A photo of Yan Xu.

Yan Xu, PhD

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



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.

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.


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

Pulmonary Biology, Biomedical Informatics


Guided construction of single cell reference for human and mouse lung. Guo, M; Morley, MP; Jiang, C; Wu, Y; Li, G; Du, Y; Zhao, S; Wagner, A; Cakar, AC; Kouril, M; et al. Nature Communications. 2023; 14:4566.

Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis. Uehara, Y; Tanaka, Y; Zhao, S; Nikolaidis, NM; Pitstick, LB; Wu, H; Yu, JJ; Zhang, E; Hasegawa, Y; Noel, JG; et al. Nature Communications. 2023; 14:1205.

Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling. Bian, F; Lan, YW; Zhao, S; Deng, Z; Shukla, S; Acharya, A; Donovan, J; Le, T; Milewski, D; Bacchetta, M; et al. Nature Communications. 2023; 14:2560.

Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia. Guo, M; Wikenheiser-Brokamp, KA; Kitzmiller, JA; Jiang, C; Wang, G; Wang, A; Preissl, S; Hou, X; Buchanan, J; Karolak, JA; et al. American Journal of Respiratory and Critical Care Medicine. 2023; 208:709-725.

An integrated cell atlas of the lung in health and disease. Sikkema, L; Ramírez-Suástegui, C; Strobl, DC; Gillett, TE; Zappia, L; Madissoon, E; Markov, NS; Zaragosi, LE; Ji, Y; Ansari, M; et al. Nature Medicine. 2023; 29:1563-1577.

Single-cell multiomic analysis identifies a HOX-PBX gene network regulating the survival of lymphangioleiomyomatosis cells. Olatoke, T; Wagner, A; Astrinidis, A; Zhang, EY; Guo, M; Zhang, AG; Mattam, U; Kopras, EJ; Gupta, N; Smith, EP; et al. Science Advances. 2023; 9:eadf8549.

Upregulation of acid ceramidase contributes to tumor progression in tuberous sclerosis complex. Astrinidis, A; Li, C; Zhang, EY; Zhao, X; Zhao, S; Guo, M; Olatoke, T; Mattam, U; Huang, R; Zhang, AG; et al. JCI insight. 2023; 8:e166850.

Estradiol Augments Tumor-Induced Neutrophil Production to Promote Tumor Cell Actions in Lymphangioleiomyomatosis Models. Minor, BM N; LeMoine, D; Seger, C; Gibbons, E; Koudouovoh, J; Taya, M; Kurtz, D; Xu, Y; Hammes, SR. Endocrinology. 2023; 164:bqad061.

Alpha-1 antitrypsin limits neutrophil extracellular trap disruption of airway epithelial barrier function. Hudock, KM; Collins, MS; Imbrogno, MA; Kramer, EL; Brewington, JJ; Ziady, A; Zhang, N; Snowball, J; Xu, Y; Carey, BC; et al. Frontiers in Immunology. 2023; 13:1023553.

Lymphangioleiomyomatosis (LAM) Cell Atlas. Du, Y; Guo, M; Wu, Y; Wagner, A; Perl, AK; Wikenheiser-Brokamp, K; Yu, J; Gupta, N; Kopras, E; Krymskaya, V; et al. Thorax. 2023; 78:85-87.

From the Blog

LungMAP Adds More Single-Cell References
Tools for Science

LungMAP Adds More Single-Cell References

Yan Xu, PhD9/8/2023