A photo of Yan Xu.

Director of Bioinformatics Core, Neonatology & Pulmonary Biology; Perinatal Institute

Professor, UC Department of PediatricsUC Department of Biomedical Informatics



Biography & Affiliation


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.

Research 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.

Academic Affiliation

Professor, UC Department of PediatricsUC Department of Biomedical Informatics


Pulmonary Biology, Biomedical Informatics

Blog Posts


BS: Pharmacology, Shanghai Medical University, China, 1986.

MS: Pathology, Shanghai Medical University, China, 1989.

PhD: Molecular and Cellular Pharmacology, University of South Alabama, Mobile, Alabama, 1997.


SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Sungnak, W; Huang, N; Bécavin, C; Berg, M; Queen, R; Litvinukova, M; Talavera-López, C; Maatz, H; Reichart, D; Sampaziotis, F; et al. Nature Medicine. 2020; 26:681-687.

Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Oherle, K; Acker, E; Bonfield, M; Wang, T; Gray, J; Lang, I; Bridges, J; Lewkowich, I; Xu, Y; Ahlfeld, S; et al. Immunity. 2020; 52:275-294.e9.

Dosing and formulation of antenatal corticosteroids for fetal lung maturation and gene expression in rhesus macaques. Schmidt, AF; Kannan, PS; Bridges, JP; Filuta, A; Lipps, D; Kemp, M; Miller, LA; Kallapur, SG; Xu, Y; Whitsett, JA; et al. Scientific Reports. 2019; 9.

Postnatal alveologenesis depends on FOXF1 signaling in c-KIT1 endothelial progenitor cells. Ren, X; Ustiyan, V; Guo, M; Wang, G; Bolte, C; Zhang, Y; Xu, Y; Whitsett, JA; Kalin, TV; Kalinichenko, VV. American Journal of Respiratory and Critical Care Medicine. 2019; 200:1164-1176.

Identification of the Lymphangioleiomyomatosis Cell and Its Uterine Origin. Guo, M; Yu, JJ; Perl, AK; Wikenheiser-Brokamp, KA; Riccetti, M; Zhang, EY; Sudha, P; Adam, M; Potter, A; Kopras, EJ; et al. 2019.

Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung. Du, Y; Clair, GC; Al Alam, D; Danopoulos, S; Schnell, D; Kitzmiller, JA; Misra, RS; Bhattacharya, S; Warburton, D; Mariani, TJ; et al. American Journal of Physiology: Lung Cellular and Molecular Physiology. 2019; 317:L347-L360.

The effect of adenotonsillectomy on ventilatory control in children with obstructive sleep apnea. Domany, KA; He, Z; Nava-Guerra, L; Khoo, MC K; Xu, Y; Hossain, MM; DiFrancesco, M; McConnell, K; Amin, RS. Sleep. 2019; 42.

BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. Prasse, A; Binder, H; Schupp, JC; Kayser, G; Bargagli, E; Jaeger, B; Hess, M; Rittinghausen, S; Vuga, L; Lynn, H; et al. American Journal of Respiratory and Critical Care Medicine. 2019; 199:622-630.

Spatial distribution of marker gene activity in the mouse lung during alveolarization. Ljungberg, MC; Sadi, M; Wang, Y; Aronow, BJ; Xu, Y; Kao, RJ; Liu, Y; Gaddis, N; Ardini-Poleske, ME; Umrod, T; et al. Data in Brief. 2019; 22:365-372.

Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth. Guo, M; Du, Y; Gokey, JJ; Ray, S; Bell, SM; Adam, M; Sudha, P; Perl, AK; Deshmukh, H; Potter, SS; et al. Nature Communications. 2019; 10:37-37.