Publications by authors named "Yingdong Zhao"

70Publications

Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products.

Mol Oncol 2020 Nov 9. Epub 2020 Nov 9.

Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, MD, USA.

View Article and Find Full Text PDF
November 2020

Bioinformatics Tools and Resources for Cancer Immunotherapy Study.

Methods Mol Biol 2020 ;2055:649-678

Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

View Article and Find Full Text PDF
November 2020

Identification of pharmacodynamic biomarkers and common molecular mechanisms of response to genotoxic agents in cancer cell lines.

Cancer Chemother Pharmacol 2019 10 31;84(4):771-780. Epub 2019 Jul 31.

Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.

View Article and Find Full Text PDF
October 2019

Single cell sequencing reveals gene expression signatures associated with bone marrow stromal cell subpopulations and time in culture.

J Transl Med 2019 01 11;17(1):23. Epub 2019 Jan 11.

Cell Processing Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health (NIH), 10 Center Drive-MSC-1184, Building 10, Room 3C720, Bethesda, MD, 20892-1184, USA.

View Article and Find Full Text PDF
January 2019

Plasma from some cancer patients inhibits adenoviral Ad5f35 vector transduction of dendritic cells.

Cytotherapy 2018 05 11;20(5):728-739. Epub 2018 Apr 11.

Cell Processing Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA. Electronic address:

View Article and Find Full Text PDF
May 2018

Longitudinal Transcriptional Response of Glycosylation-Related Genes, Regulators, and Targets in Cancer Cell Lines Treated With 11 Antitumor Agents.

Cancer Inform 2017 15;16:1176935117747259. Epub 2017 Dec 15.

Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.

View Article and Find Full Text PDF
December 2017

Concerted changes in transcriptional regulation of genes involved in DNA methylation, demethylation, and folate-mediated one-carbon metabolism pathways in the NCI-60 cancer cell line panel in response to cancer drug treatment.

Clin Epigenetics 2016 24;8:73. Epub 2016 Jun 24.

Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD 20850 USA.

View Article and Find Full Text PDF
December 2016

Analytical Validation and Application of a Targeted Next-Generation Sequencing Mutation-Detection Assay for Use in Treatment Assignment in the NCI-MPACT Trial.

J Mol Diagn 2016 Jan 18;18(1):51-67. Epub 2015 Nov 18.

Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., and Frederick National Laboratory for Cancer Research, Frederick, Maryland; Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.

View Article and Find Full Text PDF
January 2016

Application of molecular profiling in clinical trials for advanced metastatic cancers.

J Natl Cancer Inst 2015 Apr 6;107(4). Epub 2015 Feb 6.

Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD (SK, ECP, APC, LVR, YZ, RMS, BAC, JHD); Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (PMW, CJL).

View Article and Find Full Text PDF
April 2015

Mathematical modeling the pathway of human breast cancer.

Math Biosci 2014 Jul 25;253:25-9. Epub 2014 Mar 25.

Department of Computer Science and Technology, Tsinghua University, Beijing 100084, PR China.

View Article and Find Full Text PDF
July 2014

Intra-subject variability in human bone marrow stromal cell (BMSC) replicative senescence: molecular changes associated with BMSC senescence.

Stem Cell Res 2013 Nov 27;11(3):1060-73. Epub 2013 Jul 27.

Department of Transfusion Medicine, Clinical Center, National Institutes of Health, 10 Center Dr., Bethesda, MD 20892, USA. Electronic address:

View Article and Find Full Text PDF
November 2013

Quality controls in cellular immunotherapies: rapid assessment of clinical grade dendritic cells by gene expression profiling.

Mol Ther 2013 Feb 13;21(2):476-84. Epub 2012 Nov 13.

Cell Processing Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA.

View Article and Find Full Text PDF
February 2013

Influence of quercetin-rich food intake on microRNA expression in lung cancer tissues.

Cancer Epidemiol Biomarkers Prev 2012 Dec 3;21(12):2176-84. Epub 2012 Oct 3.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
December 2012

A multi-factorial genetic model for prognostic assessment of high risk melanoma patients receiving adjuvant interferon.

PLoS One 2012 24;7(7):e40805. Epub 2012 Jul 24.

Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology, National Institutes of Health, Bethesda, Maryland, United States of America.

