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Breast cancer prognostic biomarker using attractor metagenes and the FGD3-SUSD3 metagene.

Ou Yang TH, Cheng WY, Zheng T, Maurer MA, Anastassiou D.

Cancer Epidemiol Biomarkers Prev. 2014 Dec;23(12):2850-6. doi: 10.1158/1055-9965.EPI-14-0399. Epub 2014 Sep 23.


A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.

Iliadis A, Anastassiou D, Wang X.

EURASIP J Bioinform Syst Biol. 2014;2014(1):7. doi: 10.1186/1687-4153-2014-7. Epub 2014 Apr 24.


JAK2 expression is associated with tumor-infiltrating lymphocytes and improved breast cancer outcomes: implications for evaluating JAK2 inhibitors.

Miller CP, Thorpe JD, Kortum AN, Coy CM, Cheng WY, Ou Yang TH, Anastassiou D, Beatty JD, Urban ND, Blau CA.

Cancer Immunol Res. 2014 Apr;2(4):301-6. doi: 10.1158/2326-6066.CIR-13-0189. Epub 2014 Jan 15.


Notch and VEGF pathways play distinct but complementary roles in tumor angiogenesis.

Hernandez SL, Banerjee D, Garcia A, Kangsamaksin T, Cheng WY, Anastassiou D, Funahashi Y, Kadenhe-Chiweshe A, Shawber CJ, Kitajewski JK, Kandel JJ, Yamashiro DJ.

Vasc Cell. 2013 Sep 25;5(1):17. doi: 10.1186/2045-824X-5-17.


Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA.

Jajamovich GH, Iliadis A, Anastassiou D, Wang X.

BMC Bioinformatics. 2013 Sep 8;14:270. doi: 10.1186/1471-2105-14-270.


Development of a prognostic model for breast cancer survival in an open challenge environment.

Cheng WY, Ou Yang TH, Anastassiou D.

Sci Transl Med. 2013 Apr 17;5(181):181ra50. doi: 10.1126/scitranslmed.3005974.


Biomolecular events in cancer revealed by attractor metagenes.

Cheng WY, Ou Yang TH, Anastassiou D.

PLoS Comput Biol. 2013;9(2):e1002920. doi: 10.1371/journal.pcbi.1002920. Epub 2013 Feb 21.


Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data.

Iliadis A, Anastassiou D, Wang X.

BMC Genet. 2012 Oct 30;13:94. doi: 10.1186/1471-2156-13-94.


A unified framework for haplotype inference in nuclear families.

Iliadis A, Anastassiou D, Wang X.

Ann Hum Genet. 2012 Jul;76(4):312-25. doi: 10.1111/j.1469-1809.2012.00715.x. Epub 2012 May 21.


Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature.

Andreopoulos B, Anastassiou D.

Cancer Inform. 2012;11:61-75. doi: 10.4137/CIN.S9037. Epub 2012 Mar 12.


A multi-cancer mesenchymal transition gene expression signature is associated with prolonged time to recurrence in glioblastoma.

Cheng WY, Kandel JJ, Yamashiro DJ, Canoll P, Anastassiou D.

PLoS One. 2012;7(4):e34705. doi: 10.1371/journal.pone.0034705. Epub 2012 Apr 6.


Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo.

Anastassiou D, Rumjantseva V, Cheng W, Huang J, Canoll PD, Yamashiro DJ, Kandel JJ.

BMC Cancer. 2011 Dec 30;11:529. doi: 10.1186/1471-2407-11-529.


Clinical and microbiological profile of persistent coagulase-negative staphylococcal bacteraemia in neonates.

Dimitriou G, Fouzas S, Giormezis N, Giannakopoulos I, Tzifas S, Foka A, Anastassiou DE, Spiliopoulou I, Mantagos S.

Clin Microbiol Infect. 2011 Nov;17(11):1684-90. doi: 10.1111/j.1469-0691.2011.03489.x. Epub 2011 Apr 4.


Biomarker discovery using statistically significant gene sets.

Kim H, Watkinson J, Anastassiou D.

J Comput Biol. 2011 Oct;18(10):1329-38. doi: 10.1089/cmb.2010.0085. Epub 2011 Apr 1.


Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC.

Cheung YH, Watkinson J, Anastassiou D.

Hum Genet. 2011 Feb;129(2):161-76. doi: 10.1007/s00439-010-0908-2. Epub 2010 Nov 14.


Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1.

Kim H, Watkinson J, Varadan V, Anastassiou D.

BMC Med Genomics. 2010 Nov 3;3:51. doi: 10.1186/1755-8794-3-51.


A haplotype inference algorithm for trios based on deterministic sampling.

Iliadis A, Watkinson J, Anastassiou D, Wang X.

BMC Genet. 2010 Aug 23;11:78. doi: 10.1186/1471-2156-11-78.


Inference of regulatory gene interactions from expression data using three-way mutual information.

Watkinson J, Liang KC, Wang X, Zheng T, Anastassiou D.

Ann N Y Acad Sci. 2009 Mar;1158:302-13. doi: 10.1111/j.1749-6632.2008.03757.x.


Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype.

Watkinson J, Anastassiou D.

Bioinformatics. 2009 Jun 1;25(11):1445-6. doi: 10.1093/bioinformatics/btp159. Epub 2009 Mar 17.


Identification of gene interactions associated with disease from gene expression data using synergy networks.

Watkinson J, Wang X, Zheng T, Anastassiou D.

BMC Syst Biol. 2008 Jan 30;2:10. doi: 10.1186/1752-0509-2-10.

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