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Items: 35

1.

A sequential Monte Carlo algorithm for inference of subclonal structure in cancer.

Ogundijo OE, Zhu K, Wang X, Anastassiou D.

PLoS One. 2019 Jan 25;14(1):e0211213. doi: 10.1371/journal.pone.0211213. eCollection 2019.

2.

Meta-analysis of expression and methylation signatures indicates a stress-related epigenetic mechanism in multiple neuropsychiatric disorders.

Zhu K, Ou Yang TH, Dorie V, Zheng T, Anastassiou D.

Transl Psychiatry. 2019 Jan 22;9(1):32. doi: 10.1038/s41398-018-0358-5.

3.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

4.

Comment on "A COL11A1-correlated pan-cancer gene signature of activated fibroblasts for the prioritization of therapeutic targets," Cancer Lett. 2016 Nov 28; 382 (2): 203-214.

Anastassiou D.

Cancer Lett. 2017 May 1;393:125-126. doi: 10.1016/j.canlet.2017.02.002. Epub 2017 Feb 10. No abstract available.

5.

Discovering Genome-Wide Tag SNPs Based on the Mutual Information of the Variants.

Elmas A, Ou Yang TH, Wang X, Anastassiou D.

PLoS One. 2016 Dec 16;11(12):e0167994. doi: 10.1371/journal.pone.0167994. eCollection 2016.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

PMID:
19348651
24.

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.

25.

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.

26.

A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.

Liang KC, Wang X, Anastassiou D.

Bioinformatics. 2008 Jan 1;24(1):46-55. Epub 2007 Nov 17.

PMID:
18024972
27.

Bayesian basecalling for DNA sequence analysis using hidden Markov models.

Liang KC, Wang X, Anastassiou D.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):430-40.

PMID:
17666762
28.

Computational analysis of the synergy among multiple interacting genes.

Anastassiou D.

Mol Syst Biol. 2007;3:83. Epub 2007 Feb 13.

29.

Computational inference of the molecular logic for synaptic connectivity in C. elegans.

Varadan V, Miller DM 3rd, Anastassiou D.

Bioinformatics. 2006 Jul 15;22(14):e497-506.

PMID:
16873513
30.

Inference of disease-related molecular logic from systems-based microarray analysis.

Varadan V, Anastassiou D.

PLoS Comput Biol. 2006 Jun 16;2(6):e68. Epub 2006 Jun 16.

31.

Variable window binding for mutually exclusive alternative splicing.

Anastassiou D, Liu H, Varadan V.

Genome Biol. 2006;7(1):R2. Epub 2006 Jan 13.

32.

Phenotype analysis using network motifs derived from changes in regulatory network dynamics.

Cavelier G, Anastassiou D.

Proteins. 2005 Aug 15;60(3):525-46.

PMID:
15971229
33.

Data-based model and parameter evaluation in dynamic transcriptional regulatory networks.

Cavelier G, Anastassiou D.

Proteins. 2004 May 1;55(2):339-50.

PMID:
15048826
34.

Frequency-domain analysis of biomolecular sequences.

Anastassiou D.

Bioinformatics. 2000 Dec;16(12):1073-81.

PMID:
11159326
35.

Subpixel edge localization and the interpolation of still images.

Jensen K, Anastassiou D.

IEEE Trans Image Process. 1995;4(3):285-95.

PMID:
18289979

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