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Results: 1 to 20 of 117

1.

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.

PMID:
25728892
2.

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.

3.

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.

4.

Breast cancer classification: linking molecular mechanisms to disease prognosis.

Taherian-Fard A, Srihari S, Ragan MA.

Brief Bioinform. 2014 Jun 20. pii: bbu020. [Epub ahead of print]

PMID:
24950687
5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

PMID:
24407221
10.

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.

11.

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]

PMID:
24166654
12.

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.

13.

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.

14.

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.

PMID:
23877343
15.

Yeast rises to the occasion.

Ragan MA.

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

16.

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.

PMID:
23763602
17.

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.

18.

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.

19.

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.

20.

Next-generation phylogenomics.

Chan CX, Ragan MA.

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

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