View Article and Find Full Text PDF
April 2013

IRF5 gene polymorphisms in melanoma.

J Transl Med 2012 Aug 21;10:170. Epub 2012 Aug 21.

Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
August 2012

The stable traits of melanoma genetics: an alternate approach to target discovery.

BMC Genomics 2012 Apr 26;13:156. Epub 2012 Apr 26.

Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
April 2012

Molecular insights on the peripheral and intratumoral effects of systemic high-dose rIL-2 (aldesleukin) administration for the treatment of metastatic melanoma.

Clin Cancer Res 2011 Dec 5;17(23):7440-50. Epub 2011 Oct 5.

Department of Medicine/Division of Hematology-Oncology, University of Virginia Health System, Charlottesville, 22908, USA.

View Article and Find Full Text PDF
December 2011

Interaction of a traditional Chinese Medicine (PHY906) and CPT-11 on the inflammatory process in the tumor microenvironment.

BMC Med Genomics 2011 May 11;4:38. Epub 2011 May 11.

Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, Maryland 20892, USA.

View Article and Find Full Text PDF
May 2011

A signature of immune function genes associated with recurrence-free survival in breast cancer patients.

Breast Cancer Res Treat 2012 Feb 11;131(3):871-80. Epub 2011 Apr 11.

Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine and Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
February 2012

Association of IFN-gamma signal transduction defects with impaired HLA class I antigen processing in melanoma cell lines.

Clin Cancer Res 2011 May 19;17(9):2668-78. Epub 2011 Jan 19.

Martin-Luther-Universitat Halle-Wittenberg, Institute of Medical Immunology, Halle, Saale, Germany.

View Article and Find Full Text PDF
May 2011

Gene expression deconvolution in clinical samples.

Genome Med 2010 Dec 29;2(12):93. Epub 2010 Dec 29.

Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

View Article and Find Full Text PDF
December 2010

Partial immunity and vaccination for influenza.

J Comput Biol 2010 Dec;17(12):1689-96

School of Mathematics and Statistics, Central China Normal University, Wuhan, P.R. China.

View Article and Find Full Text PDF
December 2010

Evaluation of normalization methods for two-channel microRNA microarrays.

J Transl Med 2010 Jul 21;8:69. Epub 2010 Jul 21.

Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

View Article and Find Full Text PDF
July 2010

Development and validation of predictive indices for a continuous outcome using gene expression profiles.

Cancer Inform 2010 May 7;9:105-14. Epub 2010 May 7.

Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. Email:

View Article and Find Full Text PDF
May 2010

Strengths and limitations of laboratory procedures for microRNA detection.

Cancer Epidemiol Biomarkers Prev 2010 Apr 23;19(4):907-11. Epub 2010 Mar 23.

Infections and Immunepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Room 7070, Rockville, MD 20852-7248, USA.

View Article and Find Full Text PDF
April 2010

MicroRNA expression differentiates histology and predicts survival of lung cancer.

Clin Cancer Res 2010 Jan 12;16(2):430-41. Epub 2010 Jan 12.

Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, Maryland 20892-7236, USA.

View Article and Find Full Text PDF
January 2010

Combining positional scanning peptide libraries, HLA-DR transfectants and bioinformatics to dissect the epitope spectrum of HLA class II cross-restricted CD4+ T cell clones.

J Immunol Methods 2010 Feb 28;353(1-2):93-101. Epub 2009 Dec 28.

Cellular Immunology Section, Neuroimmunology Branch, NINDS, National Institutes of Health, Bethesda, Maryland 20892, USA.

View Article and Find Full Text PDF
February 2010

A comparison of phase II study strategies.

Clin Cancer Res 2009 Oct 29;15(19):5950-5. Epub 2009 Sep 29.

Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, USA.

View Article and Find Full Text PDF
October 2009

Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools.

Bioinformatics 2009 Feb 8;25(4):545-7. Epub 2009 Jan 8.

Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, USA.

View Article and Find Full Text PDF
February 2009

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

J Transl Med 2008 Oct 30;6:64. Epub 2008 Oct 30.

Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.

View Article and Find Full Text PDF
October 2008

Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China.

J Transl Med 2008 Jun 20;6:32. Epub 2008 Jun 20.

