| Year |
Citation |
Score |
| 2020 |
Mohamed AR, Chan CX, Ragan MA, Zhang J, Cooke I, Ball EE, Miller DJ. Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports. PMID 32452166 DOI: 10.1111/1758-2229.12859 |
0.314 |
|
| 2020 |
Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. Bmc Biology. 18: 56. PMID 32448240 DOI: 10.1186/S12915-020-00782-8 |
0.361 |
|
| 2019 |
Robbins SJ, Singleton CM, Chan CX, Messer LF, Geers AU, Ying H, Baker A, Bell SC, Morrow KM, Ragan MA, Miller DJ, Forêt S, Voolstra CR, Tyson GW, et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology. PMID 31548681 DOI: 10.1038/S41564-019-0532-4 |
0.335 |
|
| 2019 |
Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff SH, de Luca XM, Parsons MT, Ferguson K, Reid L, Reed AEM, Srihari S, Lakis V, Davidson AL, Mukhopadhyay P, ... ... Ragan MA, et al. Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Annals of Oncology : Official Journal of the European Society For Medical Oncology. PMID 31090900 DOI: 10.1093/Annonc/Mdz132 |
0.563 |
|
| 2019 |
González-Pech RA, Bhattacharya D, Ragan MA, Chan CX. Genome Evolution of Coral Reef Symbionts as Intracellular Residents. Trends in Ecology & Evolution. PMID 31084944 DOI: 10.1016/J.Tree.2019.04.010 |
0.367 |
|
| 2019 |
Taherian Fard A, Ragan MA. Quantitative Modelling of the Waddington Epigenetic Landscape. Methods in Molecular Biology (Clifton, N.J.). 1975: 157-171. PMID 31062309 DOI: 10.1007/978-1-4939-9224-9_7 |
0.359 |
|
| 2019 |
Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones MK, Ragan MA, Stoye J, Oleaga A, et al. Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. Plos Pathogens. 15: e1007513. PMID 30673782 DOI: 10.1371/Journal.Ppat.1007513 |
0.349 |
|
| 2019 |
Simpson P, Nones K, Johnson J, Newell F, Patch A, Thorne H, Kazakoff S, Luca XD, Parsons M, Ferguson K, Reid L, Reed AM, Srihari S, Lakis V, Davidson A, ... ... Ragan M, et al. Abstract P5-10-01: Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology Cancer Research. 79. DOI: 10.1158/1538-7445.Sabcs18-P5-10-01 |
0.552 |
|
| 2018 |
Stephens TG, Ragan MA, Bhattacharya D, Chan CX. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports. 8: 17175. PMID 30464192 DOI: 10.1038/S41598-018-35620-Z |
0.403 |
|
| 2017 |
González-Pech RA, Ragan MA, Chan CX. Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports. 7: 15021. PMID 29101370 DOI: 10.1038/S41598-017-15029-W |
0.389 |
|
| 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 |
0.37 |
|
| 2017 |
Taherian Fard A, Ragan MA. Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach. Frontiers in Genetics. 8: 48. PMID 28458684 DOI: 10.3389/Fgene.2017.00048 |
0.404 |
|
| 2017 |
Cong Y, Chan YB, Phillips CA, Langston MA, Ragan MA. Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. Frontiers in Microbiology. 8: 21. PMID 28154557 DOI: 10.3389/Fmicb.2017.00021 |
0.407 |
|
| 2017 |
Anderson AM, Kalimutho M, Harten S, Nanayakkara DM, Khanna KK, Ragan MA. The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells. Scientific Reports. 7: 39873. PMID 28051153 DOI: 10.1038/Srep39873 |
0.361 |
|
| 2017 |
Chan CX, Beiko RG, Ragan MA. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events. Methods in Molecular Biology (Clifton, N.J.). 1525: 421-432. PMID 27896730 DOI: 10.1007/978-1-4939-6622-6_16 |
0.399 |
|
| 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 |
0.524 |
|
| 2016 |
Bernard G, Ragan MA, Chan CX. Recapitulating phylogenies using k-mers: from trees to networks. F1000research. 5: 2789. PMID 28105314 DOI: 10.12688/F1000Research.10225.2 |
0.386 |
|
| 2016 |
Liu C, Rohart F, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer. Scientific Reports. 6: 34000. PMID 27666291 DOI: 10.1038/Srep34000 |
0.324 |
|
| 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 |
0.341 |
|
| 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 |
0.396 |
|
| 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 |
0.363 |
|
| 2016 |
Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ. The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology. PMID 27094992 DOI: 10.1111/Mec.13659 |
0.33 |
|
| 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 |
0.578 |
|
| 2016 |
Srihari S, Kalimutho M, Singla J, Davidson A, Wong L, Simpson P, Khanna KK, Ragan M. Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response F1000research. 5. DOI: 10.7490/F1000Research.1111789.1 |
0.525 |
|
| 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 |
0.559 |
|
| 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 |
0.614 |
|
| 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 |
0.552 |
|
| 2015 |
Fard AT, Srihari S, Mar JC, Ragan MA. Modeling the landscape of cellular development using the Hopfield network F1000research. 6. DOI: 10.7490/F1000Research.1097980.1 |
0.517 |
|
| 2015 |
Voolstra CR, Miller DJ, Ragan MA, Hoffmann AA, Hoegh-Guldberg O, Bourne DG, Ball EE, Ying H, Forêt S, Takahashi S, Weynberg KD, Oppen MJHv, Morrow K, Chan CX, Rosic N, et al. The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change Frontiers in Marine Science. 2. DOI: 10.3389/Fmars.2015.00068 |
0.337 |
|
| 2015 |
