Departments & Divisions
Institutes & Centers
Yidong Chen, Ph.D.
Dr.Yidong Chen received his B.S./M.S. degrees in Electrical Engineering from Fudan University, Shanghai, China, and Ph.D. in Imaging Science from Rochester Institute of Technology, Rochester, NY. He has been with Hewlett Packard Co as a Research Engineer before he joined National Institutes of Health (NIH) at 1996. At NIH, Dr. Chen joined microarray technology development effort at National Human Genome Research Institute (NHGRI), as a Special Expert, Staff Scientist, and later Associate Investigator for microarray image, statistical analysis, and bioinformatics. From 2006-2008 he joined the Genetics branch at National Cancer Institute (NCI) as a staff scientist. During the 13-year period with NHGRI and NCI, he has contributed about 90 peer reviewed publications and book chapters. Currently, Chen Lab works on computational biology and bioinformatics and focuses on developing computational solution and statistical modeling to bridge between quantitative science and the basic biology and translational research within Greehey Children’s Cancer Research Institute and around UT Health San Antonio. Our research contributions are in:
Genome Sequencing Facility (GSF) bioinformatics operation
Next-Generation Sequencing (NGS) data analysis methods
computational biology and biostatistics collaboration for pediatric cancer
Deep Learning/machine learning methodologies for genome analysis, drug response
prediction, disease prognosis, and their applications to precision medicine, and
of estimating individual ancestry admixture from standard whole exome
sequencing, and genetic analysis methods for admixture population.
Computational Biology and Bioinformatics program is the home for High-Performance Computing (HPC) infrastructure, large data storage, bioinformatics expertise, and interdisciplinary research experience to manage and distribute complex genomic data sets, to develop and perform bioinformatics tasks, machine learning techniques, and systems biology using genomic data. We aim to establish as world-leading bioinformatics group of developing new biomedical technologies and computational methods to the varieties of high-throughput and multi-omics datasets. Our research area includes Systems biology, pan-cancer bioinformatics; Deep Learning methods in genomics, analysis using gene regulatory networks, novel bioinformatics algorithm for NGS applications, and bioinformatics tools in proteo-genomics data analysis. By working with faculty from the Biostatistics Division, we will provide a wide range of research collaboration and education partners.
- 1995 - PhD - Imaging Science - Rochester Institute of Technology
- 1986 - MS - Electrical Engineering - Fudan University
- 1983 - BS - Electrical Engineering - Fudan University
- 9/2019 - Professor - UT Health San Antonio, Population Health Science, San Antonio
- 8/2014 - Co-Director of Mays Cancer Center Next-Generation Sequencing Shared Resource - UT Health Science Center at San AntonioSan Antonio
- 9/2008 - Director of Computational Biology and Bioinformatics - UT Health Science Center at San Antonio, Greehey Children`s Cancer Research Institute, San Antonio
Instruction & Training
- 3/2019 - Present, Gene Expression, UT Health San Antonio
- 01/2014-Present, Functional Genomics Data Analysis, UT Health San Antonio
Research & Grants
Computational Biology and Bioinformatics program is the home for High-Performance Computing (HPC) infrastructure,large data storage,bioinformatics expertise,interdisciplinary research experience to manage and distribute complex genomic data sets, to develop and perform bioinformatics tasks, machine learning techniques, and systems using genomic data. Establishing the world-leading bioinformatics group of developing new biomedical technologies and methods to the varieties of high-throughput and multi-omics data sets. With faculty from Biostatistics Division,we will provide a wide range of research collaboration and education partners.
