Yan Xu, PhD

Director of Bioinformatics Core, Neonatology & Pulmonary Biology
Perinatal Institute
Professor, UC Department of Pediatrics
UC Department of Biomedical Informatics

yan.xu@cchmc.org

About

Biography

Dr. Xu’s research interest is to develop and apply bioinformatics and systems biology approaches to gain a better understanding of molecular mechanisms behind big data sets. Her current lines of research are focusing on the identification of gene signatures, regulatory networks, and biological pathways controlling lung maturation and diseases.

She is actively involved in using high-throughput single cell genomics for the development of LungMAP, a web-based data resource funded by the National Heart, Lung and Blood Institute to provide useful tools and resources for the lung research community.

Interests

Yan Xu: main area of research interests are bioinformatics and systems biology application in pulmonary research. Our current focus is to systemically identify the critical components in the transcriptional/signaling programs and determine genetic networks regulating lung maturation, surfactant homeostasis, lung cell type specific signaling and asthma associated pathology. We applied systems biology approach that integrates expression profiling with expression-independent data resources including protein interaction, functional annotation, promoter and literature mining to enable the elucidation of genetic networks. Important regulator-target relationships will be selected for experimental validation in vivo and in vitro through collaborations with experimental biologists.

Research Areas

Publications

In situ treatment with a TLR9 agonist virus-like particle to promote immune responses against oral epithelial dysplasia progression. Xu, Y; Mcmillan, A; Gupta, N; Lemke-Miltner, CD; Rataan, AO; Areecheewakul, S; Bhat, DS; Lanzel, EA; Geary, SM; Simons, AL; Weiner, GJ; Salem, AK. Cancer Immunology, Immunotherapy. 2025; 74:189.

Wnt5a and Notum influence the temporal dynamics of cartilaginous mesenchymal condensations in developing trachea. Bottasso-Arias, N; Mohanakrishnan, M; Trovillion, S; Burra, K; Russell, NX; Wu, Y; Xu, Y; Sinner, D. Frontiers in Cell and Developmental Biology. 2025; 13:1523833.

Development of a 3D bioengineered human lung submucosal gland ductal airway model to study mucociliary clearance in vitro. Kim, H; Yi, S; Liyanage, P; Zhao, S; Wikenheiser-Brokamp, KA; McMillin, L; Xu, Y; Kitzmiller, JA; Whitsett, JA; Naren, AP; Mun, KS. 2025; 1:100013.

3D bioprinted ferret mesenchymal stem cell-laden cartilage grafts for laryngotracheal reconstruction in a ferret surgical model. McMillan, A; Hoffman, MR; Xu, Y; Wu, Z; Thayer, E; Peel, A; Guymon, A; Kanotra, S; Salem, AK. Biomaterials Science. 2025; 13:1304-1322.

Targeting transforming growth factor-β1 by methylseleninic acid/seleno-L-methionine in clear cell renal cell carcinoma: Mechanisms and therapeutic potential. Rataan, AO; Xu, Y; Geary, SM; Zakharia, Y; Kamel, ES; Rustum, YM; Salem, AK. Cancer Treatment and Research Communications. 2025; 42:100864.

PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. He, H; Bell, SM; Davis, AK; Zhao, S; Sridharan, A; Na, CL; Guo, M; Xu, Y; Snowball, J; Swarr, DT; Zacharias, WJ; Whitsett, JA. Nature Communications. 2024; 15:8112.

ISG12a promotes immunotherapy of HBV-associated hepatocellular carcinoma through blocking TRIM21/AKT/β-catenin/PD-L1 axis. Deng, R; Tian, R; Li, X; Xu, Y; Li, Y; Wang, X; Li, H; Wang, L; Xu, B; Yang, D; Tang, S; Xue, B; Zuo, C; Zhu, H. iScience. 2024; 27:109533.

Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Bhattacharya, S; Myers, JA; Baker, C; Guo, M; Danopoulos, S; Myers, JR; Bandyopadhyay, G; Romas, ST; Huyck, HL; Misra, RS; Whitsett, JA; Xu, Y; Pryhuber, GS; Mariani, TJ. Genes. 2024; 15:298.

PZR suppresses innate immune response to RNA viral infection by inhibiting MAVS activation in interferon signaling mediated by RIG-I and MDA5. Deng, R; Zhang, L; Chen, S; Li, X; Xue, B; Li, H; Xu, Y; Tian, R; Liu, Q; Wang, L; Liu, S; Yang, D; Li, P; Tang, S; Zhu, H. Antiviral Research. 2024; 222:105797.

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; Xu, Y; Tickle, T; Aronow, BJ; Salomonis, N. American Journal of Respiratory Cell and Molecular Biology. 2024; 70:129-139.