Yidong Chen

发表

Expression profiling using cDNA microarrays

M. Bittner, P. Meltzer, J. Trent, 1999, Nature Genetics.

Gray-scale morphological granulometric texture classification

E. Dougherty, Yidong Chen, 1994 .

Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses

M. Bittner, P. Meltzer, J. Trent, 1999, Oncogene.

Coefficient of determination in nonlinear signal processing

Edward R. Dougherty, Yidong Chen, Seungchan Kim, 2000, Signal Process..

E-CAST: A Data Mining Algorithm for Gene Expression Data

Abdelghani Bellaachia, Yidong Chen, David Portnoy, 2002, BIOKDD.

Data management and analysis for gene expression arrays

M. Bittner, M. Boguski, P. Meltzer, 1998, Nature Genetics.

Molecular classification of familial non-BRCA1/BRCA2 breast cancer

M. Ringnér, P. Meltzer, Z. Yakhini, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Predicting hepatitis B virus–positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning

X. Wang, Yidong Chen, R. Simon, 2003, Nature Medicine.

Gene expression profiling of human sarcomas: insights into sarcoma biology.

P. Meltzer, A. Glatfelter, C. Antonescu, 2005, Cancer research.

Cancer‐associated molecular signature in the tissue samples of patients with cirrhosis

X. Wang, Yidong Chen, Q. Ye, 2004, Hepatology.

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).

M. Daly, E. H. Margulies, T. Wolfsberg, 2005, Genome research.

Optimal and adaptive design of logical granulometric filters

E. Dougherty, Yidong Chen, 2001 .

The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles.

Sven Bilke, Markus Ringnér, Paul S Meltzer, 2003, Cancer research.

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen.

John N Weinstein, Mark Reimers, Michael L Bittner, 2008, Cancer research.

Mutation of melanosome protein RAB38 in chocolate mice

M. Bittner, W. Pavan, Yidong Chen, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Remarkably Distinct Gene Expression Patterns Estrogen Receptor Status in Breast Cancer Is Associated with Updated

S. Gruvberger, M. Ringnér, S. Panavally, 2001 .

MicroRNA expression, survival, and response to interferon in liver cancer.

Stephanie Roessler, Xin Wei Wang, Zhipeng Yu, 2009, The New England journal of medicine.

Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.

P. Meltzer, E. Jaffe, J. Hipp, 2009, Cancer research.

Quality-based distance measures and applications to clustering

E. Dougherty, Yidong Chen, D. M. Taverna, 2006, 2006 IEEE/NLM Life Science Systems and Applications Workshop.

Development of a normalization algorithm for array comparative genomic hybridization

Yidong Chen, E. Chuang, M. Tsai, 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics.

Sensitive and specific method for detecting G protein–coupled receptor mRNAs

Z. Qi, Yidong Chen, M. Palkovits, 2007, Nature Methods.

Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.

James B. Mitchell, Mong-Hsun Tsai, Shuping Zhao, 2002, Cancer research.

Chain-reaction, a model of gene expression dynamics

Yidong Chen, 2012 .

Effects of ligand and thyroid hormone receptor isoforms on hepatic gene expression profiles of thyroid hormone receptor knockout mice

P. Meltzer, Yidong Chen, R. Walker, 2003, EMBO reports.

91 FADS AND FALLACIES IN THE NAME OF SMALL-SAMPLE MICROARRAY CLASSIFICATION

Rabab K. Ward, Petar M. Djuric, Sergios Theodoridis, 2007 .

Elucidation of the Downstream Targets of the PAX3-FKHR Fusion Oncogene Found in Aveolar Rhabdomyosarcoma Using cDNA Microarrays

M. Bittner, L. Saal, P. Meltzer, 1999 .

Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer

E. Dougherty, E. Serpedin, Yidong Chen, 2012, BMC Genomics.

Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling

Spyro Mousses, Michael Bittner, Lukas Bubendorf, 2001, Oncogene.