Funding Agency NIH-NCATS Title Institute for Integration of Medicine & Science (IIMS): A Partnership to Improve Health Status Active Period 5/2018 - 4/2023 Role Contributor Grant Detail The vision of the Institute for Integration of Medicine and Science is to improve health and reduce disparities by
accelerating scientific discoveries and applications across the full translational research spectrum. We will
accomplish this by strategic resource deployment, focusing on prevalent challenges in our region, including: 1)
the health needs of our underserved Hispanic and rural populations, 2) the special health issues facing activeduty
military and veteran populations, and 3) limitations in the translational science workforce required to fill in
critical knowledge gaps and improve health in South Texas and the US. I will serve in the capacity of Medical Director of the CTSA hub liaison team with the Trial Innovation Network Funding Agency NIH/NIDDK Title Human hypothalamic neuronal epigenomics and risk for obesity Status Active Period 9/2018 - 9/2022 Role Contributor Grant Detail ABSTRACT: Translating information on genetic risk for body weight regulation into molecular mechanisms can have a significant impact on intervention and therapies. We are seeking to identify genetic variation and their molecular mechanisms that influences obesity through direct effects on the hypothalamus as it is the brain hub that regulates energy homeostasis and there is now considerable evidence for genetic influence to impact this brain region. However, the majority of genetic loci associated with this common, chronic disorder in the general population are located in noncoding regions of the genome, suggesting their influence on energy homeostasis is manifested through changes to the regulome. Thus, pinpointing the causal human variants and connecting them to their downstream targets in brain presents challenges of tissue access for study because much epigenetic control is species-, tissue- and context-specific. To overcome the barrier of limited human tissue access, we have developed a robust protocol for generating human induced pluripotent stem cell (iPSC)derived neuronal cultures that recapitulate many of the features of hypothalamic neurons from the arcuate nucleus, including by benchmarking this in vitro model to in vivo events that are pivotal in hypothalamic development. We will use this human model and state of the art high throughput assays to map the currently uncharted regulatory landscape of the human hypothalamic neurons across 3 stages in development (early, mid, and late) and under experimental obesogenic conditions. Next, in order to precisely pinpoint the functional variants in BMI GWAS loci that have influence on body weight regulation through hypothalamic epigenomic regulation, we will identify those that influence chromatin accessibility and/or target gene expression by assay in 100 iPSC-derived neuronal lines generated from subjects of the San Antonio Mexican American Family Studies. GWAS variants with both properties have high potential Funding Agency Title NCI (PQ#3) Novel tumor intrinsic PD-L1 signals direct tumor immune cell infiltration Status Active Period 4/2017 - 3/2022 Role Contributor Grant Detail Council Meeting Date: 2017/01
