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Results: 16

1.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M.

Genome Biol. 2015 Jun 25;16:133. doi: 10.1186/s13059-015-0694-1.

2.

Development of a Drug-Response Modeling Framework to Identify Cell Line Derived Translational Biomarkers That Can Predict Treatment Outcome to Erlotinib or Sorafenib.

Li B, Shin H, Gulbekyan G, Pustovalova O, Nikolsky Y, Hope A, Bessarabova M, Schu M, Kolpakova-Hart E, Merberg D, Dorner A, Trepicchio WL.

PLoS One. 2015 Jun 24;10(6):e0130700. doi: 10.1371/journal.pone.0130700. eCollection 2015.

3.

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era.

Su Z, Fang H, Hong H, Shi L, Zhang W, Zhang W, Zhang Y, Dong Z, Lancashire LJ, Bessarabova M, Yang X, Ning B, Gong B, Meehan J, Xu J, Ge W, Perkins R, Fischer M, Tong W.

Genome Biol. 2014 Dec 3;15(12):523. doi: 10.1186/s13059-014-0523-y.

4.

Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms.

Riley BE, Gardai SJ, Emig-Agius D, Bessarabova M, Ivliev AE, Schüle B, Alexander J, Wallace W, Halliday GM, Langston JW, Braxton S, Yednock T, Shaler T, Johnston JA.

PLoS One. 2014 Aug 29;9(8):e102909. doi: 10.1371/journal.pone.0102909. eCollection 2014.

5.

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.

6.

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.

7.

An integrated map of HIV-human protein complexes that facilitate viral infection.

Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T.

PLoS One. 2014 May 9;9(5):e96687. doi: 10.1371/journal.pone.0096687. eCollection 2014.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

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