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Items: 1 to 50 of 141


Deciphering the nature of the coral-Chromera association.

Mohamed AR, Cumbo VR, Harii S, Shinzato C, Chan CX, Ragan MA, Satoh N, Ball EE, Miller DJ.

ISME J. 2018 Mar;12(3):776-790. doi: 10.1038/s41396-017-0005-9. Epub 2018 Jan 10.


Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium.

González-Pech RA, Ragan MA, Chan CX.

Sci Rep. 2017 Nov 3;7(1):15021. doi: 10.1038/s41598-017-15029-w.


Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence.

Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, Ragan MA, Schmidt S, Hugenholtz P.

Nat Commun. 2017 Aug 9;8(1):215. doi: 10.1038/s41467-017-00262-8.


Palmitoylation: a protein S-acylation with implications for breast cancer.

Anderson AM, Ragan MA.

NPJ Breast Cancer. 2016 Oct 19;2:16028. doi: 10.1038/npjbcancer.2016.28. eCollection 2016. Review.


Alignment-free inference of hierarchical and reticulate phylogenomic relationships.

Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA.

Brief Bioinform. 2017 Jun 30. doi: 10.1093/bib/bbx067. [Epub ahead of print]


Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach.

Taherian Fard A, Ragan MA.

Front Genet. 2017 Apr 18;8:48. doi: 10.3389/fgene.2017.00048. eCollection 2017.


Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.

Cong Y, Chan YB, Phillips CA, Langston MA, Ragan MA.

Front Microbiol. 2017 Jan 19;8:21. doi: 10.3389/fmicb.2017.00021. eCollection 2017.


Recapitulating phylogenies using k-mers: from trees to networks.

Bernard G, Ragan MA, Chan CX.

Version 2. F1000Res. 2016 Nov 29 [revised 2016 Jan 1];5:2789. doi: 10.12688/f1000research.10225.2. eCollection 2016.


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

Anderson AM, Kalimutho M, Harten S, Nanayakkara DM, Khanna KK, Ragan MA.

Sci Rep. 2017 Jan 4;7:39873. doi: 10.1038/srep39873.


Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

Chan CX, Beiko RG, Ragan MA.

Methods Mol Biol. 2017;1525:421-432.


Crosstalk between sugarcane and a plant-growth promoting Burkholderia species.

Paungfoo-Lonhienne C, Lonhienne TG, Yeoh YK, Donose BC, Webb RI, Parsons J, Liao W, Sagulenko E, Lakshmanan P, Hugenholtz P, Schmidt S, Ragan MA.

Sci Rep. 2016 Nov 21;6:37389. doi: 10.1038/srep37389.


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

Liu C, Rohart F, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA.

Sci Rep. 2016 Sep 26;6:34000. doi: 10.1038/srep34000.


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

Cong Y, Chan YB, Ragan MA.

Sci Rep. 2016 Jul 25;6:30308. doi: 10.1038/srep30308.


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

Cong Y, Chan YB, Ragan MA.

Sci Rep. 2016 Jul 25;6:29319. doi: 10.1038/srep29319.


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

Bissett A, Fitzgerald A, Meintjes T, Mele PM, Reith F, Dennis PG, Breed MF, Brown B, Brown MV, Brugger J, Byrne M, Caddy-Retalic S, Carmody B, Coates DJ, Correa C, Ferrari BC, Gupta VV, Hamonts K, Haslem A, Hugenholtz P, Karan M, Koval J, Lowe AJ, Macdonald S, McGrath L, Martin D, Morgan M, North KI, Paungfoo-Lonhienne C, Pendall E, Phillips L, Pirzl R, Powell JR, Ragan MA, Schmidt S, Seymour N, Snape I, Stephen JR, Stevens M, Tinning M, Williams K, Yeoh YK, Zammit CM, Young A.

Gigascience. 2016 May 18;5:21. doi: 10.1186/s13742-016-0126-5. eCollection 2016.


