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Items: 1 to 20 of 30

1.

Reconstitution of the ERG Gene Expression Network Reveals New Biomarkers and Therapeutic Targets in ERG Positive Prostate Tumors.

Dubovenko A, Serebryiskaya T, Nikolsky Y, Nikolskaya T, Perlina A, JeBailey L, Bureeva S, Katta S, Srivastava S, Dobi A, Khasanova T.

J Cancer. 2015 Apr 1;6(6):490-501. doi: 10.7150/jca.8213. eCollection 2015.

2.

Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.

Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K.

Cell Stem Cell. 2013 Jul 3;13(1):117-30. doi: 10.1016/j.stem.2013.05.004. Epub 2013 Jun 13.

3.

Knowledge-based analysis of proteomics data.

Bessarabova M, Ishkin A, JeBailey L, Nikolskaya T, Nikolsky Y.

BMC Bioinformatics. 2012;13 Suppl 16:S13. doi: 10.1186/1471-2105-13-S16-S13. Epub 2012 Nov 5. Review.

4.

Putative multifunctional signature of lung metastases in dedifferentiated chondrosarcoma.

Malchenko S, Seftor EA, Nikolsky Y, Hasegawa SL, Kuo S, Stevens JW, Poyarkov S, Nikolskaya T, Kucaba T, Wang M, Abdulkawy H, Casavant T, Morcuende J, Buckwalter J, Hohl R, Deyoung B, Kernstine K, Bonaldo Mde F, Hendrix MJ, Soares MB, Soares VM.

Sarcoma. 2012;2012:820254. doi: 10.1155/2012/820254. Epub 2012 Feb 16.

5.

The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.

Marotta LL, Almendro V, Marusyk A, Shipitsin M, Schemme J, Walker SR, Bloushtain-Qimron N, Kim JJ, Choudhury SA, Maruyama R, Wu Z, Gönen M, Mulvey LA, Bessarabova MO, Huh SJ, Silver SJ, Kim SY, Park SY, Lee HE, Anderson KS, Richardson AL, Nikolskaya T, Nikolsky Y, Liu XS, Root DE, Hahn WC, Frank DA, Polyak K.

J Clin Invest. 2011 Jul;121(7):2723-35. doi: 10.1172/JCI44745.

6.

Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.

Maruyama R, Choudhury S, Kowalczyk A, Bessarabova M, Beresford-Smith B, Conway T, Kaspi A, Wu Z, Nikolskaya T, Merino VF, Lo PK, Liu XS, Nikolsky Y, Sukumar S, Haviv I, Polyak K.

PLoS Genet. 2011 Apr;7(4):e1001369. doi: 10.1371/journal.pgen.1001369. Epub 2011 Apr 21.

7.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS.

Genome Res. 2010 Dec;20(12):1730-9. doi: 10.1101/gr.108217.110. Epub 2010 Nov 2.

8.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD; MAQC Consortium.

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30.

9.

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.

Shi W, Bessarabova M, Dosymbekov D, Dezso Z, Nikolskaya T, Dudoladova M, Serebryiskaya T, Bugrim A, Guryanov A, Brennan RJ, Shah R, Dopazo J, Chen M, Deng Y, Shi T, Jurman G, Furlanello C, Thomas RS, Corton JC, Tong W, Shi L, Nikolsky Y.

Pharmacogenomics J. 2010 Aug;10(4):310-23. doi: 10.1038/tpj.2010.35.

10.

Genomic indicators in the blood predict drug-induced liver injury.

Huang J, Shi W, Zhang J, Chou JW, Paules RS, Gerrish K, Li J, Luo J, Wolfinger RD, Bao W, Chu TM, Nikolsky Y, Nikolskaya T, Dosymbekov D, Tsyganova MO, Shi L, Fan X, Corton JC, Chen M, Cheng Y, Tong W, Fang H, Bushel PR.

Pharmacogenomics J. 2010 Aug;10(4):267-77. doi: 10.1038/tpj.2010.33.