Meeting Date: 11/15/201 Funding Agency NIH/NIDDK Title The Role of AEG-1 in NASH and NASH-HCC Status Active Period 7/2016 - 6/2021 Role Co-Investigator Grant Detail Funding Agency NIH/NCI Title Aging mammary stem cells and breast cancer prevention Status Active Period 9/2015 - 6/2020 Role Co-Investigator Grant Detail Our long-term goal is to determine how aging-related breast cancer can be specifically targeted and prevented. Funding Agency NIH/NCI Title miRNAs: Safe and effective therapeutic adjuvants for treating drug resistant TNBCs Status Active Period 2/2015 - 1/2020 Role Co-Investigator Grant Detail This work will determine if candidate miRNA sensitizes cellular response to taxol by targeting microtubule-associated proteins, and if candidate miRNA affects taxol response by targeting DNA damage surveillance pathway. In addition, we will study the therapeutic potential of candidate miRNAs in improving the efficacy of taxol for treating therapy resistant TNBC using a tumor xenograft mouse model and syngeneic mouse model with intact immune system. Funding Agency NIH/NCI Title Cancer Therapy and Research Center/Caner Center Admin Status Active Period 5/2014 - 4/2019 Role Contributor Grant Detail This is a P30 Cancer Center Support Grant at the University of Texas Health Science Center at San Antonio. This grant provides funding for the conduct of cancer clinical trials, prevention studies and assistance with statistical design and analysis of translational cancer research projects. Specifically, this is for support of the biostatistics and medical informatics core. Funding Agency NIH/NCATS Title Institute for Integration of Medicine & Science (IIMS): A Partnership to Improve Health Status Active Period 9/2013 - 8/2018 Role Contributor Grant Detail Funding Agency NIH/NIGMS Title Graphical models for characterizing global RNA methylation Status Active Period 9/2014 - 8/2017 Role Co-Principal Investigator Grant Detail The goal of this project is to develop, for the first time, computational graphical models to enable 1) accurate and reproducible detection of global mRNA methylations, and 2) context-specific differential RNA methylations in normal and disease states
Funding Agency San Antonio Life Science Institute Title A Cloud Computing Pipeline for Precision Medicine Status Complete Period 5/2016 - 4/2017 Role Principal Investigator Grant Detail
Funding Agency Cancer Prevention & Research Institute of Texas Title Predicting drug response from genomic data using deep learning methods Status Active Period 9/2019 - 8/2022 Role Principal Investigator Grant Detail Funding Agency Cancer Prevention & Research Institute of Texas Title UTHSCSA Cancer Genome Sequencing and Computation Core (UTHSCSA-CGSCC) Status Active Period 6/2016 - 5/2021 Role Principal Investigator Grant Detail Funding Agency CPRIT Title Functional Genomics and Computation Core Status Active Period 8/2012 - 8/2017 Role Principal Investigator Grant Detail A computational genomic core to perform integrative genomic analysis for a collection of soft-tissue sarcoma tumors from children?s in Texas, and genomic data from model organisms
Ruan J, Jin V, Huang Y, Xu H, Edwards JS, Chen Y, Zhao Z. Education, collaboration, and innovation: intelligent biology and medicine in the era of big data BMC Genomics 2015 Jun;16.
