News and updates:

• 9-29-2022: New Team Member We are happy to announce that Adnan Cihan Cakar joined our team as an analyst and a web developer. To meet the rest of our team check out About Us.
• 9-29-2022: New Team Member We are happy to announce that Jiang Cheng joined our team as an analyst. To meet the rest of our team check out About Us.
• 9-29-2022: New Team Member We are happy to announce that Ashley Kuenzi Davis joined our team as an analyst. To meet the rest of our team check out About Us.
• 9-29-2022: New web development Check out LAM Cell Atlas Web-Portal (LCA) for LAM projects and datasets with lung, kidney and uterus cells from LAM patients.
• 9-29-2022: New publication Stevens J, Steinmeyer S, Bonfield M, Peterson L, Wang T, Gray J, Lewkowich I, Xu Y, Du Y, Guo M, Wynn JL, Zacharias W, Salomonis N, Miller L, Chougnet C, O'Connor DH, Deshmukh H. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Sci Transl Med 2022; 14: eabl3981. PubMed bioRxiv
• 9-29-2022: New publicationDu Y, Guo M, Wu Y, Wagner A, Perl AK, Wikenheiser-Brokamp K, Yu J, Gupta N, Kopras E, Krymskaya V, Obraztsova K, Tang Y, Kwiatkowski D, Henske EP, McCormack F, Xu Y. Lymphangioleiomyomatosis (LAM) Cell Atlas. Thorax 2022: thoraxjnl-2022-218772
• 9-29-2022: New publicationGuo M, Morley MP, Wu Y, Du Y, Zhao S, Wagner A, Kouril M, Jin K, Gaddis N, Kitzmiller JA, Stewart K, Basil MC, Lin SM, Ying Y, Babu A, Wikenheiser-Brokamp KA, Mun KS, Naren AP, Lin S, Clair G, Adkins JN, Pryhuber GS, Misra RS, Aronow BJ, Tickle TL, Salomonis N, Sun X, Morrisey EE, Whitsett JA, Xu Y, Consortium NL. Guided construction of single cell reference for human and mouse lung. bioRxiv 2022: 2022.2005.2018.491687
• 9-29-2022: New publicationToth A, Steinmeyer S, Kannan P, Gray J, Jackson CM, Mukherjee S, Demmert M, Sheak JR, Benson D, Kitzmiller J, Wayman JA, Presicce P, Cates C, Rubin R, Chetal K, Du Y, Miao Y, Gu M, Guo M, Kalinichenko VV, Kallapur SG, Miraldi ER, Xu Y, Swarr D, Lewkowich I, Salomonis N, Miller L, Sucre JS, Whitsett JA, Chougnet CA, Jobe AH, Deshmukh H, Zacharias WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Sci Transl Med 2022; 14: eabl8574. PubMed bioRxiv
• 9-29-2022: New publicationSun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE, Consortium NL. A census of the lung: CellCards from LungMAP. Dev Cell 2022; 57: 112-145 e112. PubMed
• 9-29-2022: New publicationBottasso-Arias N, Leesman L, Burra K, Snowball J, Shah R, Mohanakrishnan M, Xu Y, Sinner D. BMP4 and Wnt signaling interact to promote mouse tracheal mesenchyme morphogenesis. Am J Physiol Lung Cell Mol Physiol 2022; 322: L224-L242. AJPLCMP PubMed
• 1-1-2022: New publicationGokey 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 signaling.. Thorax 2021; 76: 456-467. thoraxjnl PubMed
• 1-1-2022: New publicationDu Y, Ouyang W, Kitzmiller JA, Guo M, Zhao S, Jeffrey A Whitsett JA, Xu Y. Lung Gene Expression Analysis (LGEA) Web Portal v3: Lung at a Glance. AJRCMB. 2021. AJRCMB PubMed bioRxiv
• 1-1-2022: New publicationWen B, Li E, Ustiyan V, Wang G, Guo M, Na CL, Kalin GT, Galvan V, Xu Y, Weaver TE, Kalin TV, Whitsett JA, Kalinichenko VV. In Vivo Generation of Lung and Thyroid Tissues from Embryonic Stem Cells Using Blastocyst Complementation. Am J Respir Crit Care Med 2021; 203: 471-483. AJRCMB PubMed
• 1-1-2022: New publicationWang 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. Am J Respir Crit Care Med 2021; 204: 326-338. PubMed
• 1-1-2022: New publicationSitaraman S, Martin EP, Na CL, Zhao S, Green J, Deshmukh H, Perl AT, Bridges JP, Xu Y, Weaver TE. Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease. . JCI Insight 2021; 6. JCI PubMed
• 1-1-2022: New publicationMilewski D, Shukla S, Gryder BE, Pradhan A, Donovan J, Sudha P, Vallabh S, Pyros A, Xu Y, Barski A, Szabo S, Turpin B, Pressey JG, Millay DP, Khan J, Kalinichenko VV, Kalin TV. FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene 2021; 40: 2182-2199. Nature PubMed
• 1-1-2022: New publicationGokey 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: 102967. PubMed
