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Results: 1 to 20 of 61

1.

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.

Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Łabaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W.

Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24.

PMID:
25150839
[PubMed - in process]
Free PMC Article
2.

JARID1B is a luminal lineage-driving oncogene in breast cancer.

Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K.

Cancer Cell. 2014 Jun 16;25(6):762-77. doi: 10.1016/j.ccr.2014.04.024.

PMID:
24937458
[PubMed - indexed for MEDLINE]
3.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

Yu Y, Fuscoe JC, Zhao C, Guo C, Jia M, Qing T, Bannon DI, Lancashire L, Bao W, Du T, Luo H, Su Z, Jones WD, Moland CL, Branham WS, Qian F, Ning B, Li Y, Hong H, Guo L, Mei N, Shi T, Wang KY, Wolfinger RD, Nikolsky Y, Walker SJ, Duerksen-Hughes P, Mason CE, Tong W, Thierry-Mieg J, Thierry-Mieg D, Shi L, Wang C.

Nat Commun. 2014;5:3230. doi: 10.1038/ncomms4230.

PMID:
24510058
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
23770079
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Drug target prediction and repositioning using an integrated network-based approach.

Emig D, Ivliev A, Pustovalova O, Lancashire L, Bureeva S, Nikolsky Y, Bessarabova M.

PLoS One. 2013 Apr 4;8(4):e60618. doi: 10.1371/journal.pone.0060618. Print 2013.

PMID:
23593264
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23176192
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genomic characterization of explant tumorgraft models derived from fresh patient tumor tissue.

Monsma DJ, Monks NR, Cherba DM, Dylewski D, Eugster E, Jahn H, Srikanth S, Scott SB, Richardson PJ, Everts RE, Ishkin A, Nikolsky Y, Resau JH, Sigler R, Nickoloff BJ, Webb CP.

J Transl Med. 2012 Jun 18;10:125. doi: 10.1186/1479-5876-10-125.

PMID:
22709571
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Prediction of organ toxicity endpoints by QSAR modeling based on precise chemical-histopathology annotations.

Myshkin E, Brennan R, Khasanova T, Sitnik T, Serebriyskaya T, Litvinova E, Guryanov A, Nikolsky Y, Nikolskaya T, Bureeva S.

Chem Biol Drug Des. 2012 Sep;80(3):406-16. doi: 10.1111/j.1747-0285.2012.01411.x. Epub 2012 Jun 27.

PMID:
22583392
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
22448124
[PubMed]
Free PMC Article
10.

A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium.

Galat V, Malchenko S, Galat Y, Ishkin A, Nikolsky Y, Kosak ST, Soares BM, Iannaccone P, Crispino JD, Hendrix MJ.

Stem Cells Dev. 2012 May 20;21(8):1250-63. doi: 10.1089/scd.2010.0578. Epub 2011 Oct 19.

PMID:
21861759
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A systems biology strategy for predicting similarities and differences of drug effects: evidence for drug-specific modulation of inflammation in atherosclerosis.

Kleemann R, Bureeva S, Perlina A, Kaput J, Verschuren L, Wielinga PY, Hurt-Camejo E, Nikolsky Y, van Ommen B, Kooistra T.

BMC Syst Biol. 2011 Aug 12;5:125. doi: 10.1186/1752-0509-5-125.

PMID:
21838869
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21633165
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
21533021
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.

Bessarabova M, Pustovalova O, Shi W, Serebriyskaya T, Ishkin A, Polyak K, Velculescu VE, Nikolskaya T, Nikolsky Y.

Cancer Res. 2011 May 15;71(10):3471-81. doi: 10.1158/0008-5472.CAN-10-3038. Epub 2011 Mar 11.

PMID:
21398405
[PubMed - indexed for MEDLINE]
Free Article
15.

Quantitative knowledge-based analysis in compound safety assessment.

Bureeva S, Nikolsky Y.

Expert Opin Drug Metab Toxicol. 2011 Mar;7(3):287-98. doi: 10.1517/17425255.2011.553191. Epub 2011 Jan 22. Review.

PMID:
21254873
[PubMed - indexed for MEDLINE]
16.

The genetic landscape of the childhood cancer medulloblastoma.

Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE.

Science. 2011 Jan 28;331(6016):435-9. doi: 10.1126/science.1198056. Epub 2010 Dec 16.

PMID:
21163964
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Altered antisense-to-sense transcript ratios in breast cancer.

Maruyama R, Shipitsin M, Choudhury S, Wu Z, Protopopov A, Yao J, Lo PK, Bessarabova M, Ishkin A, Nikolsky Y, Liu XS, Sukumar S, Polyak K.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2820-4. doi: 10.1073/pnas.1010559107. Epub 2010 Nov 22.

PMID:
21098291
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Systems biology approaches to the study of cardiovascular drugs.

Nikolsky Y, Kleemann R.

Methods Mol Biol. 2010;662:221-43. doi: 10.1007/978-1-60761-800-3_11.

PMID:
20824474
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
20676074
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20676069
[PubMed - indexed for MEDLINE]
Free PMC Article

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