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A meiotic recombination checkpoint controlled by mitotic checkpoint genes.
Lydall D, Nikolsky Y, Bishop DK, Weinert T. Lydall D, et al. Nature. 1996 Oct 31;383(6603):840-3. doi: 10.1038/383840a0. Nature. 1996. PMID: 8893012
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. Wang C, et al. Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24. Nat Biotechnol. 2014. PMID: 25150839 Free PMC article.
Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer.
Triska M, Ivliev A, Nikolsky Y, Tatarinova TV. Triska M, et al. Among authors: nikolsky y. Methods Mol Biol. 2017;1613:291-310. doi: 10.1007/978-1-4939-7027-8_11. Methods Mol Biol. 2017. PMID: 28849565
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. Shi L, et al. Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30. Nat Biotechnol. 2010. PMID: 20676074 Free PMC article.
Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.
Thomas RS, Bao W, Chu TM, Bessarabova M, Nikolskaya T, Nikolsky Y, Andersen ME, Wolfinger RD. Thomas RS, et al. Toxicol Sci. 2009 Dec;112(2):311-21. doi: 10.1093/toxsci/kfp233. Epub 2009 Sep 23. Toxicol Sci. 2009. PMID: 19776212
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. Yu Y, et al. Nat Commun. 2014;5:3230. doi: 10.1038/ncomms4230. Nat Commun. 2014. PMID: 24510058 Free PMC article.
Knowledge-based analysis of proteomics data.
Bessarabova M, Ishkin A, JeBailey L, Nikolskaya T, Nikolsky Y. Bessarabova M, et al. BMC Bioinformatics. 2012;13 Suppl 16(Suppl 16):S13. doi: 10.1186/1471-2105-13-S16-S13. Epub 2012 Nov 5. BMC Bioinformatics. 2012. PMID: 23176192 Free PMC article. Review.
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. Myshkin E, et al. Chem Biol Drug Des. 2012 Sep;80(3):406-16. doi: 10.1111/j.1747-0285.2012.01411.x. Epub 2012 Jun 27. Chem Biol Drug Des. 2012. PMID: 22583392
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. Emig D, et al. PLoS One. 2013 Apr 4;8(4):e60618. doi: 10.1371/journal.pone.0060618. Print 2013. PLoS One. 2013. PMID: 23593264 Free PMC article.
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. Popovici V, et al. Breast Cancer Res. 2010;12(1):R5. doi: 10.1186/bcr2468. Epub 2010 Jan 11. Breast Cancer Res. 2010. PMID: 20064235 Free PMC article.
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