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen (Cancer Research (January 15, 2008) 68 (415-424))

Albert J. Fornace, Sally A. Amundson, Mark Reimers, 2008 .

Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment.

Xin Wei Wang, Krista A. Zanetti, X. Wang, 2006, Cancer cell.

EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma.

Jin Woo Kim, Wei Wang, Xin Wei Wang, 2008, Cancer research.

Application of gene set enrichment method to ChIP-chip data analysis

P. Meltzer, Yidong Chen, Fan Yang, 2008, 2008 IEEE International Workshop on Genomic Signal Processing and Statistics.

Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer

A. Dutra, Yidong Chen, A. Elkahloun, 2007, Genes, chromosomes & cancer.

Expression profiling of synovial sarcoma by cDNA microarrays: association of ERBB2, IGFBP2, and ELF3 with epithelial differentiation.

M. Bittner, P. Meltzer, M. Ladanyi, 2002, The American journal of pathology.

Defective Immune Function of Primary Effusion Lymphoma Cells is Associated with Distinct KSHV Gene Expression Profiles

Christian Brander, B. Walker, Yidong Chen, 2004, Leukemia & lymphoma.

Transcription Program of Human Herpesvirus 8 (Kaposi's Sarcoma-Associated Herpesvirus)

Michael Bittner, M. Bittner, J. Trent, 2001, Journal of Virology.

Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease

Bonnie LaFleur, K. Peterson, C. Lawlor, 2001, Nature Genetics.

Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer

Michael L. Bittner, Spyro Mousses, Anne Kallioniemi, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease.

Javed Khan, Markus Ringnér, Michael L Bittner, 2003, Human molecular genetics.

Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival.

Stephanie Roessler, Xin Wei Wang, Paul S Meltzer, 2012, Gastroenterology.

cDNA Microarrays Gene Expression Profiling of Alveolar Rhabdomyosarcoma with

M. Bittner, P. Meltzer, J. Trent, 2006 .

High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression.

Yidong Chen, O. Kallioniemi, O. Monni, 2004, Neoplasia.

Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles

Edward R. Dougherty, Erchin Serpedin, Yidong Chen, 2011, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome.

Yidong Chen, T. Ried, B. Ghadimi, 2008, Cancer research.

Comparison of expression profiles of metastatic versus primary mammary tumors in MMTV-Wnt-1 and MMTV-Neu transgenic mice.

Yidong Chen, K. Podsypanina, Shixia Huang, 2008, Neoplasia.

Identification of molecular markers for endometriosis in blood lymphocytes by using deoxyribonucleic acid microarrays.

Yidong Chen, Idhaliz Flores, S. Mousses, 2006, Fertility and sterility.

Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice

H. Varmus, A. Olshen, Yidong Chen, 2005, Genome Biology.

Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer

Tony Pawson, Sampsa Hautaniemi, Spyro Mousses, 2004, Nature Genetics.

Prognostic Subtypes of Hepatocellular Carcinoma-Fetoprotein Expression Defines Novel α EpCAM and Updated

Krista A. Zanetti, X. Wang, Yidong Chen, 2008 .

Wnt-1 is Dominant over Neu in Specifying Mammary Tumor Expression Profiles

S. Hilsenbeck, Yidong Chen, K. Podsypanina, 2006, Technology in cancer research & treatment.

Microarray Image Analysis and Gene Expression Ratio Statistics

Michael L. Bittner, Edward R. Dougherty, Yidong Chen, 2006 .

Ratio statistics of gene expression levels and applications to microarray data analysis

Michael L. Bittner, Edward R. Dougherty, Jeffrey M. Trent, 2002, Bioinform..

Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic

Edward R. Dougherty, Erchin Serpedin, Yidong Chen, 2012, IEEE Transactions on Biomedical Engineering.

Inference from Clustering with Application to Gene-Expression Microarrays

Roberto Marcondes Cesar Junior, Michael L. Bittner, Edward R. Dougherty, 2002, J. Comput. Biol..