Mostavi, M., Chiu, Y., Huang, Y., Chen, Y. (2020). Convolutional neural network models for cancer type prediction based on gene expression. BMC Medical Genomics. Vol.13. Article number 44. doi:10.1186/s12920-020-0677-2, Liss, M., Chen, Y., Rodriguez, R., Pruthi, D., Johnson-Pais, T., Wang, H., Mansour, A., White, J., Kaushik, D. (2020). Microbiome within Primary Tumor Tissue from Renal Cell Carcinoma May Be Associated with PD-L1 Expression of the Venous Tumor Thrombus. Advances in Urology. Article ID 9068068. doi.org/10.1155/2020/9068068,Wang, L., Zhang, C.W., Su, S.C., Chen, H., Chiu, Y., Lai, Z., Bouamar, H., Ramirez, A., Cigarroa, F., Sun, L., Chen, Y. (2019). An ancestry infomrative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data. BMC Genomics. 20, Article number: 1007. doi.org/10.1186/s12864-019-633-6 Jariwala N, Mendoza RG, Garcia D, Lai Z, Subler MA, Windle JJ, Mukhopadhyay ND, Fisher PB, Chen Y, Sarkar D. Posttranscriptional Inhibition of Protein Tyrosine Phosphatase Nonreceptor Type 23 by Staphylococcal Nuclease and Tudor Domain Containing 1: Implications for Hepatocellular Carcinoma Hepatology Communications 2019 Sep;3(9). Liu J, Gao M, Nipper M, Deng J, Sharkey FE, Johnson RL, Crawford HC, Chen Y, Wang P. Activation of the intrinsic fibroinflammatory program in adult pancreatic acinar cells triggered by Hippo signaling disruption PLoS Biology 2019 Sep;17(9). She L, Alanazi HH, Yan L, Zou Y, Sun Y, Dube PH, Brooks EG, Barrera GD, Lai Z, Chen Y, Liu Y, Zhang X, Li XD. Immune Sensing of Aeroallergen-Associated Double-Stranded RNA Triggers an IFN Response and Modulates Type 2 Lung Inflammation Journal of Immunology 2019 Sep;. Liss MA, Chen Y, Rodriguez R, Pruthi D, Johnson-Pais T, Wang H, Mansour A, Kaushik D. Immunogenic Heterogeneity of Renal Cell Carcinoma With Venous Tumor Thrombus Urology 2019 Feb;124:168-173. Mohammad TA, Tsai YS, Ameer S, Chen HH, Chiu YC, Chen Y. CeL-ID: cell line identification using RNA-seq data. BMC Genomics BMC Genomics 2019 Feb;. Zhou M, Humbert M, Mukhtar MM, Scinto HB, Vyas HK, Lakhashe SK, Byrareddy SN, Maurer G, Thorat S, Owuor J, Lai Z, Chen Y, Griffiths A, Chenine AL, Gumber S, Villinger F, Montefiori D, Ruprecht RM. Adaptation of an R5 Simian-human Immunodeficiency Virus Encoding an HIV Clade A Envelope With or Without Ablation of Adaptive Host Immunity: Differential Selection of Viral Mutants J Virology 2019 Feb;. Zhang SY, Zhang SW, Fan XN, Meng J, Chen Y, Gao SJ, Huang Y. Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods PLoS Computational Biology 2019 Jan;. Chiu YC, Chen HH, Zhang T, Zhang S, Gorthi A, Wang LJ, Huang Y, Chen Y. Predicting drug response of tumors from integrated genomic profiles by deep neural networks BMC Med Genomics 2019 Jan;. Chiu YC, Hsiao TH, Wang LJ, Chen Y, Shao YJ. scdNet: a computational tool for single-cell differential network analysis BMC Systems Biology 2018 Dec;. Chen HH, Chiu YC, Zhang T, Zhang S, Huang Y, Chen Y. GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization BMC Systems Biology 2018 Dec;. Abdelfattah N, Rajamanickam S, Panneerdoss S, Timilsina S, Yadav P, Onyeagucha BC, Garcia M, Vadlamudi R, Chen Y, Brenner A, Houghton P, Rao MK. MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma Nature Communications 2018 Oct;. Panneerdoss S, Eedunuri VK, Yadav P, Timilsina S, Rajamanickam S, Viswanadhapalli S, Abdelfattah N, Onyeagucha BC, Cui X, Lai Z, Mohammad TA, Gupta YK, Huang TH, Huang Y, Chen Y, Rao MK. Cross-talk among writers, readers, and erasers of m6A regulates cancer growth and progression Science