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Items: 1 to 50 of 73

1.

Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer.

Triska M, Ivliev A, Nikolsky Y, Tatarinova TV.

Methods Mol Biol. 2017;1613:291-310. doi: 10.1007/978-1-4939-7027-8_11.

PMID:
28849565
2.

Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

Dubovenko A, Nikolsky Y, Rakhmatulin E, Nikolskaya T.

Methods Mol Biol. 2017;1613:101-124. doi: 10.1007/978-1-4939-7027-8_6.

PMID:
28849560
3.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.

Ozerov IV, Lezhnina KV, Izumchenko E, Artemov AV, Medintsev S, Vanhaelen Q, Aliper A, Vijg J, Osipov AN, Labat I, West MD, Buzdin A, Cantor CR, Nikolsky Y, Borisov N, Irincheeva I, Khokhlovich E, Sidransky D, Camargo ML, Zhavoronkov A.

Nat Commun. 2016 Nov 16;7:13427. doi: 10.1038/ncomms13427.

4.

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer.

Ivliev AE, 't Hoen PA, Borisevich D, Nikolsky Y, Sergeeva MG.

PLoS One. 2016 Nov 8;11(11):e0165059. doi: 10.1371/journal.pone.0165059. eCollection 2016.

5.

Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes.

Marusyk A, Tabassum DP, Janiszewska M, Place AE, Trinh A, Rozhok AI, Pyne S, Guerriero JL, Shu S, Ekram M, Ishkin A, Cahill DP, Nikolsky Y, Chan TA, Rimawi MF, Hilsenbeck S, Schiff R, Osborne KC, Letai A, Polyak K.

Cancer Res. 2016 Nov 15;76(22):6495-6506. doi: 10.1158/0008-5472.CAN-16-1457. Epub 2016 Sep 26.

6.

Nucleotide diversity analysis highlights functionally important genomic regions.

Tatarinova TV, Chekalin E, Nikolsky Y, Bruskin S, Chebotarov D, McNally KL, Alexandrov N.

Sci Rep. 2016 Oct 24;6:35730. doi: 10.1038/srep35730.

7.

Toward high-resolution population genomics using archaeological samples.

Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV.

DNA Res. 2016 Aug;23(4):295-310. doi: 10.1093/dnares/dsw029. Epub 2016 Jul 19. Review.

8.

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry.

Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV.

Sci Rep. 2016 Feb 11;6:20768. doi: 10.1038/srep20768.

9.

The mysterious orphans of Mycoplasmataceae.

Tatarinova TV, Lysnyansky I, Nikolsky YV, Bolshoy A.

Biol Direct. 2016 Jan 8;11(1):2. doi: 10.1186/s13062-015-0104-3.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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
28.

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.

29.

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.

30.

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
31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.
39.

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.

Toxicol Sci. 2009 Dec;112(2):311-21. doi: 10.1093/toxsci/kfp233. Epub 2009 Sep 23.

PMID:
19776212
40.

Protein networks and pathway analysis. Preface.

Nikolsky Y, Bryant J.

Methods Mol Biol. 2009;563:v-vii. No abstract available.

PMID:
19760825
41.

MetaMiner (CF): a disease-oriented bioinformatics analysis environment.

Wright JM, Nikolsky Y, Serebryiskaya T, Wetmore DR.

Methods Mol Biol. 2009;563:353-67. doi: 10.1007/978-1-60761-175-2_18.

PMID:
19597794
42.

Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform.

Nikolsky Y, Kirillov E, Zuev R, Rakhmatulin E, Nikolskaya T.

Methods Mol Biol. 2009;563:177-96. doi: 10.1007/978-1-60761-175-2_10.

PMID:
19597786
43.

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.

44.

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.

45.

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.

46.

Genome-wide functional synergy between amplified and mutated genes in human breast cancer.

Nikolsky Y, Sviridov E, Yao J, Dosymbekov D, Ustyansky V, Kaznacheev V, Dezso Z, Mulvey L, Macconaill LE, Winckler W, Serebryiskaya T, Nikolskaya T, Polyak K.

Cancer Res. 2008 Nov 15;68(22):9532-40. doi: 10.1158/0008-5472.CAN-08-3082.

47.

The transcriptomic signature of fasting murine liver.

Sokolović M, Sokolović A, Wehkamp D, Ver Loren van Themaat E, de Waart DR, Gilhuijs-Pederson LA, Nikolsky Y, van Kampen AH, Hakvoort TB, Lamers WH.

BMC Genomics. 2008 Nov 6;9:528. doi: 10.1186/1471-2164-9-528.

48.

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.

49.

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.

50.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.

Science. 2008 Sep 26;321(5897):1801-6. doi: 10.1126/science.1164368. Epub 2008 Sep 4.

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