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

Stephens TG, Bhattacharya D, Ragan MA, Chan CX.

PeerJ. 2016 May 12;4:e2038. doi: 10.7717/peerj.2038. eCollection 2016.


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

Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ.

Mol Ecol. 2016 Jul;25(13):3127-41. doi: 10.1111/mec.13659. Epub 2016 May 18.


Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks.

Fard AT, Srihari S, Mar JC, Ragan MA.

NPJ Syst Biol Appl. 2016 Feb 18;2:16001. doi: 10.1038/npjsba.2016.1. eCollection 2016.


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

Srihari S, Kalimutho M, Lal S, Singla J, Patel D, Simpson PT, Khanna KK, Ragan MA.

Mol Biosyst. 2016 Mar;12(3):963-72. doi: 10.1039/c5mb00655d.


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

Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA.

Mol Oncol. 2016 Jan;10(1):179-93. doi: 10.1016/j.molonc.2015.09.007. Epub 2015 Sep 26.


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

Srihari S, Singla J, Wong L, Ragan MA.

Biol Direct. 2015 Oct 1;10:57. doi: 10.1186/s13062-015-0086-1.


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

Yeoh YK, Paungfoo-Lonhienne C, Dennis PG, Robinson N, Ragan MA, Schmidt S, Hugenholtz P.

Environ Microbiol. 2016 May;18(5):1338-51. doi: 10.1111/1462-2920.12925. Epub 2015 Jul 30.


Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.

Paungfoo-Lonhienne C, Yeoh YK, Kasinadhuni NR, Lonhienne TG, Robinson N, Hugenholtz P, Ragan MA, Schmidt S.

Sci Rep. 2015 Mar 2;5:8678. doi: 10.1038/srep08678.


Complex-based analysis of dysregulated cellular processes in cancer.

Srihari S, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA.

BMC Syst Biol. 2014;8 Suppl 4:S1. doi: 10.1186/1752-0509-8-S4-S1. Epub 2014 Dec 8.


Inferring phylogenies of evolving sequences without multiple sequence alignment.

Chan CX, Bernard G, Poirion O, Hogan JM, Ragan MA.

Sci Rep. 2014 Sep 30;4:6504. doi: 10.1038/srep06504.


Breast cancer classification: linking molecular mechanisms to disease prognosis.

Taherian-Fard A, Srihari S, Ragan MA.

Brief Bioinform. 2015 May;16(3):461-74. doi: 10.1093/bib/bbu020. Epub 2014 Jun 20. Review.


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

Liu C, Srihari S, Cao KA, Chenevix-Trench G, Simpson PT, Ragan MA, Khanna KK.

Nucleic Acids Res. 2014 Jun;42(10):6106-27. doi: 10.1093/nar/gku284. Epub 2014 May 3. Review.


INsPeCT: INtegrative Platform for Cancer Transcriptomics.

Madhamshettiwar PB, Maetschke SR, Davis MJ, Reverter A, Ragan MA.

Cancer Inform. 2014 Mar 12;13:59-66. doi: 10.4137/CIN.S13630. eCollection 2014.


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

Ragan MA, Bernard G, Chan CX.

RNA Biol. 2014;11(3):176-85. doi: 10.4161/rna.27505. Epub 2014 Jan 14. Review.


RMaNI: Regulatory Module Network Inference framework.

Madhamshettiwar PB, Maetschke SR, Davis MJ, Ragan MA.

BMC Bioinformatics. 2013;14 Suppl 16:S14. doi: 10.1186/1471-2105-14-S16-S14. Epub 2013 Oct 22.


Characterizing cancer subtypes as attractors of Hopfield networks.

Maetschke SR, Ragan MA.

Bioinformatics. 2014 May 1;30(9):1273-9. doi: 10.1093/bioinformatics/btt773. Epub 2014 Jan 8.


Evolution and Controllability of Cancer Networks: A Boolean Perspective.