Advances 2018 Oct;4(10). Ignatius MS, Hayes MN, Moore FE, Tang Q, Garcia SP, Blackburn PR, Baxi K, Wang L, Jin A, Ramakrishnan A, Reeder S, Chen Y, Nielsen GP, Chen EY, Hasserjian RP, Tirode F, Ekker SC, Langenau DM. tp53 deficiency causes a wide tumor spectrum and increases embryonal rhabdomyosarcoma metastasis in zebrafish eLife 2018 Sep;. Zanotto-Filho A, Rajamanickam S, Loranc E, Masamsetti VP, Gorthi A, Romero JC, Tonapi S, Goncalves RM, Reddick RL, Benavides R, Kuhn J, Chen Y, Bishop AJR. Sorafenib improves alkylating therapy by blocking induced inflammation, invasion and angiogenesis in breast cancer cells Cancer Letter 2018 Jul;425. Gorthi A, Romero JC, Loranc E, Cao L, Lawrence LA, Goodale E, Iniguez AB, Bernard X, Masamsetti VP, Roston S, Lawlor ER, Toretsky JA, Stegmaier K, Lessnick SL, Chen Y, Bishop AJR. EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma Nature 2018 Mar;555(7696). Cui X, Zhang L, Meng J, Rao MK, Chen Y, Huang Y. A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data IEEE/ACM Transactions on Computational Biology and Bioinformatics 2018 Mar;15(2). Antonarakis ES, Lu C, Luber B, Liang C, Wang H, Chen Y, Silberstein JL, Piana D, Lai Z, Chen Y, Isaacs WB, Luo J. Germline DNA-repair Gene Mutations and Outcomes in Men with Metastatic Castration-resistant Prostate Cancer Receiving First-line Abiraterone and Enzalutamide European Urology 2018 Feb;. Wei Z, Panneerdoss S, Timilsina S, Zhu J, Mohammad TA, Lu ZL, de Magalh?es JP, Chen Y, Rong R, Huang Y, Rao MK, Meng J. Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing International Journal of Genomics 2018 Jan;. Hsiao TH, Chiu YC, Chen YH, Hsu YC, Chen HH, Chuang EY, Chen Y. Utilizing Cancer - Functional Gene set - Compound Networks to Identify Putative Drugs for Breast Cancer Combinatorial Chemistry & High Throughput Screening 2018 Jan;. Liu Y, Wu P, Zhou J, Johnson-Pais TL, Lai Z, Chowdhury WH, Rodriguez R, Chen Y. XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation BMC Bioinformatics 2017 Oct;. Chiu YC, Wang LJ, Hsiao TH, Chuang EY, Chen Y. Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer BMC Genomics 2017 Oct;18. Onyeagucha B, Subbarayalu P, Abdelfattah N, Rajamanickam S, Timilsina S, Guzman R, Zeballos C, Eedunuri V, Bansal S, Mohammad T, Chen Y, Vadlamudi RK, Rao MK. Novel post-transcriptional and post-translational regulation of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 determine the fate of breast cancer cells to survive or die Oncotarget 2017 Sep;8(49). Panneerdoss S, Viswanadhapalli S, Abdelfattah N, Onyeagucha BC, Timilsina S, Mohammad TA, Chen Y, Drake M, Vuori K, Kumar TR, Rao MK. Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells Nature Communications 2017 Sep;8(1). Srivastava J, Robertson CL, Ebeid K, Dozmorov M, Rajasekaran D, Mendoza R, Siddiq A, Akiel MA, Jariwala N, Shen XN, Windle JJ, Subler MA, Mukhopadhyay ND, Giashuddin S, Ghosh S, Lai Z, Chen Y, Fisher PB, Salem AK, Sanyal AJ, Sarkar D. A novel role of astrocyte elevated gene-1 (AEG-1) in regulating nonalcoholic steatohepatitis (NASH) Hepatology 2017 Aug;66(2). Akiel M, Guo C, Li X, Rajasekaran D, Mendoza RG, Robertson CL, Jariwala N, Yuan F, Subler MA, Windle J, Garcia DK, Lai Z, Chen HH, Chen Y, Giashuddin S, Fisher PB, Wang XY, Sarkar D. IGFBP7 Deletion Promotes Hepatocellular Carcinoma Cancer Research 2017 Aug;16(4). Sanchez-Diaz PC, Chang