• 2-5-2021: New web development Check out LGEA (LungMAP phase 2) for more datasets from normal and disease lungs.
• 1-4-2021: New publication 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. Am J Respir Cell Mol Biol. 2021 Jan;64(1):146-149. AJRCMB PubMed bioRxiv
• 12-8-2020: New web development LGEA provides query links to access DESCARTES (Human Gene Expression During Development) website in LungDTC panel.
• 7-1-2020: New publication Basil MC, Katzen J, Engler AE, Guo M, Herriges MJ, Kathiriya JJ, Windmueller R, Ysasi AB, Zacharias WJ, Chapman HA, Kotton DN, Rock JR, Snoeck HW, Vunjak-Novakovic G, Whitsett JA, Morrisey EE. The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future. Cell Stem Cell. 2020 Apr 2;26(4):482-502. PubMed PubMed Central
• 6-18-2020: Our recent research activities related to SARS-CoV-2 Sungnak W, et al, and Network HCALB. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med 26: 681-687, 2020. Drs. Jeffrey Whitsett, Xin Sun, Yan Xu and Minzhe Guo from LungMAP are involved in this study, investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNAseq data from healthy human donors. Access these data at www.covid19cellatlas.org
• 6-18-2020: Our recent research activities related to SARS-CoV-2 Muus C, et al. Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells. bioRxiv 2020.
• 6-18-2020: Our recent research activities related to SARS-CoV-2 Wang A, et al. Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection. bioRxiv 2020.
• 6-18-2020: New publication Guo M, Yu JJ, Perl AK, Wikenheiser-Brokamp KA, Riccetti M, Zhang EY, Sudha P, Adam M, Potter A, Kopras EJ, Giannikou K, Potter SS, Sherman S, Hammes SR, Kwiatkowski DJ, Whitsett JA, McCormack FX, and Xu Y. Identification of the lymphangioleiomyomatosis cell and its uterine origin. Am J Respir Crit Care Med. In press. 2020. bioRxiv AJRCCM PubMed
• 6-18-2020: New publication J. P. Bridges, P. Sudha, D. Lipps, M. Guo, Y. Du, K. Brown, A. Filuta, Joseph Kitzmiller, C. Stockman, X. Chen, Alan H. Jobe, J. Whitsett, M. Weirauch, and Y. Xu. Glucocorticoid Dependent Mesenchymal Cell Differentiation is Required for Perinatal Lung Morphogenesis and Lung Function. Am J Physiol Lung Cell Mol Physiol. 2020. AJP-Lung
• 6-18-2020: New publication Oherle K, Acker E, Bonfield M, Wang T, Gray J, Lang I, Bridges J, Lewkowich I, Xu Y, Ahlfeld S, Zacharias W, Alenghat T, and Deshmukh H. Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity 52: 275-294 e279, 2020.PubMed
• 11-4-2019: Dr. whitsett and Dr. Wert's manuscript : "Comprehensive Anatomic Ontologies for Lung Development: A Comparison of Alveolar Formation and Maturation within Mouse and Human Lung" has been published online. <PubMed>
• 7-9-2019: Check out our recent publication: Integration of Transcriptomic and Proteomic Data Identifies Biological Functions in Cell Populations From Human Infant Lung.
• 4-23-2019: New analyses of mouse sorted cells at PND1 and PND 14 are available in LungSortedCell Panel.
• 3-18-2019: ATS Webinar on the LungMAP PART 1 & PART 2.
• 2-6-2019: LGEA added in mouse E16.5 dropseq dataset, mouse PND7 dropseq dataset, and mouse PND28 dropseq dataset.
• 1-23-2019: LGEA added in a study of A revised airway epithelial hierarchy includes CFTR-expressing ionocytes from Rajagopal Lab in LGEA-ExternalData panel. Check out its analyses: Gene query(dropseq), Cell type query(dropseq), Gene query(C1 scRNA-seq), Cell type query(C1 scRNA-seq) and Gene query(pulse-seq).
• 1-3-2019: Check out our recent publication, "Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth" published in Nature Communication.
• 11-20-2018: Check out our recent publication: Whitsett, Jeffrey A., et al. Building and Regenerating the Lung Cell by Cell. Physiological reviews 99.1 (2018): 513-554.
• 10-29-2018: LGEA added in a study of Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung from Morrisey's Lab in LGEA-ExternalData panel. Check out its analyses: Gene query and Cell type query.
• 9-10-2018: LGEA added in mouse PND3 dropseq dataset and human PND1 dropseq dataset.
  
