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


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; et al. American Journal of Respiratory Cell and Molecular Biology. 2022.

The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Stevens, J; Steinmeyer, S; Bonfield, M; Peterson, L; Wang, T; Gray, J; Lewkowich, I; Xu, Y; Du, Y; Guo, M; et al. Science Translational Medicine. 2022; 14.

Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; et al. Science Translational Medicine. 2022; 14.

BMP4 and Wnt signaling interact to promote mouse tracheal mesenchyme morphogenesis. Bottasso-Arias, N; Leesman, L; Burra, K; Snowball, J; Shah, R; Mohanakrishnan, M; Xu, Y; Sinner, D. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2022; 322:L224-L242.

A census of the lung: CellCards from LungMAP. Sun, X; Perl, AK; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; et al. Developmental Cell. 2022; 57:112-145.e2.

YAP regulates alveolar epithelial cell differentiation and AGER via NFIB/KLF5/NKX2-1. Gokey, JJ; Snowball, J; Sridharan, A; Sudha, P; Kitzmiller, JA; Xu, Y; Whitsett, JA. iScience. 2021; 24.

Generation of Pulmonary Endothelial Progenitor Cells for Cell-based Therapy Using Interspecies Mouse-Rat Chimeras. Wang, G; Wen, B; Ren, X; Li, E; Zhang, Y; Guo, M; Xu, Y; Whitsett, JA; Kalin, TV; Kalinichenko, VV. American Journal of Respiratory and Critical Care Medicine. 2021; 204:326-338.

Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease. Sitaraman, S; Martin, EP; Na, CL; Zhao, S; Green, J; Deshmukh, H; Perl, AK T; Bridges, JP; Xu, Y; Weaver, TE. JCI insight. 2021; 6.

Pretreatment of aged mice with retinoic acid supports alveolar regeneration via upregulation of reciprocal PDGFA signalling. Gokey, JJ; Snowball, J; Green, J; Waltamath, M; Spinney, JJ; Black, KE; Hariri, LP; Xu, Y; Perl, AK. Thorax. 2021; 76:456-467.

FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Milewski, D; Shukla, S; Gryder, BE; Pradhan, A; Donovan, J; Sudha, P; Vallabh, S; Pyros, A; Xu, Y; Barski, A; et al. Oncogene. 2021; 40:2182-2199.

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