Amine-modified random primers to label probes for DNA microarrays.

Yidong Chen, J. Inman, M. Brownstein, 2002 .

Amine-modified random primers to label probes for DNA microarrays

Yidong Chen, J. Inman, M. Brownstein, 2002, Nature Biotechnology.

Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome

M. Bittner, R. Strausberg, P. Meltzer, 2004, Oncogene.

Identification and Mapping of Origins of DNA Replication in the Human Genome

Yidong Chen, S. Bilke, R. Walker, 2013 .

Comparative Genomic Hybridization Analysis of 38 Breast Cancer Cell Lines : A Basis for Interpreting Complementary DNA Microarray Data 1

Yidong Chen, O. Kallioniemi, Yuan Jiang, 2000 .

Obtaining and Evaluating Gene Expression Profiles with cDNA Microarrays

Michael L. Bittner, Edward R. Dougherty, Paul S. Meltzer, 2002 .

Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples.

P. Meltzer, Yidong Chen, S. Davis, 2012, Methods in molecular biology.

Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences

Mirit I. Aladjem, Sean Davis, Paul S. Meltzer, 2011, PloS one.

Identification of Tumor‐Suppressor Genes Using Human Melanoma Cell Lines UACC903, UACC903(+6), and SRS3 by Comparison of Expression Profiles

Yan A. Su, M. Bittner, D. Stephan, 2000, Molecular carcinogenesis.

Issues associated with microarray data analysis and integration

Michael L. Bittner, Edward R. Dougherty, E. Dougherty, 1999 .

Simulation of cDNA microarrays via a parameterized random signal model.

Yoganand Balagurunathan, Yidong Chen, Edward R Dougherty, 2002, Journal of biomedical optics.

Strong Feature Sets from Small Samples

Michael L. Bittner, Edward R. Dougherty, Junior Barrera, 2002, J. Comput. Biol..

Gene Expression Profiling Reveals Potential Biomarkers of Human Hepatocellular Carcinoma

Xin Wei Wang, Lu Wang, X. Wang, 2007, Clinical Cancer Research.

massively parallel signature sequencing (MPSS) Genome-wide mapping of DNase hypersensitive sites using

M. Daly, T. Wolfsberg, S. Luo, 2006 .

Mouse Embryo Fibroblasts Lacking the Tumor Suppressor Menin Show Altered Expression of Extracellular Matrix Protein Genes

F. Collins, Yidong Chen, A. Elkahloun, 2007, Molecular Cancer Research.

Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-κB activation

M. Bittner, P. Meltzer, J. Trent, 2001, Oncogene.

Finding robust linear expression-based classifiers

Michael L. Bittner, Edward R. Dougherty, Junior Barrera, 2001, SPIE BiOS.

Microarray ratio analysis under noisy background

E. Dougherty, M. Bittner, P. Meltzer, 1999, Nature Genetics.

Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy

Edward R. Dougherty, Erchin Serpedin, Yidong Chen, 2013, IEEE Transactions on Biomedical Engineering.

Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile.

M. Ringnér, P. Meltzer, J. Carpten, 2001, Cancer research.

Adaptive reconstructive tau-openings: convergence and the steady-state distribution

Edward R. Dougherty, Yidong Chen, E. Dougherty, 1996, J. Electronic Imaging.

Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In situ hybridization

Edward R. Dougherty, E. Dougherty, Yidong Chen, 1996, Pattern Recognit..

Optimal morphological peak classification

Edward R. Dougherty, Yidong Chen, E. Dougherty, 1995, Optics + Photonics.

Classification of trabecular structure in magnetic resonance images based on morphological granulometries

Y. Chen, E. Dougherty, E. Dougherty, 1993, Magnetic resonance in medicine.

Optimal robust classifiers

Zixiang Xiong, Edward R. Dougherty, Yidong Chen, 2005, Pattern Recognit..

