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Items: 36

1.

Tracking the Evolution of Resistance to ALK Tyrosine Kinase Inhibitors through Longitudinal Analysis of Circulating Tumor DNA.

Dagogo-Jack I, Brannon AR, Ferris LA, Campbell CD, Lin JJ, Schultz KR, Ackil J, Stevens S, Dardaei L, Yoda S, Hubbeling H, Digumarthy SR, Riester M, Hata AN, Sequist LV, Lennes IT, Iafrate AJ, Heist RS, Azzoli CG, Farago AF, Engelman JA, Lennerz JK, Benes CH, Leary RJ, Shaw AT, Gainor JF.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00160. Epub 2018 Jan 23.

2.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

PMID:
29092936
3.

The Warburg effect: persistence of stem-cell metabolism in cancers as a failure of differentiation.

Riester M, Xu Q, Moreira A, Zheng J, Michor F, Downey RJ.

Ann Oncol. 2018 Jan 1;29(1):264-270. doi: 10.1093/annonc/mdx645.

PMID:
29045536
4.

"Let's Bring Her Home First." Patient Characteristics and Place of Death in Specialized Pediatric Palliative Home Care.

Bender HU, Riester MB, Borasio GD, Führer M.

J Pain Symptom Manage. 2017 Aug;54(2):159-166. doi: 10.1016/j.jpainsymman.2017.04.006. Epub 2017 Jun 8.

PMID:
28602938
5.

Distance in cancer gene expression from stem cells predicts patient survival.

Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F.

PLoS One. 2017 Mar 23;12(3):e0173589. doi: 10.1371/journal.pone.0173589. eCollection 2017.

6.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X.

Nucleic Acids Res. 2017 Jun 2;45(10):e77. doi: 10.1093/nar/gkx026.

7.

PureCN: copy number calling and SNV classification using targeted short read sequencing.

Riester M, Singh AP, Brannon AR, Yu K, Campbell CD, Chiang DY, Morrissey MP.

Source Code Biol Med. 2016 Dec 15;11:13. doi: 10.1186/s13029-016-0060-z. eCollection 2016.

8.

The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles.

Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M.

J Natl Cancer Inst. 2016 Jul 5;108(11). doi: 10.1093/jnci/djw146. Print 2016 Nov.

9.

Molecular analysis of a male breast cancer patient with prolonged stable disease under mTOR/PI3K inhibitors BEZ235/everolimus.

Brannon AR, Frizziero M, Chen D, Hummel J, Gallo J, Riester M, Patel P, Cheung W, Morrissey M, Carbone C, Cottini S, Tortora G, Melisi D.

Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000620. doi: 10.1101/mcs.a000620.

10.

Molecular Alterations and Everolimus Efficacy in Human Epidermal Growth Factor Receptor 2-Overexpressing Metastatic Breast Cancers: Combined Exploratory Biomarker Analysis From BOLERO-1 and BOLERO-3.

André F, Hurvitz S, Fasolo A, Tseng LM, Jerusalem G, Wilks S, O'Regan R, Isaacs C, Toi M, Burris H, He W, Robinson D, Riester M, Taran T, Chen D, Slamon D.

J Clin Oncol. 2016 Jun 20;34(18):2115-24. doi: 10.1200/JCO.2015.63.9161. Epub 2016 Apr 18.

PMID:
27091708
11.

Meta-Analysis in Gene Expression Studies.

Waldron L, Riester M.

Methods Mol Biol. 2016;1418:161-76. doi: 10.1007/978-1-4939-3578-9_8.

PMID:
27008014
12.

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer.

Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F.

PLoS Comput Biol. 2015 Sep 17;11(9):e1004350. doi: 10.1371/journal.pcbi.1004350. eCollection 2015 Sep.

13.

Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors.

Bellmunt J, Werner L, Leow JJ, Mullane SA, Fay AP, Riester M, Van Hummelen P, Taplin ME, Choueiri TK, Van Allen E, Rosenberg J.

PLoS One. 2015 Jun 3;10(6):e0124711. doi: 10.1371/journal.pone.0124711. eCollection 2015.

14.

DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors.

Bambury RM, Bhatt AS, Riester M, Pedamallu CS, Duke F, Bellmunt J, Stack EC, Werner L, Park R, Iyer G, Loda M, Kantoff PW, Michor F, Meyerson M, Rosenberg JE.

BMC Cancer. 2015 Apr 9;15:242. doi: 10.1186/s12885-015-1192-2.

15.

HER2 as a target in invasive urothelial carcinoma.

Bellmunt J, Werner L, Bamias A, Fay AP, Park RS, Riester M, Selvarajah S, Barletta JA, Berman DM, de Muga S, Salido M, Gallardo E, Rojo F, Guancial EA, Bambury R, Mullane SA, Choueiri TK, Loda M, Stack E, Rosenberg J.

Cancer Med. 2015 Jun;4(6):844-52. doi: 10.1002/cam4.432. Epub 2015 Feb 26.

16.

JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response.

Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL.

Cancer Discov. 2015 Mar;5(3):316-31. doi: 10.1158/2159-8290.CD-14-0736. Epub 2015 Jan 8.

17.

Molecular subtypes of high-grade serous ovarian cancer: the holy grail?

Waldron L, Riester M, Birrer M.

J Natl Cancer Inst. 2014 Sep 30;106(10). pii: dju297. doi: 10.1093/jnci/dju297. Print 2014 Oct. No abstract available.

PMID:
25269490
18.

Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma.

Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC.

Cancer Cell. 2014 Aug 11;26(2):288-300. doi: 10.1016/j.ccr.2014.06.005.

19.

Cross-study validation for the assessment of prediction algorithms.

Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L.

Bioinformatics. 2014 Jun 15;30(12):i105-12. doi: 10.1093/bioinformatics/btu279.

20.

FGFR3 expression in primary and metastatic urothelial carcinoma of the bladder.

Guancial EA, Werner L, Bellmunt J, Bamias A, Choueiri TK, Ross R, Schutz FA, Park RS, O'Brien RJ, Hirsch MS, Barletta JA, Berman DM, Lis R, Loda M, Stack EC, Garraway LA, Riester M, Michor F, Kantoff PW, Rosenberg JE.

Cancer Med. 2014 Aug;3(4):835-44. doi: 10.1002/cam4.262. Epub 2014 May 21.

21.

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju048. doi: 10.1093/jnci/dju048.

22.

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju049. doi: 10.1093/jnci/dju049. Review.

23.

Influence of pulmonary artery size on early outcome after the Fontan operation.

Lehner A, Schuh A, Herrmann FE, Riester M, Pallivathukal S, Dalla-Pozza R, Kozlik-Feldmann R, Netz H, Malec E, Januszewska K.

Ann Thorac Surg. 2014 Apr;97(4):1387-93. doi: 10.1016/j.athoracsur.2013.11.068. Epub 2014 Feb 14.

PMID:
24529483
24.

Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma.

Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FA, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, Michor F, Rosenberg JE.

Clin Cancer Res. 2014 Apr 1;20(7):1873-83. doi: 10.1158/1078-0432.CCR-13-0759. Epub 2014 Jan 31.

25.

Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value.

Chekaluk Y, Wu CL, Rosenberg J, Riester M, Dai Q, Lin S, Guo Y, McDougal WS, Kwiatkowski DJ.

PLoS One. 2013 Apr 4;8(4):e60927. doi: 10.1371/journal.pone.0060927. Print 2013.

26.

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.

Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L.

Database (Oxford). 2013 Apr 2;2013:bat013. doi: 10.1093/database/bat013. Print 2013.

27.

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F.

PLoS Genet. 2013;9(1):e1003137. doi: 10.1371/journal.pgen.1003137. Epub 2013 Jan 10.

28.

Evolution of the cancer genome.

Podlaha O, Riester M, De S, Michor F.

Trends Genet. 2012 Apr;28(4):155-63. doi: 10.1016/j.tig.2012.01.003. Epub 2012 Feb 16. Review.

29.

Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer.

Riester M, Taylor JM, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F.

Clin Cancer Res. 2012 Mar 1;18(5):1323-33. doi: 10.1158/1078-0432.CCR-11-2271. Epub 2012 Jan 6.

30.

1,2:3,4-Diepoxybutane in blood of male B6C3F1 mice and male Sprague-Dawley rats exposed to 1,3-butadiene.

Csanády GA, Steinhoff R, Riester MB, Semder B, Pütz C, Li Q, Richter N, Kessler W, Klein D, Filser JG.

Toxicol Lett. 2011 Dec 15;207(3):286-90. doi: 10.1016/j.toxlet.2011.09.027. Epub 2011 Oct 1.

31.

Reconstruction of pedigrees in clonal plant populations.

Riester M, Stadler PF, Klemm K.

Theor Popul Biol. 2010 Sep;78(2):109-17. doi: 10.1016/j.tpb.2010.05.002. Epub 2010 May 23.

PMID:
20566407
32.

A differentiation-based phylogeny of cancer subtypes.

Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S, Michor F.

PLoS Comput Biol. 2010 May 6;6(5):e1000777. doi: 10.1371/journal.pcbi.1000777.

33.

FRANz: reconstruction of wild multi-generation pedigrees.

Riester M, Stadler PF, Klemm K.

Bioinformatics. 2009 Aug 15;25(16):2134-9. doi: 10.1093/bioinformatics/btp064. Epub 2009 Feb 8.

34.

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata.

Dreyer C, Hoffmann M, Lanz C, Willing EM, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D.

BMC Genomics. 2007 Aug 8;8:269.

35.

Highly specific gene silencing by artificial microRNAs in Arabidopsis.

Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D.

Plant Cell. 2006 May;18(5):1121-33. Epub 2006 Mar 10.

36.

Specific effects of microRNAs on the plant transcriptome.

Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D.

Dev Cell. 2005 Apr;8(4):517-27.

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