Youping Deng, PhD

The long-term goal of the Deng lab is to develop precision medicine for cancer using both bioinformatics and experimental approaches.

My research is mainly centered on 4 areas:

1. New computational method development. My lab has developed a series of innovative methods including novel algorithms for data normalization, clustering, feature selection, classification, differential expression, gene function ontology, gene network modeling and so on. We are currently developing new methods for alternative splicing and DNA somatic mutation for biomarker identification based on sequencing data.
   
   
2. Identification of non-invasive biomarkers for early detection of cancer. We are searching for novel accurate circulating biomarkers for early detection of lung cancer and breast cancer. Based on a variety of high throughput “omics” methods including small RNA-seq, metabolomics, DNA-seq, and proteomics plus bioinformatics data mining, we have found and are seeking for circulating metabolite, ncRNA, protein, and CtDNA markers for early diagnosis of cancer.
   
   
3. Characterization of biomarkers for predicting clinical outcomes of human diseases including cancer. We are mining public “omics” data such as TCGA data as well as generating our own high-throughput data to identify biomarkers to predict clinical outcomes of human diseases including cancer. For instance, we have found novel DNA mutation and gene expression signatures to predict better response to cancer drugs such as PARP inhibitor. New cellular and animal experiments are being designed to evaluate these biomarkers and understand their mechanisms.
   
   
4. Integrative data analysis of “omics” and clinical data. We are integrating different types of “omics” data such as genomics, transcriptomics, metabolomics, epigenomics and proteomics data, as well as clinical factors, using a systems biology approach to understand carcinogenesis, cancer development, and find better biomarkers for precision medicine.

In addition to independent research, my team also provides bioinformatics data science services, which primarily focuses on the analysis and management of high-throughput data such as microarray data, real-time PCR data, proteomics, metabolomics, multiple biomarker data and next-generation sequence data including DNA-seq, RNA-seq, Chip-seq and microbiota (metagenomics) data and so on. The core also supports routine bioinformatics applications, such as phylogenetic, protein function prediction.

Y. Deng, Co-I; S. Kwee, PI
NIH/NCI
1R01CA262460
“Evaluation of treatment predictors reflecting beta-catenin activation in hepatocellular carcinoma”
07/01/2021 - 06/30/2026

Y. Deng, PI
NIH/NCI
1R01CA230514
“Circulating Lipid and miRNA Markers for Early Detection of Breast Cancer among Women with Abnormal Mammograms”
08/01/2019 – 07/31/2024

Y. Deng, PI
NIH/NCI
1R01CA223490
“Profiling Genome-wide Circulating ncRNAs for the Early Detection of Lung Cancer”
09/01/2018 – 08/31/2023

Y. Deng, Co-Leader, Genomics & Informatics Shared Resource; J. Ramos, PI
NIH/NCI
5P30CA071789
“University of Hawaii Cancer Center CCSG”
07/01/2018 – 06/30/2023

Y. Deng, Director, Bioinformatics Core; Nichols, PI
NIH/NIGMS
5P20GM103466-18
“INBRE IV: Hawaii Statewide Research and Education Partnership”
05/01/2018 - 04/30/2023

Y. Deng, Director, Bioinformatics Core; Yanagihara, PI
NIH/NIGMS
Y5P30GM114737
“Pacific Center for Emerging Infectious Diseases Research”
07/01/2015 – 06/30/2022

Y. Deng, Co-Director, Research Infrastructure Core; Hedges, PI
NIH/NIMHD
5U54MD007601
“Ola HAWAII – Health And Wellness Attained by Impacting Inequities”
09/01/2017 – 06/30/2022