11.

Consistency of predictive signature genes and classifiers generated using different microarray platforms.

Fan X, Lobenhofer EK, Chen M, Shi W, Huang J, Luo J, Zhang J, Walker SJ, Chu TM, Li L, Wolfinger R, Bao W, Paules RS, Bushel PR, Li J, Shi T, Nikolskaya T, Nikolsky Y, Hong H, Deng Y, Cheng Y, Fang H, Shi L, Tong W.

Pharmacogenomics J. 2010 Aug;10(4):247-57. doi: 10.1038/tpj.2010.34.

12.

Integrated network analysis of transcriptomic and proteomic data in psoriasis.

Piruzian E, Bruskin S, Ishkin A, Abdeev R, Moshkovskii S, Melnik S, Nikolsky Y, Nikolskaya T.

BMC Syst Biol. 2010 Apr 8;4:41. doi: 10.1186/1752-0509-4-41.

13.

Bimodal gene expression patterns in breast cancer.

Bessarabova M, Kirillov E, Shi W, Bugrim A, Nikolsky Y, Nikolskaya T.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S8. doi: 10.1186/1471-2164-11-S1-S8.

14.

Proteins That Underlie Neoplastic Progression of Ulcerative Colitis.

Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, Jebailey L, Goodlett DR, McIntosh M, Aebersold R, Rabinovitch PS, Chen R.

Proteomics Clin Appl. 2009 Sep 14;3(11):1326.

15.

Effect of training-sample size and classification difficulty on the accuracy of genomic predictors.

Popovici V, Chen W, Gallas BG, Hatzis C, Shi W, Samuelson FW, Nikolsky Y, Tsyganova M, Ishkin A, Nikolskaya T, Hess KR, Valero V, Booser D, Delorenzi M, Hortobagyi GN, Shi L, Symmans WF, Pusztai L.

Breast Cancer Res. 2010;12(1):R5. doi: 10.1186/bcr2468. Epub 2010 Jan 11.

16.

Network analysis of human glaucomatous optic nerve head astrocytes.

Nikolskaya T, Nikolsky Y, Serebryiskaya T, Zvereva S, Sviridov E, Dezso Z, Rahkmatulin E, Brennan RJ, Yankovsky N, Bhattacharya SK, Agapova O, Hernandez MR, Shestopalov VI.

BMC Med Genomics. 2009 May 9;2:24. doi: 10.1186/1755-8794-2-24.

17.

Identifying disease-specific genes based on their topological significance in protein networks.

Dezso Z, Nikolsky Y, Nikolskaya T, Miller J, Cherba D, Webb C, Bugrim A.

BMC Syst Biol. 2009 Mar 23;3:36. doi: 10.1186/1752-0509-3-36.

18.

A comprehensive functional analysis of tissue specificity of human gene expression.

Dezso Z, Nikolsky Y, Sviridov E, Shi W, Serebriyskaya T, Dosymbekov D, Bugrim A, Rakhmatulin E, Brennan RJ, Guryanov A, Li K, Blake J, Samaha RR, Nikolskaya T.

BMC Biol. 2008 Nov 12;6:49. doi: 10.1186/1741-7007-6-49.

19.

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers.

Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjöblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky Y, Kopelovich L, Papadopoulos N, Pennacchio LA, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE.

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16224-9. doi: 10.1073/pnas.0808041105. Epub 2008 Oct 13.

20.

Cell type-specific DNA methylation patterns in the human breast.

Bloushtain-Qimron N, Yao J, Snyder EL, Shipitsin M, Campbell LL, Mani SA, Hu M, Chen H, Ustyansky V, Antosiewicz JE, Argani P, Halushka MK, Thomson JA, Pharoah P, Porgador A, Sukumar S, Parsons R, Richardson AL, Stampfer MR, Gelman RS, Nikolskaya T, Nikolsky Y, Polyak K.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):14076-81. doi: 10.1073/pnas.0805206105. Epub 2008 Sep 9.

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