Xu Lab

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

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

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

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

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

Muus, C; Luecken, MD; Eraslan, G; Sikkema, L; Waghray, A; Heimberg, G; Kobayashi, Y; Vaishnav, ED; Subramanian, A; Smillie, C; et al. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine. 2021; 27:546-559.

Wen, B; Li, E; Ustiyan, V; Wang, G; Guo, M; Na, CL; Kalin, GT; Galvan, V; Xu, Y; Weaver, TE; et al. In Vivo Generation of Lung and Thyroid Tissues from Embryonic Stem Cells Using Blastocyst Complementation. American Journal of Respiratory and Critical Care Medicine. 2021; 203:471-483.

Du, Y; Ouyang, W; Kitzmiller, JA; Guo, M; Zhao, S; Whitsett, JA; Xu, Y. Lung Gene Expression Analysis Web Portal Version 3: Lung-at-a-Glance. American Journal of Respiratory Cell and Molecular Biology. 2021; 64:146-149.

Guo, M; Yu, JJ; Perl, AK; Wikenheiser-Brokamp, KA; Riccetti, M; Zhang, EY; Sudha, P; Adam, M; Potter, A; Kopras, EJ; et al. Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell. American Journal of Respiratory and Critical Care Medicine. 2020; 202:1373-1387.

Wang, A; Chiou, J; Poirion, OB; Buchanan, J; Valdez, MJ; Verheyden, JM; Hou, X; Kudtarkar, P; Narendra, S; Newsome, JM; et al. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes. eLife. 2020; 9.

Hudock, KM; Collins, MS; Imbrogno, M; Snowball, J; Kramer, EL; Brewington, JJ; Gollomp, K; McCarthy, C; Ostmann, AJ; Kopras, EJ; et al. Neutrophil extracellular traps activate IL-8 and IL-1 expression in human bronchial epithelia. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2020; 319:L137-L147.

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

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

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

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

Ren, X; Ustiyan, V; Guo, M; Wang, G; Bolte, C; Zhang, Y; Xu, Y; Whitsett, JA; Kalin, TV; Kalinichenko, VV. Postnatal Alveologenesis Depends on FOXF1 Signaling in c-KIT+ Endothelial Progenitor Cells. American Journal of Respiratory and Critical Care Medicine. 2019; 200:1164-1176.

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

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

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

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

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

Whitsett, JA; Kalin, TV; Xu, Y; Kalinichenko, VV. Building and Regenerating the Lung Cell by Cell. Physiological Reviews. 2019; 99:513-554.

Kyle, JE; Clair, G; Bandyopadhyay, G; Misra, RS; Zink, EM; Bloodsworth, KJ; Shukla, AK; Du, Y; Lillis, J; Myers, JR; et al. Cell type-resolved human lung lipidome reveals cellular cooperation in lung function. Scientific Reports. 2018; 8.

Ustiyan, V; Bolte, C; Zhang, Y; Han, L; Xu, Y; Yutzey, KE; Zorn, AM; Kalin, TV; Shannon, JM; Kalinichenko, VV. FOXF1 transcription factor promotes lung morphogenesis by inducing cellular proliferation in fetal lung mesenchyme. Developmental Biology. 2018; 443:50-63.

Bandyopadhyay, G; Huyck, HL; Misra, RS; Bhattacharya, S; Wang, Q; Mereness, J; Lillis, J; Myers, JR; Ashton, J; Bushnell, T; et al. Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2018; 315:L576-L583.

Gokey, JJ; Snowball, J; Sridharan, A; Speth, JP; Black, KE; Hariri, LP; Perl, AT; Xu, Y; Whitsett, JA. MEG3 is increased in idiopathic pulmonary fibrosis and regulates epithelial cell differentiation. JCI insight. 2018; 3.

Black, M; Milewski, D; Le, T; Ren, X; Xu, Y; Kalinichenko, VV; Kalin, TV. FOXF1 Inhibits Pulmonary Fibrosis by Preventing CDH2-CDH11 Cadherin Switch in Myofibroblasts. Cell Reports. 2018; 23:442-458.

Gokey, JJ; Sridharan, A; Xu, Y; Green, J; Carraro, G; Stripp, BR; Perl, AT; Whitsett, JA. Active epithelial Hippo signaling in idiopathic pulmonary fibrosis. JCI insight. 2018; 3.

Guo, M; Xu, Y. Single-Cell Transcriptome Analysis Using SINCERA Pipeline. Methods in Molecular Biology. 2018; 1751:209-222.

Rindler, TN; Stockman, CA; Filuta, AL; Brown, KM; Snowball, JM; Zhou, W; Veldhuizen, R; Zink, EM; Dautel, SE; Clair, G; et al. Alveolar injury and regeneration following deletion of ABCA3. JCI insight. 2017; 2.

Tang, X; Snowball, JM; Xu, Y; Na, C; Weaver, TE; Clair, G; Kyle, JE; Zink, EM; Ansong, C; Wei, W; et al. EMC3 coordinates surfactant protein and lipid homeostasis required for respiration. Journal of Clinical Investigation. 2017; 127:4314-4325.

Ardini-Poleske, ME; Clark, RF; Ansong, C; Carson, JP; Corley, RA; Deutsch, GH; Hagood, JS; Kaminski, N; Mariani, TJ; Potter, SS; et al. LungMAP: The Molecular Atlas of Lung Development Program. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2017; 313:L733-L740.

Endale, M; Ahlfeld, S; Bao, E; Chen, X; Green, J; Bess, Z; Weirauch, M; Xu, Y; Perl, AK. Dataset on transcriptional profiles and the developmental characteristics of PDGFRα expressing lung fibroblasts. Data in Brief. 2017; 13:415-431.

Endale, M; Ahlfeld, S; Bao, E; Chen, X; Green, J; Bess, Z; Weirauch, MT; Xu, Y; Perl, AK. Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development. Developmental Biology. 2017; 425:161-175.

Du, Y; Kitzmiller, JA; Sridharan, A; Perl, AK; Bridges, JP; Misra, RS; Pryhuber, GS; Mariani, TJ; Bhattacharya, S; Guo, M; et al. Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax. 2017; 72:481-484.

Guo, M; Bao, EL; Wagner, M; Whitsett, JA; Xu, Y. SLICE: determining cell differentiation and lineage based on single cell entropy. Nucleic Acids Research. 2017; 45.

Guo, M; Tomoshige, K; Meister, M; Muley, T; Fukazawa, T; Tsuchiya, T; Karns, R; Warth, A; Fink-Baldauf, IM; Nagayasu, T; et al. Gene signature driving invasive mucinous adenocarcinoma of the lung. EMBO Molecular Medicine. 2017; 9:462-481.