CAN MARKOV CHAIN MODELS MIMIC BIOLOGICAL REGULATION

Edward R. Dougherty, Seungchan Kim, Huai Li, 2002 .

Analysis of Expression Patterns: The Scope of the Problem, the Problem of Scope

Zohar Yakhini, Amir Ben-Dor, Edward Dougherty, 2002, Disease markers.

Microarrays: Optical Technologies and Informatics

Michael L. Bittner, Andreas N. Dorsel, M. Bittner, 2001 .

High-resolution CGH analysis on cDNA microarrays for direct identification of amplification target genes

M. Bittner, Yidong Chen, O. Kallioniemi, 2001, Nature Genetics.

Use of a cDNA microarray to analyse gene expression patterns in human cancer

L. Penland, P. Brown, M. Bittner, 1996, Nature Genetics.

Molecular classification of cutaneous malignant melanoma by gene expression profiling

N. Sampas, E. Dougherty, M. Bittner, 2000, Nature.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Yidong Chen, Sean R. Davis, Paul S. Meltzer, 2008, Bioinform..

Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays.

E Mahlamäki, T C Gasser, Y. Chen, 1999, Journal of the National Cancer Institute.

Texture classification by gray-scale morphological granulometries

Edward R. Dougherty, Yidong Chen, E. Dougherty, 1992, Other Conferences.

Multivariate measurement of gene expression relationships.

E. Dougherty, M. Bittner, P. Meltzer, 2000, Genomics.

Complexity-Reduced Tumor Classification System using Microarray Gene Expression Dataset

Allam Appa Rao, O. Naga Raju, A. A. Rao, 2013 .

Gene expression profiling of human bone marrow stromal cells with FGFR-3 mutation (K650M) using cDNA microarrays

M. Bittner, J. Powell, Liming Yang, 1999, Nature Genetics.

Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.

Y. Chen, Y. Jiang, Yidong Chen, 2000, Cancer research.

Advances in Brief Human Prostate Cancer and Benign Prostatic Hyperplasia : Molecular Dissection by Gene Expression Profiling 1

Michael L. Bittner, Jun Luo, William B. Isaacs, 2001 .

Which is better for cDNA-microarray-based classification: ratios or direct intensities

Michael L. Bittner, Edward R. Dougherty, Jeffrey M. Trent, 2004, Bioinform..

Gene Expression Analysis via Multidimensional Scaling

Yidong Chen, Paul S Meltzer, P. Meltzer, 2005, Current protocols in bioinformatics.

MicroRNA expression, survival, and response to interferon in liver cancer.

P. Meltzer, X. Wang, Yidong Chen, 2009, The New England journal of medicine.

Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins.

Yidong Chen, C. Harris, K. Valerie, 2007, Carcinogenesis.

Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses

M. Bittner, P. Meltzer, J. Trent, 1999, Oncogene.

Gene Expression Profiling Reveals Potential Biomarkers of Human Hepatocellular Carcinoma

X. Wang, Yidong Chen, Q. Ye, 2007, Clinical Cancer Research.

Morphological pattern-spectra-based Tau-opening optimization

Robert M. Haralick, Edward R. Dougherty, Yidong Chen, 1991, Other Conferences.

Optimal and adaptive reconstructive granulometric bandpass filters

Edward R. Dougherty, Yidong Chen, E. Dougherty, 1997, Signal Process..

Gene Expression Analysis via Multidimensional Scaling

P. Meltzer, Yidong Chen, 2005, Current Protocols in Bioinformatics.

Evaluating Dynamic Effects of Copy Number Alterations on Gene Expression Using a Single Transcription Model

Edward R. Dougherty, Erchin Serpedin, Yidong Chen, 2012, IEEE Transactions on Biomedical Engineering.

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen (Cancer Research (January 15, 2008) 68 (415-424))

M. Bittner, P. Meltzer, J. Weinstein, 2008 .