Srihari S, Raman V, Leong HW, Ragan MA.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):83-94. doi: 10.1109/TCBB.2013.128.


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

Paungfoo-Lonhienne C, Lonhienne TG, Yeoh YK, Webb RI, Lakshmanan P, Chan CX, Lim PE, Ragan MA, Schmidt S, Hugenholtz P.

Microb Biotechnol. 2014 Mar;7(2):142-54. doi: 10.1111/1751-7915.12105. Epub 2013 Dec 19.


Evolution and Controllability of Cancer Networks: A Boolean Perspective.

Srihari S, Raman V, Leong HW, Ragan MA.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Oct 22. [Epub ahead of print]


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

Fearnley LG, Davis MJ, Ragan MA, Nielsen LK.

Brief Bioinform. 2014 Nov;15(6):973-83. doi: 10.1093/bib/bbt058. Epub 2013 Aug 14.


Understanding cellular function and disease with comparative pathway analysis.

Davis MJ, Ragan MA.

Genome Med. 2013 Jul 26;5(7):64. doi: 10.1186/gm468. eCollection 2013.


Biological intuition in alignment-free methods: response to Posada.

Ragan MA, Chan CX.

J Mol Evol. 2013 Aug;77(1-2):1-2. doi: 10.1007/s00239-013-9573-0. Epub 2013 Jul 23.


Yeast rises to the occasion.

Ragan MA.

Elife. 2013 Jun 18;2:e00933. doi: 10.7554/eLife.00933.


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

Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA.

Mol Ecol. 2013 Jun;22(12):3216-41. doi: 10.1111/mec.12309. Review.


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

Maetschke SR, Madhamshettiwar PB, Davis MJ, Ragan MA.

Brief Bioinform. 2014 Mar;15(2):195-211. doi: 10.1093/bib/bbt034. Epub 2013 May 21.


Systematic tracking of dysregulated modules identifies novel genes in cancer.

Srihari S, Ragan MA.

Bioinformatics. 2013 Jun 15;29(12):1553-61. doi: 10.1093/bioinformatics/btt191. Epub 2013 Apr 23.


Clustering evolving proteins into homologous families.

Chan CX, Mahbob M, Ragan MA.

BMC Bioinformatics. 2013 Apr 8;14:120. doi: 10.1186/1471-2105-14-120.


Next-generation phylogenomics.

Chan CX, Ragan MA.

Biol Direct. 2013 Jan 22;8:3. doi: 10.1186/1745-6150-8-3.


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

Muscat GE, Eriksson NA, Byth K, Loi S, Graham D, Jindal S, Davis MJ, Clyne C, Funder JW, Simpson ER, Ragan MA, Kuczek E, Fuller PJ, Tilley WD, Leedman PJ, Clarke CL.

Mol Endocrinol. 2013 Feb;27(2):350-65. doi: 10.1210/me.2012-1265. Epub 2013 Jan 4.


mCOPA: analysis of heterogeneous features in cancer expression data.

Wang C, Taciroglu A, Maetschke SR, Nelson CC, Ragan MA, Davis MJ.

J Clin Bioinforma. 2012 Dec 10;2(1):22. doi: 10.1186/2043-9113-2-22.


The mammalian PYHIN gene family: phylogeny, evolution and expression.

Cridland JA, Curley EZ, Wykes MN, Schroder K, Sweet MJ, Roberts TL, Ragan MA, Kassahn KS, Stacey KJ.

BMC Evol Biol. 2012 Aug 7;12:140.


Rewiring the dynamic interactome.

Davis MJ, Shin CJ, Jing N, Ragan MA.

Mol Biosyst. 2012 Aug;8(8):2054-66, 2013. doi: 10.1039/c2mb25050k. Epub 2012 Jun 22.


Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets.

Madhamshettiwar PB, Maetschke SR, Davis MJ, Reverter A, Ragan MA.

Genome Med. 2012 May 1;4(5):41. doi: 10.1186/gm340.

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