Selected Publications

The Gene Expression Response of Breast Cancer to Growth Regulators: Patterns and Correlation with Tumor Expression Profiles
Heather E. Cunliffe, Markus Ringnér, Sven Bilke, Robert L. Walker, Jennifer M. Cheung, Yidong Chen, and Paul S. Meltzer

Cancer Research, 63:7158-7166. (2003)

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Gastrointestinal Stromal Tumors with KIT Mutations Exhibit a Remarkably Homogeneous Gene Expression Profile
Susanne V. Allander, Nina N. Nupponen, Markus Ringnér, Galen Hostetter, Greg W. Maher, Natalie Goldberger, Yidong Chen, John Carpten, Abdel G. Elkahloun, and Paul S. Meltzer

Cancer Research, 61:8624-8628. (2001)

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Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
Javed Khan, Jun S. Wei, Markus Ringnér, Lao H. Saal, Marc Ladanyi, Frank Westermann, Frank Berthold, Manfred Schwab, Cristina R. Antonescu, Carsten Peterson, and Paul S. Meltzer

Nature Medicine, Volume 7, Number 6, June 2001

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Gene Expression Profiles in Hereditary Breast Cancer.
Ingrid Hedenfalk, David Duggan, Yidong Chen, Michael Radmacher, Michael Bittner, Richard Simon, Paul Meltzer, Barry Gusterson, Manel Esteller, Mark Raffeld, Zohar Yakhini, Amir Ben-Dor, Edward Dougherty, Juha Kononen, Lukas Bubendorf, Wilfrid Fehrle, Stefania Pittaluga, Sofia Gruvberger, Niklas Loman, Oskar Johannsson, Håkan Olsson, Benjamin Wilfond, Guido Sauter, Olli-P. Kallioniemi, Åke Borg and Jeffrey Trent

New England Journal of Medicine, 244:539-548. (2001)

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Estrogen Receptor Status in Breast Cancer Is Associated with Remarkably Distinct Gene Expression Patterns
Sofia Gruvberger, Markus Ringnér, Yidong Chen, Sujatha Panavally, Lao H. Saal, Åke Borg, Mårten Fernö, Carsten Peterson and Paul S. Meltzer

Cancer Research, 61:5979-5984. (2001)

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Human Prostate Cancer and Benign Prostatic Hyperplasia: Molecular Dissection by Gene Expression Profiling
Jun Luo, David J. Duggan, Yidong Chen, Jurga Sauvageot, Charles Ewing, Michael Bittner, Jeffrey M. Trent, and William B. Isaacs

Cancer Research, 61:4683-4688. (2001)

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Transcription Program of Human Herpesvirus 8 (Kaposi's Sarcoma-Associated Herpesvirus)
Mini Paulose-Murphy, Nguyen-Khoi Ha, Chunsheng Xiang, Yidong Chen, Laura Gillim, Robert Yarchoan, Paul Meltzer, Michael Bittner, Jeffrey Trent, and Steven Zeichner

Journal of Virology, Volume 75, Number 10, May 2001

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Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.
Forozan F, Mahlamaki EH, Monni O, Chen Y, Veldman R, Jiang Y, Gooden GC, Ethier SP, Kallioniemi A, Kallioniemi OP.

Cancer Research, 60:4519-4525. (2000)

Supplemental Information

Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling.
M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, A. Ben-Dor, E. Dougherty, E. Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, E. Gillanders, D. Leja, K. Dietrich, C., M. Berens, D. Alberts, V. Sondak, N. Hayward, and J. Trent

Nature 406: 536-540 (2000)

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Multivariate Measurement of Gene Expression Relationships
Seungchan Kim, Edward R. Dougherty, Yidong Chen, Krishnamoorthy Sivakumar, Paul Meltzer, Jeffery M. Trent, Michael Bittner

Genomics 2000 July;Vol. 67, No. 2 ISSN 0888-7543

Article(PDF)

Development of a prostate cDNA microarray and statistical gene expression analysis package.
Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB

Mol Carcinog 2000 May;28(1):12-22

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cDNA microarrays detect activation of a myogenic transcription program by the PAX3 FKHR fusion oncogene.
Khan J, Bittner ML, Saal LH, Teichmann U, Azorsa DO, Gooden GC, Pavan WJ, Trent JM, Meltzer PS

Proc Natl Acad Sci USA 1999 Nove 9;96(23):13264-9

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Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays.
Bubendorf L, Kolmer M, Kononen J, Koivisto P, Mousses S, Chen Y, Mahlamaki E, Schraml P, Moch H, Willi N, Elkahloun AG, Pretlow TG, Gasser TC, Mihatsch MJ, Sauter G, Kallioniemi OP Pavan WJ, Trent JM, Meltzer PS

J Natl Cancer Inst 1999 Oct 20;91(20):1758-64

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Analysis of gene expression in mutiple sclerosis lesions using cDNA microarrays.
Whitney LW, Becker KG, Tresser NJ, Caballero-Ramos CI, Munson PJ, Prabhu VV, Trent JM, McFarland HF, Biddison WE

Ann Neurol 1999 Sep;46(3):425-8

Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis.
Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, Hilliard M, Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W

Proc Natl Acad Sci USA 1999 Aug 3;96(16):9277-80

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Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses.
Amundson SA, Bittner M, Chen Y, Trent J, Meltzer P, Fornace AJ Jr Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W

Oncogene 1999 Jun 17;18(24):3666-72

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High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma.
Moch H, Schraml P, Bubendorf L, Mirlacher M, Kononen J, Gasser T, Mihatsch MJ, Kallioniemi OP, Sauter G

Am J Pathol 1999 Apr:154(4):981-6

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Microarrays and toxicology: the advent of toxicogenomics.
Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA

Mol Carcingo 1999 Mar;24(3):153-9

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Expression profiling in cancer using cDNA microarrays.
Khan J, Saal LH, Bittner ML, Chen Y, Trent JM, Meltzer PS

Electrophoresis 1999 Feb;20(2):223-9

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The transcriptional program in the response of human fibroblasts to serum.
Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO

Science 1999 Jan 1;283(5398):83-7

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Expression profiling using cDNA microarrays.
Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM

Nat Genet 1999 Jan 21(1 Suppl):10-14

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The complexity of radiation stress responses: analysis by informatics and functional genomics approaches.
Fornace AJ Jr, Amundson SA, Bittner M, Myers TG, Meltzer P, Weinsten JN, Trent J

Gene Expr 1999; 7(4-6):387-400

Data management and analysis for gene expression arrays.
Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS

Nat Genet 1998 Sep 20(1):19-23

Article(PDF)

Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays.
Khan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS

Cancer Res 1998 Nov 15;58(22):5009-13

Use of a cDNA microarray to analyse gene expression patterns in human cancer.
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM

Nat Genet 1996 Dec;14(4):457-60