Yan Xu, PhD

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

Academic Affiliations

Professor, UC Department of Pediatrics

UC Department of Biomedical Informatics

Phone 513-636-8921

Fax 513-636-7868

Email yan.xu@cchmc.org

Bioinformatics; systems biology application in pulmonary research; lung cell type specific signaling; asthma associated pathology

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.

View PubMed Publications

Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y. Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. BMC Med Genomics. 2015;8(1):67.

Guo M, Wang H, Potter SS, Whitsett JA, Xu Y. SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis. PLoS Comput Biol. 2015;11(11):e1004575.

Du Y, Guo M, Whitsett JA, Xu Y. 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung. Thorax. 2015 Jun 30.

Xu Y, Wang Y, Besnard V, Ikegami M, Wert SE, Heffner C, Murray SA, Donahue LR, Whitsett JA. Transcriptional programs controlling perinatal lung maturation. PLoS One. 2012;7(8):e37046.

Xu Y, Zhang M, Wang Y, Kadambi P, Dave V, Lu LJ, Whitsett JA. A systems approach to mapping transcriptional networks controlling surfactant homeostasis. BMC Genomics. 2010;11(1):451.

“Lung Map” Atlas Research Center. Co-Investigator. National Heart, Lung, and Blood Institute. Jan 2014-Jan 2019.

Transcriptional Programming of Asthma Related Pathology in Respiratory Epithelial. Co-Investigator. National Heart, Lung, and Blood Institute. Apr 2013-Mar 2018.

Airway Progenitor Cell Proliferation and Differentiation During Lung Repair. Co-Investigator. National Heart, Lung, and Blood Institute. Jan 2012-Dec 2016.

Mechanisms Underlying DICER1 Suppression of Pleuropulmonary Blastoma. Co-Investigator. St. Baldrick's Foundation. Jul 2011-Jun 2016.

Stard7, a Novel Inhibitor of Allergic Lung Disease. Co-Investigator. National Institutes of Health/National Heart, Lung, and Blood Institute. Dec 2013-Nov 2018. HL122130.

Matrix fibroblasts are required for alveolar homeostasis and regrowth. Co-Investigator. National Institutes of Health/National Heart, Lung, and Blood Institute. Sep 2015-Aug 2016. R56 HL123969.

Transcriptional regulation of pulmonary fibrosis. Co-Investigator. National Institutes of Health/National Heart, Lung, and Blood Institute. Sep 2015-Aug 2016. R56 HL126660.