Chan CX, Stephens TG, Ling EYS, Foret S, Morrow K, Bourne DG, Voolstra CR, Leggat W, Miller DJ, Ragan MA. Genome Analysis of Two Symbiodinium Isolates European Journal of Phycology. 50: 57-58. DOI: 10.1080/09670262.2015.1069489 |
0.301 |
|
| 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 |
0.615 |
|
| 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 |
0.773 |
|
| 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 |
0.339 |
|
| 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 |
0.549 |
|
| 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 |
0.772 |
|
| 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 |
0.339 |
|
| 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 |
0.353 |
|
| 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 |
0.301 |
|
| 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 |
0.756 |
|
| 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 |
0.42 |
|
| 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 |
0.774 |
|
| 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 DOI: 10.7490/F1000Research.1094485.1 |
0.738 |
|
| 2013 |
Davis MJ, Ragan MA. Understanding cellular function and disease with comparative pathway analysis. Genome Medicine. 5: 64. PMID 23889971 DOI: 10.1186/Gm468 |
0.384 |
|
| 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 |
0.348 |
|
| 2013 |
Ragan MA. Yeast rises to the occasion. Elife. 2: e00933. PMID 23795300 DOI: 10.7554/Elife.00933 |
0.368 |
|
| 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 |
0.385 |
|
| 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 |
0.602 |
|
| 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 |
0.309 |
|
| 2013 |
Chan CX, Ragan MA. Next-generation phylogenomics. Biology Direct. 8: 3. PMID 23339707 DOI: 10.1186/1745-6150-8-3 |
0.387 |
|
| 2013 |
Srihari S, Liu C, Taherian-Fard A, Simpson PT, Khanna KK, Ragan MA. Harnessing DNA-damage response pathways for breast cancer therapy: a synthetic lethality paradigm F1000research. 4. DOI: 10.7490/F1000Research.1094535.1 |
0.516 |
|
| 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 |
0.706 |
|
| 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: 10.1111/Bju.12293 |
0.362 |
|
| 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 |
0.739 |
|
| 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 |
0.375 |
|
| 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 |
0.345 |
|
| 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 |
0.785 |
|
| 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 |
0.759 |
|
| 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 |
0.303 |
|
| 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 |
0.342 |
|
| 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 |
0.756 |
|
| 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 |
0.41 |
|
| 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 |
0.724 |
|
| 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 |
0.339 |
|
| 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 |
0.307 |
|
| 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 |
0.332 |
|
| 2009 |
Chan CX, Beiko RG, Darling AE, Ragan MA. Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution. 1: 429-38. PMID 20333212 DOI: 10.1093/Gbe/Evp044 |
0.422 |
|
| 2009 |
Ragan MA. Thinking laterally about genomes. Genome Informatics. International Conference On Genome Informatics. 23: 221-2. PMID 20180279 |
0.31 |
|
| 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 |
0.321 |
|
| 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 |
0.327 |
|
| 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 |
0.37 |
|
| 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 |
0.346 |
|
| 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 |
0.411 |
|
| 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 |
0.345 |
|
| 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 |
0.41 |
|
| 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 |
0.329 |
|
| 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 |
0.382 |
|
| 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 |
0.348 |
|
| 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 |
0.429 |
|
| 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 |
0.394 |
|
| 2008 |
Ragan M. Genomics and evolution of microbial eukaryotes Botanica Marina. 51. DOI: 10.1515/Bot.2008.008 |
0.317 |
|
| 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 |
0.323 |
|
| 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 |
0.428 |
|
| 2006 |
Höhl M, Rigoutsos I, Ragan MA. Pattern-based phylogenetic distance estimation and tree reconstruction. Evolutionary Bioinformatics Online. 2: 359-75. PMID 19455227 DOI: 10.4137/Ebo.S0 |
0.31 |
|
| 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 |
0.326 |
|
| 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 |
0.317 |
|
| 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 |
0.414 |
|
| 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 |
0.32 |
|
| 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 |
0.31 |
|
| 2003 |
Ragan MA. Automated Inference Pipeline for Assessment of Lateral Gener Transfer among Microbial Genomes Genome Informatics. 14: 709-709. DOI: 10.11234/Gi1990.14.709 |
0.308 |
|
| 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: 10.1099/00207713-52-3-777 |
