 0
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 23   35 0
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 61   8 Cited 10 times in Scopus10 0
Ragan, MA (1997) A third kingdom of eukaryotic life: History of an idea - ISEP president's address. Archiv Fur Protistenkunde, 148 3: 225-243. 24   10
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. In: Proceedings of the First Southern African Bioinformatics Workshop (SABioinf 2007). The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, (9-16). 28-30 January 2007. 233 65
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007) A two-phase strategy for detecting recombination in nucleotide sequences. 142 409
Ragan, M. A. (2003). Automated computational genomics: a case study. In: Australian Partnership in Advanced Computing APAC03. Australian Partnership in Advanced Computing APAC03, Queensland, Australia, (18-19). 2003. 35  
Ragan, M.A. (2003). Automated inference pipeline for assessment of lateral genetic transfer among microbial genomes. In: Gribskov, M. Kanehisa, S. Miyano and T. Takagi, Genome Informatics 2003 - Part III - The first annual symposium of Association of Asian Societies for Bioinformatics (AASBI 2003). Genome Informatics 2003, Yokohama Pacifico/Yokohama, Japan, (709-709). 14-17 December 2003. 43  
Davis, Melissa J., Sehgal, Muhammad Shoaib B. and Ragan, Mark A. (2010) Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics, 11 498-1-498-13. doi:10.1186/1471-2105-11-498 65   10 Cited 10 times in Scopus10 0
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: 851-857. doi:10.1093/bioinformatics/btr720 38   1 Cited 2 times in Scopus2 0
Ragan, MA (2006). Automating the search for lateral gene transfer. In: Proceedings of the 4th Asia-Pacific Bioinformatics Conference. 4th Asia-Pacific Bioinformatics Conference, Taipei Taiwan, (3-3). Feb 13-16, 2006. doi:10.1142/9781860947292_0002 15   1 0
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: 737-744. doi:10.1093/bioinformatics/btq042 77   7 Cited 9 times in Scopus9 0
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 220 190 10 Cited 9 times in Scopus9 0
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 8.1-8.20. doi:10.1186/1471-2148-5-8 124   23 Cited 23 times in Scopus23 0
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Benchmarking the Detection and Analysis of Recombination. In: Proceedings of the 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB). 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB), Glasgow, UK, (160-160). 31 July - 4 August 2004. 194 366
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. 17  
Ragan, Mark A. (1989). Biochemical pathways and the phylogeny of the eukaryotes.. In: Bo Fernholm, Kare Bremer and Hans Jörnvall, The hierarchy of life : molecules and morphology in phylogenetic analysis : proceedings from Nobel Symposium 70. 1988 Nobel Symposium "The Hierarchy of Life", Karlskoge, Sweden, (145-160). 29 August-2 September 1988. 16  
Ragan, Mark A. (2014). Bioinformatics. In Mehdi Khosrow-Pour (Ed.), Encyclopedia of Information Science and Technology 3rd ed. (pp. 393-401) United Kingdom: Sweet and Maxwell. doi:10.4018/978-1-4666-5888-2 15   0
Ragan, M.A. (2003) Bioinformatics: a glimpse of the future. BIOSILICO, 1 4: 119-120. 48   Cited 0 times in Scopus0
Garcia, Alexander, Thoraval, Samuel, Garcia, Leyla J., Chen, Yi-Ping Phoebe and Ragan, Mark A. (2005). Bioinformatic workflows: G-PIPE as an implementation. In: A. Facchiano and P. Romano, Proceedings. NETTAB 2005: Workflows management: new abilities for the biological information overflow, Second University of Naples, Naples, (61-64). 5-7 October 2005. 85  
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 47   2 Cited 2 times in Scopus2 0
Chen, L. C.-M., McCracken, I. and Ragan, M. A. (1990) Biotechnology potential for hoshi-nori production. World Aquaculture, 21 3: 106-107. 25  
Taherian-Fard, Atefeh, Srihari, Sriganesh and Ragan, Mark A. (2014) Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings in Bioinformatics, . doi:10.1093/bib/bbu020 45   6
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 13   7 0
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 8   7 0
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 21   25 Cited 15 times in Scopus15 0
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 21   12 Cited 13 times in Scopus13 0
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 22   12 Cited 14 times in Scopus14 0
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 22   11 Cited 10 times in Scopus10 1

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