• 9-7-2018: Check out our recent publication MEG3 is increased in idiopathic pulmonary fibrosis and regulates epithelial cell differentiation. .
  
• 8-13-2018: Video: SLICE and single cell Entrope -- Dr.Minzhe Guo.
  
• 5-31-2018: LGEA added in a study of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium from Kotton's Lab in LGEA new section "LGEA-ExternalData".
  Check out its three analyses: Time Course Microarray Analysis, hPSC-Derived Airway Epithelium cell clusters in scRNA-seq and hPSC-Derived Airway vs. Alveolar Epithelium in scRNA-Seq.
• 4-11-2018: LGEA added in mouse P10 scRNA-seq dataset.
  
• 3-13-2018: LGEA has been selected to be featured in February issue, Editors' Picks section of Biomedical Advances.
  
• 3-12-2018: Check out our book chapter: Single-Cell Transcriptome Analysis Using SINCERA Pipeline.
  
• 2-5-2018: LGEA added in mouse time course protein dataset in LungProteomics panel.
  
• 2-5-2018: LGEA added in mouse P14 scRNA-seq dataset and mouse PND1 Drop-seq dataset in LungGENS panel.
  
• 8-28-2017: LGEA added in mouse P28 scRNA-seq dataset.
  
• 8-28-2017: Check out our new section: "LungProteomics" and human protein dataset.
  
• 8-2-2017: Check out our paper: SLICE : 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(7):e54.
  
• 7-19-2017: LGEA added in mouse P3 scRNA-seq dataset
  
  
• 5-8-2017: LGEA added in mouse P7 scRNA-seq dataset and Human iPSC-derived NKX2-1 lung scRNA-seq dataset from Kotton Lab.
  
  
• 4-22-2017: Dr.Whitsett and Dr.Xu's new published chapter: Transcriptional Networks-Control of Lung Maturation.
  
  
• 4-22-2017: Check out our 3 new sections: "LungEpigenetics", "LungImage" and "LGEA-ToolBox".
  
  
• 4-10-2017: LGEA web portal has just been published by Thorax. (PubMed)
  
  
• 1-10-2017: LGEA web portal adds a new section "LungDisease" and IPF study is available.
  
  
• 12-22-2016: Mouse single cell P01 database from 4 pools analysis is available.
  
  
• 12-12-2016: Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax. (PubMed)
  
  
• 12-08-2016: "Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis" has been published in JCI Insight.
  
  
• 12-01-2016: SLICE: determing cell differentiation and lineage based on single cell entropy. Nucleic Acids Research. (In press)
  
  
• 10-08-2016: Single cell E18.5 database has been updated from 3 pools analysis.
  
  
• 8-26-2016: Mouse P7 sorted cells has been added into LGEA web portal database.
  
  
• 7-15-2016: Mouse single cell E18.5 database has been updated from 2 pools analysis.
  
  
• 7-14-2016: Mouse P28 sorted cells has been added into LGEA web portal database
  
  
• 6-15-2016: Mouse single cell E16.5 database has been updated from 3 pools analysis.
  
  
• 6-9-2016: Check out this new book "Fetal and Neonatal Lung Development: Clinical Correlates and Technologies for the Future (Lung Growth, Development, and Disease)" (1st Edition by Alan Jobe (Editor), Jeffrey Whitsett(Editor), Steven Abman (Editor)). [Amazon]
• Feb-2016: LGEA Web Portal has been open to public.
  
  
• Feb-2016: LGEA Web Portal has been open to LungMAP community for test.
  
  
• 12-10-2015: Introduction of LungMAP -- Dr.Jeffrey Whitsett
• Nov-2015: SINCERA has accepted and published @ PLOS Computational Biology
  
  
• June-2015: LungGENS has accepted and published @ Thorax
  
  
• May-2015: LungGENS added in "gene list query" functions for mouse E16.5 and E18.5 single cell data
  
  
• April-2015: LungGENS has been open to public with "gene query" and "cell type query" functions of E16.5 and E18.5 mouse single cell data.