0.333 |
|
| 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 |
0.38 |
|
| 2002 |
Ragan M. Reconciling the many faces of lateral gene transfer - Response from Ragan Trends in Microbiology. 10: 4-4. DOI: 10.1016/S0966-842X(01)02283-1 |
0.378 |
|
| 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 |
0.397 |
|
| 2001 |
Ragan MA. On surrogate methods for detecting lateral gene transfer. Fems Microbiology Letters. 201: 187-91. PMID 11470360 DOI: 10.1111/J.1574-6968.2001.Tb10755.X |
0.351 |
|
| 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 |
0.345 |
|
| 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 |
0.303 |
|
| 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 |
0.305 |
|
| 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 = Gã©Nome / Conseil National De Recherches Canada. 43: 116-36. PMID 10701121 DOI: 10.1139/G99-108 |
0.383 |
|
| 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 |
0.415 |
|
| 1998 |
Ragan MA, Gaasterland T. Microbial genescapes: a prokaryotic view of the yeast genome. Microbial & Comparative Genomics. 3: 219-35. PMID 10027191 DOI: 10.1089/Omi.1.1998.3.219 |
0.342 |
|
| 1998 |
Gaasterland T, Ragan MA. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microbial & Comparative Genomics. 3: 199-217. PMID 10027190 DOI: 10.1089/Omi.1.1998.3.199 |
0.338 |
|
| 1998 |
Gaasterland T, Ragan MA. Constructing multigenome views of whole microbial genomes. Microbial & Comparative Genomics. 3: 177-92. PMID 9775388 DOI: 10.1089/Omi.1.1998.3.177 |
0.342 |
|
| 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 |
0.383 |
|
| 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 |
0.377 |
|
| 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 |
0.398 |
|
| 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 |
0.359 |
|
| 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 |
0.343 |
|
| 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 |
0.348 |
|
| 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 DOI: 10.1111/J.1550-7408.1996.Tb03998.X |
0.326 |
|
| 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 |
0.365 |
|
| 1996 |
Zhou YH, Ragan MA. Nuclear-encoded protein-coding genes of the agarophyte Gracilaria verrucosa (Gracilariales, Rhodophyta) Hydrobiologia. 326: 429-436. DOI: 10.1007/Bf00047842 |
0.37 |
|
| 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 |
0.345 |
|
| 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 |
0.387 |
|
| 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 |
0.329 |
|
| 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 |
0.382 |
|
| 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 |
0.318 |
|
| 1995 |
Saunders GW, Bird CJ, Ragan MA, Rice EL. PHYLOGENETIC RELATIONSHIPS OF SPECIES OF UNCERTAIN TAXONOMIC POSITION WITHIN THE ACROCHAETIALES-PALMARIALES COMPLEX (RHODOPHYTA): INFERENCES FROM PHENOTYPIC AND 18S rDNA SEQUENCE DATA1 Journal of Phycology. 31: 601-611. DOI: 10.1111/J.1529-8817.1995.Tb02556.X |
0.342 |
|
| 1995 |
Oliveira MC, Kurniawan J, Bird CJ, Rice EL, Murphy CA, Singh RK, Gutell RR, Ragan MA. A preliminary investigation of the order Bangiales (Bangiophycidae, Rhodophyta) based on sequences of nuclear small-subunit ribosomal RNA genes Phycological Research. 43: 71-79. DOI: 10.1111/J.1440-1835.1995.Tb00007.X |
0.331 |
|
| 1995 |
Ragan MA, Gutell RR. Are red algae plants? Botanical Journal of the Linnean Society. 118: 81-105. DOI: 10.1111/J.1095-8339.1995.Tb00463.X |
0.32 |
|
| 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 |
0.339 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A040102 |
0.352 |
|
| 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 DOI: 10.1128/Jb.176.15.4597-4609.1994 |
0.327 |
|
| 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 |
0.364 |
|
| 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 |
0.325 |
|
| 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. DOI: 10.1111/J.0022-3646.1994.00490.X |
0.323 |
|
| 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 |
0.301 |
|
| 1994 |
Cerff R, Bohnert HJ, Ragan M, Sachs MM. Plant-wide nomenclature of nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases Plant Molecular Biology Reporter. 12. DOI: 10.1007/Bf02671565 |
0.306 |
|
| 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 |
0.329 |
|
| 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 |
0.304 |
|
| 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 |
0.325 |
|
| 1992 |
Bird CJ, Rice EL, Murphy CA, Ragan MA. Phylogenetic relationships in the Gracilariales (Rhodophyta) as determined by 18S rDNA sequences Phycologia. 31: 510-522. DOI: 10.2216/I0031-8884-31-6-510.1 |
0.341 |
|
| 1992 |
Destombe C, Cembella AD, Murphy CA, Ragan MA. Nucleotide sequence of the 18S ribosomal RNA genes from the marine dinoflagellate Alexandrium tamarense (Gonyaulacales, Dinophyta) Phycologia. 31: 121-124. DOI: 10.2216/I0031-8884-31-1-121.1 |
0.326 |
|
| 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 |
0.361 |
|
| 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 |
0.318 |
|
| 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 |
0.331 |
|
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