Cancer Research Institute of Southern Medical University, Key Lab for Transcriptomics and Proteomics of Human Fatal Diseases Supported by Ministry of Education and Guangdong Province, 510515, PR China.

View Article and Find Full Text PDF
June 2008

Artificial intelligence methods for predicting T-cell epitopes.

Methods Mol Biol 2007 ;409:217-25

National Cancer Institute, National Institutes of Health, Rockville, MD, USA.

View Article and Find Full Text PDF
June 2008

Conservation of genetic alterations in recurrent melanoma supports the melanoma stem cell hypothesis.

Cancer Res 2008 Jan;68(1):122-31

Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Warren G. Magnuson Clinical Center, Biometrics Research Branch, National Cancer Institute, NIH, Bethesda, Maryland 20892-1184, USA.

View Article and Find Full Text PDF
January 2008

How large a training set is needed to develop a classifier for microarray data?

Clin Cancer Res 2008 Jan;14(1):108-14

Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Rockville, Maryland 20852, USA.

View Article and Find Full Text PDF
January 2008

BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource.

Cancer Inform 2008 21;6:9-15. Epub 2008 Apr 21.

Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.

View Article and Find Full Text PDF
May 2010

Gene Set Expression Comparison kit for BRB-ArrayTools.

Bioinformatics 2008 Jan 15;24(1):137-9. Epub 2007 Nov 15.

Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434, USA.

View Article and Find Full Text PDF
January 2008

Analysis of gene expression data using BRB-ArrayTools.

Cancer Inform 2007 Feb 4;3:11-7. Epub 2007 Feb 4.

Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892-7434, USA.

View Article and Find Full Text PDF
February 2007

Common cancer biomarkers.

Cancer Res 2006 Mar;66(6):2953-61

Department of Transfusion Medicine, Warren G. Magnuson Clinical Center, National Cancer Institute, NIH, Bethesda, Maryland 20892-1184, USA.

View Article and Find Full Text PDF
March 2006

Redundancy in antigen-presenting function of the HLA-DR and -DQ molecules in the multiple sclerosis-associated HLA-DR2 haplotype.

J Immunol 2006 Feb;176(3):1951-61

Cellular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
February 2006

Recognition of conserved amino acid motifs of common viruses and its role in autoimmunity.

PLoS Pathog 2005 Dec 16;1(4):e41. Epub 2005 Dec 16.

Cellular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.

View Article and Find Full Text PDF
December 2005

HLAMatchmaker-driven analysis of responses to HLA-typed platelet transfusions in alloimmunized thrombocytopenic patients.

Blood 2006 Feb 3;107(4):1680-7. Epub 2005 Nov 3.

Department of Transfusion Medicine, Bldg 10, 1C711, National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
February 2006

An adaptive method for cDNA microarray normalization.

BMC Bioinformatics 2005 Feb 11;6:28. Epub 2005 Feb 11.

Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.

View Article and Find Full Text PDF
February 2005

Selection and validation of endogenous reference genes using a high throughput approach.

BMC Genomics 2004 Aug 13;5(1):55. Epub 2004 Aug 13.

Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, NIH Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
August 2004

Application of support vector machines for T-cell epitopes prediction.

Bioinformatics 2003 Oct;19(15):1978-84

Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
October 2003

A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings.

J Transl Med 2003 Aug 20;1(1). Epub 2003 Aug 20.

Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA.

View Article and Find Full Text PDF
August 2003

Molecular differentiation of high- and moderate-grade human prostate cancer by cDNA microarray analysis.

Diagn Mol Pathol 2003 Jun;12(2):63-70

Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

View Article and Find Full Text PDF
June 2003

Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes.

Proc Natl Acad Sci U S A 2002 Sep 6;99(19):12037-42. Epub 2002 Sep 6.

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7260, USA.

View Article and Find Full Text PDF
September 2002

T-cell epitope prediction with combinatorial peptide libraries.

J Comput Biol 2002 ;9(3):527-39

Molecular Statistics and Bioinformatics Section, Biometric Research Branch, National Cancer Institute, National Institutes of Health, 6130 Executive Boulevard, EPN 8146, MSC 7434, Bethesda, MD 20892-7434, USA.

View Article and Find Full Text PDF
January 2003