Yate-Ching Yuan Ph.D.
Director, Translational Bioinformatics
Research Background
- Oversight of TBI Division budget, resource and personnel development
- Provide platform independent OMIC analysis pipelines for NGS, microarray, NanoString, Fulidign using Partek, Qiagen IPA/IVA, Matlab to support HPC resource on premise, TGEN, Amazon AWS/MS Azure Cloud cyberinfrastructure
- Teach graduate school and coordinate regional bioinformatics workshops such as NCBI, EBI, UCSC , and commercial software/database trainings
- Published 9 joined manuscripts in FY18 and facilitate pilot grant submissions
- Participated NCI CCSG site visit since 1999 and awarded exceptional merit scores for past 2 grant cycles
Research Highlights
1. TBI has developed computational methodology and tools to integrate public open source bioinformatics resource for data sharing, standardize analysis pipeline and visualization support for data generated from sanger sequence, microarray, and next generation genomics sequencing as well as public accessible disease focus patient cohorts from NCBI, EBI, TCGA, CPTAC, BROAD, GTEX, and cBioportal, etc. We also developed BRAVO (Biomarker Recognition and Validation Online) database with more than more than 1,000,000 human disease samples from 58 cancer studies including NCI CPTAC/TCGA for 17 cancer and diabetes disease (brain, breast, bladder, colorectal, endometrial, heck & neck, glioblastoma, kidney, liver, lung, leukemia, lymphoma, gastric, melanoma, ovarian, pancreatic, prostate), and T1D/T2D Diabetes public cohort studies to assist in characterization gene panels derived from high throughput assay-driven predictive biomarker evaluation using clinical specimens for genotype-phenotype correlation to establish actionable biomarker for targeted therapy to support precision medicine.
a. Zhao ZM, Yost SE, Hutchinson KE, Li SM, Yuan YC, Noorbakhsh J, Liu Z, Warden C, Johnson RM, Wu X, Chuang JH, Yuan Y. CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer. BMC Cancer. 2019 Jan 21;19(1):96. PubMed PMID: 30665374; PubMed Central PMCID: PMC6341717.
b. Chen SF, Liu Z, Chaurasiya S, Dellinger TH, Lu J, Wu X, Qin H, Wang J, Fong Y, Yuan YC. Identification of core aberrantly expressed microRNAs in serous ovarian carcinoma. Oncotarget. 2018 Apr 17;9(29):20451-20466. PubMed PMID: 29755664; PMCID: PMC5945511.
c. Zhang XH, Nam S, Wu J, Chen CH, Liu X, Li H, McKeithan T, Gong Q, Chan WC, Yin HH, Yuan YC, Pillai R, Querfeld C, Horne D, Chen Y, Rosen ST. Multi-Kinase Inhibitor with Anti-p38? Activity in Cutaneous T-Cell Lymphoma. J Invest Dermatol. 2018 Nov;138(11):2377-2387. Epub 2018 Jul 14. PubMed PMID: 29758280.
d. Zhang B, Nguyen LXT, Li L, Zhao D, Kumar B, Wu H, Lin A, Pellicano F, Hopcroft L, Su YL, Copland M, Holyoake TL, Kuo CJ, Bhatia R, Snyder DS, Ali H, Stein AS, Brewer C, Wang H, McDonald T, Swiderski P, Troadec E, Chen CC, Dorrance A, Pullarkat V, Yuan YC, Perrotti D, Carlesso N, Forman SJ, Kortylewski M, Kuo YH, Marcucci G. Bone marrow niche trafficking of miR-126 controls the self-renewal of leukemia stem cells in chronic myelogenous leukemia. Nat Med. 2018 May;24(4):450-462. PubMed PMID: 29505034; PubMed Central PMCID: PMC5965294.
2. We also developed open source bioinformatics programs hosted on public sourceforge for developing a streamlined and integrated genomic algorithm and pipeline for predicting down-stream activation and inhibition of pathways for genomic expression and DNA methylation profiles generating deep sequencing and microarray platforms.
a. Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res, 2019, Sep 5;47(15):8335-8336. PubMed PMID: 31340028
b. Warden CD, Kanaya N, Chen S, Yuan YC. BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. 2013 1: e159. PubMed PMID: 24058887; PubMed Central PMCID: PMC3775632.
3. We have developed analysis pipelines for computer assisted molecular design of novel small molecule(s) and nanoparticles as prognosis probe targeting biomarkers and their underlining molecular mechanisms and molecular dynamic simulations the binding modes of protein-protein and protein-DNA tertiary interactions with nature substrate(s) and therapeutics for personalized medicine to treating cancer, diabetic and immune-deficient life threaten diseases. Three of COH in-house developed potent inhibitors have awarded patent award for clinical trials.
a. Zhang XH, Nam S, Wu J, Chen CH, Liu X, Li H, McKeithan T, Gong Q, Chan WC, Yin HH, Yuan YC, Pillai R, Querfeld C, Horne D, Chen Y, Rosen ST. Multi-Kinase Inhibitor with Anti-p38? Activity in Cutaneous T-Cell Lymphoma. J Invest Dermatol. 2018 Nov;138(11):2377-2387. Epub 2018 Jul 14. PubMed PMID: 29758280.
b. Awasthi S, Singhal SS, Singhal J, Nagaprashantha L, Li H, Yuan YC, Liu Z, Berz D, Igid H, Green WC, Tijani L, Tonk V, Rajan A, Awasthi Y, Singh SP. Anticanceractivity of 2'-hydroxyflavanone towards lung cancer. Oncotarget. 2018 Nov 16;9(90):36202-36219. 2018 PubMed PMID: 30546837; PubMed Central PMCID: PMC6281421.
c. Gu L, Lingeman R, Yakushijin F, Sun E, Cui Q, Chao J, Hu W, Li H, Hickey RJ, Stark JM, Yuan YC, Chen Y, Vonderfecht SL, Synold TW, Shi Y, Reckamp KL, Horne D, Malkas LH. The Anticancer Activity of a First-in-class Small-molecule Targeting PCNA. Clin Cancer Res. 2018 Jul 2. CCR-18-0592. [Epub ahead of print] PubMed PMID: 29967249
d. Awasthi S, Tompkins J, Singhal J, Riggs AD, Yadav S, Wu X, Singh S, Warden C, Liu Z, Wang J, Slavin TP, Weitzel JN, Yuan YC, Awasthi M, Srivastava SK, Awasthi YC, Singhal SS. (2018) Rlip depletion prevents spontaneous neoplasia in TP53 null mice. Proc Natl Acad Sci 2018 Apr 10;115(15):3918-3923. PubMed PMID: 29572430; PubMed Central; PMCID: PMC5899455.
Bio
1995-present ● Director, Translational Bioinformatics. More than 20 years at COH.
1995 ● Postdoc in pharmaceutical chemistry, University of California at San Francisco
1992 ● Postdoc in pharmaceutical chemistry, University of Texas at Austin
1991 ● Ph.D. in computational chemistry, University of Texas at Austin