JC, Moses ES, Dao T, Chen Y, Hung JY. Ubiquitin carboxyl-terminal esterase L1 (UCHL1) is associated with stem-like cancer cell functions in pediatric high-grade glioma PLoS One 2017 May;12(5). Zhang N, Valentine JM, Zhou Y, Li ME, Zhang Y, Bhattacharya A, Walsh ME, Fischer KE, Austad SN, Osmulski P, Gaczynska M, Shoelson SE, Van Remmen H, Chen HI, Chen Y, Liang H, Musi N. Sustained NFκB inhibition improves insulin sensitivity but is detrimental to muscle health Aging Cell 2017 May;16(4). Zhang L, Liu H, Huang Y, Wang X, Chen Y, Meng J. Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net IEEE/ACM Transactions on Computational Biology and Bioinformatics 2017 Jan;14(1). Chiu YC, Wang LJ, Lu TP, Hsiao TH, Chuang EY, Chen Y. Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival BMC bioinformatics 2017 Jan;18(1). Yao L, Liu Y, Qiu Z, Kumar S, Curran JE, Blangero J, Chen Y, Lehman DM. Molecular Profiling of Human Induced Pluripotent Stem Cell-Derived Hypothalamic Neurones Provides Developmental Insights into Genetic Loci for Body Weight Regulation Journal of neuroendocrinology 2017 Jan;29(2). Zanotto-Filho A, Masamsetti VP, Loranc E, Tonapi SS, Gorthi A, Bernard Gonaives RM, Moreira JC, Chen Y, Bishop AJ. Alkylating Agent-Induced NRF2 Blocks Endoplasmic Reticulum Stress-Mediated Apoptosis via Control of Glutathione Pools and Protein Thiol Homeostasis. Molecular cancer therapeutics Molecular cancer therapeutics 2016 Dec;15(12). Zhao Z, Ma X, Shelton SD, Sung DC, Li M, Hernandez D, Zhang M, Losiewicz MD, Chen Y, Pertsemlidis A, Yu X, Liu Y, Du L. A combined gene expression and functional study reveals the crosstalk between N-Myc and differentiation-inducing microRNAs in neuroblastoma cells Oncotarget 2016 Nov;7(48). Chiu YC, Hsiao TH, Wang LJ, Chen Y, Chuang EY. Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme IEEE/ACM Transactions on Computational Biology and Bioinformatics 2016 Nov;. Sumazin P, Chen Y, Trevino LR, Sarabia SF, Hampton OA, Patel K, Mistretta TA, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, Parsons DW, Lopez-Terrada D. Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups Hepatology 2016 Nov;65(1). Dong Q, Gao H, Shi Y, Zhang F, Gu X, Wu A, Wang D, Chen Y, Bandyopadhyay A, Yeh IT, Daniel BJ, Chen Y, Zou Y, Rebel VL, Walter CA, Lu J, Huang C, Sun LZ. Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential Aging 2016 Nov;8(11). Comerford SA, Hinnant EA, Chen Y, Bansal H, Klapproth S, Rakheja D, Finegold MJ, Lopez-Terrada D, O`Donnell KA, Tomlinson GE, Hammer RE. Hepatoblastoma modeling in mice places Nrf2 within a cancer field established by mutant β-catenin JCI Insight 2016 Oct;1(16). Wu HL, Hsiao TH, Chen PJ, Wong SH, Kao JH, Chen DS, Lu JY, Lu TP, Chen Y, Chuang EY, Tu HC, Liu CJ. Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients Scientific Reports 2016 Aug;. Ma C, Sastry KS, Flore M, Gehani S, Al-Bozom I, Feng Y, Serpedin E, Chouchane L, Chen Y, Huang Y. CrossLink: a novel method for cross-condition classification of cancer subtypes BMC Genomics 2016 Aug;17. Liu Y, Wilson D, Leach RJ, Chen Y. MBDDiff: an R package designed specifically for processing MBDcap-seq datasets BMC Genomics 2016 Aug;. Cui X, Meng J, Zhang S, Rao MK, Chen Y, Huang Y. A hierarchical model for clustering m(6)A methylation peaks in MeRIP-seq data BMC Genomics 2016 Aug;17. Chen HI, Jin Y, Huang Y, Chen Y. Detection of high variability in gene expression from single-cell RNA-seq profiling BMC Genomics 2016 Aug;17. Hsu YC, Chiu YC, Chen Y, Hsiao TH, Chuang EY. A simple gene set-based method accurately predicts the synergy of drug pairs BMC Systems Biology 2016 Aug;7(48). Rajamanickam S, Panneerdoss S, Gorthi A, Timilsina S, Onyeagucha B, Kovalskyy D, Ivanov D, Hanes MA, Vadlamudi RK, Chen Y, Bishop AJ, Arbiser JL, Rao MK. Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis Clinical Cancer Research 2016 Jul;22(14). Cui X, Meng J, Zhang S, Chen Y, Huang Y. A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data Bioinformatics 2016 Jun;32(12). Toledo RA, Qin Y, Cheng ZM, Gao Q, Iwata S, Silva GM, Prasad ML, Ocal IT, Rao S, Aronin N, Barontini M, Bruder J, Reddick RL, Chen Y, Aguiar RC, Dahia PL. Recurrent Mutations of Chromatin-Remodeling Genes and Kinase Receptors in Pheochromocytomas and Paragangliomas Clinical Cancer Research 2016 May;22(9). Elzi DJ, Song M, Blackman B, Weintraub ST, Lopez-Terrada D, Chen Y, Tomlinson GE, Shiio Y. FGF19 functions as autocrine growth factor for hepatoblastoma Genes & Cancer 2016 Mar;7(3-4). Hsiao TH, Chiu YC, Hsu PY, Lu TP, Lai LC, Tsai MH, Huang TH, Chuang EY, Chen Y. Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers Scientific Reports 2016 Mar;11(4). Wang Y, Jadhav RR, Liu J, Wilson D, Chen Y, Thompson IM, Troyer DA, Hernandez J, Shi H, Leach RJ, Huang TH, Jin VX. Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis Scientific Reports 2016 Feb;. Zanotto-Filho A, Dashnamoorthy R, Loranc E, de Souza LH, Moreira JC, Suresh U, Chen Y, Bishop AJ. Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human PLoS One 2016 Jan;11(4). Sareddy GR, Zhang Q, Wang R, Scott E, Zou Y, O'Connor JC, Chen Y, Dong Y, Vadlamudi RK, Brann D,. Proline-, glutamic acid-, and leucine-rich protein 1 mediates estrogen rapid signaling and neuroprotection in the brain Proceedings of the National Academy of Sciences of the United States of America 2015 Dec;112(48). Horning AM, Awe JA, Wang CM, Liu J, Lai Z, Wang VY, Jadhav RR, Louie AD, Lin CL, Kroczak T, Chen Y, Jin VX, Abboud-Werner SL, Leach RJ, Hernandez J, Thompson IM, Saranchuk J, Drachenberg D, Chen CL, Mai S, Huang TH. DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence The Prostate 2015 Nov;75(15). Elzi DJ, Song M, Houghton PJ, Chen Y, Shiio Y. The role of FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1, in Ewing sarcoma 2015 Nov;6(11-12). Chuang MK, Chiu YC, Chou WC, Hou HA, Tseng MH, Kuo YY, Chen Y, Chuang EY, Tien HF. An mRNA expression signature for prognostication in de novo acute myeloid leukemia patients with normal karyotype Oncotarget 2015 Oct;6(36). Liu XS, Genet MD, Haines JE, Mehanna EK, Wu S, Chen HI, Chen Y, Qureshi AA, Han J, Chen X, Fisher DE, Pandolfi PP, Yuan ZM. ZBTB7A Suppresses Melanoma Metastasis by Transcriptionally Repressing MCAM Molecular Cancer Research 2015 Aug;13(8). Chen HI, Liu Y, Zou Y, Lai Z, Sarkar D, Huang Y, Chen Y. Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads BMC Genomics 2015 Jun;16. Chiu YC, Wu CT, Hsiao TH, Lai YP, Hsiao C, Chen Y, Chuang EY. Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes BMC Genomics 2015 Jun;7. Zhao Z, Ma X, Sung D, Li M, Kosti A, Lin G, Chen Y, Pertsemlidis A, Hsiao TH, Du L. microRNA-449a functions as a tumor suppressor in neuroblastoma through inducing cell differentiation and cell cycle arrest RNA Biology 2015 May;12(5):538-554. Cui X, Meng J, Rao MK, Chen Y, Huang Y. HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data BMC Genomics 2015 Apr;16. Chiu YC, Hsiao TH, Chen Y, Chuang EY. Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers BMC Genomics 2015 Apr;16. Srivastava J, Siddiq A, Gredler R, Shen XN, Rajasekaran D, Robertson CL, Subler MA, Windle JJ, Dumur CI, Mukhopadhyay ND, Garcia D, Lai Z, Chen Y, Balaji U, Fisher PB, Sarkar D.. Astrocyte elevated gene-1 and c-Myc cooperate to promote hepatocarcinogenesis in mice Hepatology 2015 Mar;61(3). Kosti A, Harry Chen HI, Mohan S, Liang S, Chen Y, Habib SL. Microarray profile of human kidney from diabetes, renal cell carcinoma and renal cell carcinoma with diabetes Genes & Cancer 2015 Jan;6(1-2):62-70. Zhou Y, Chen HI, Lin AL, Dang H, Haack K, Cole SA, Huang Y, Yu H, Chen Y, Yeh CK. Early gene expression in salivary gland after isoproterenol treatment J Cell Biochem 2014 Oct;116(3):431-437. Mao Z, Ma C, Huang TH, Chen Y, Huang Y. BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data BMC Bioinformatics 2014 Oct;. Antonarakis ES, Lu C, Wang H, Luber B, Nakazawa M, Roeser JC, Chen Y, Mohammad TA, Chen Y, Fedor HL, Lotan TL, Zheng Q, De Marzo AM, Isaacs JT, Isaacs WB, Nadal R, Paller CJ, Denmeade SR, Carducci MA, Eisenberger MA, Luo J. AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer N Engl J Med 2014 Sep;371(10):1028-1038. Fok W.C., Livi CB, Bokov A, Yu Z., Chen Y, Richardson AG, Perez VI. Short-term rapamycin treatment in mice has few effects on the transcriptome of white adipose tissue compared to dietary restriction Mech Ageing Dev 2014 Sep;140:23-29. Flores M, Chen Y, Huang Y. TraceRNA: a web application for competing endogenous RNA exploration Circ Cardiovasc Genet 2014 Aug;7(4). Abraham J, Nu?ez-Alvarez Y, Hettmer S, Carrio E, Chen HI, Nishijo K, Huang ET, Prajapati SI, Walker RL, Davis S, Rebeles J, Wiebush H, McCleish AT, Hampton ST, Bjornson CR, Brack AS, Wagers AJ, Rando TA, Capecchi MR, Marini FC, Ehler BR, Zarzabal LA, Goros MW, Michalek JE, Meltzer PS, Langenau DM, LeGallo RD, Mansoor A, Chen Y, Suelves M, Rubin BP, Keller C. Lineage of origin in rhabdomyosarcoma informs pharmacological response Genes Dev 2014 Jul;28(14). Zhao Z, Ma, Xiuye, Hsiao, Tzu-Hung, Lin, Gregory, Kosti, Adam, Yu, Xiaojie, Suresh, Uthra, Chen Y, Tomlinson GE, Pertsemlidis A, Du L. A high-content morphological screen identifies novel microRNAs that regulate neuroblastoma cell differentiation OncoTarget 2014 May;15;5(9):2499-2512. Fok, Wilson C, Bokov A, Gelfond JA, Yu, Zhen, Zhang Y, Doderer, Mark, Chen Y, Javors MA, Wood, William, Zhang, Yongqing, Becker, Kevin G, Richardson AG, Perez, Viviana I. Combined treatment of rapamycin and dietary restriction has a larger effect on the transcriptome and metabolome of liver Aging Cell 2014 Apr;13(2):311-319. Pan H, Qin K, Guo Z, Ma Y, April C, Gao X, Andrews TG, Bokov A, Zhang J, Chen Y, Weintraub ST, Fan J-B, Wang D, Hu Y, Aune GJ, Lindsey ML, Li R. Negative elongation factor controls energy homeostasis in cardiomyocytes Cell Reports 2014 Mar;7(1):79-85. Fok, Wilson C, Chen Y, Bokov A, Zhang Y, Salmon A, Diaz, Vivian, Javors MA, Becker, KG, Zhang, Yongqing, Becker, KG, Perez VI, Richardson AG. Mice Fed Rapamycin Have an Increase in Lifespan Associated with Major Changes in the Liver Transcriptome PLoS One 2014 Jan;9(1):e83988-e83988.