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

Pulmonary Biology, Biomedical Informatics

Publications

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.

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:eabl3981.

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:eabl8574.

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.