A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

[1]  J. Sage,et al.  A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs , 2022, Nature Communications.

[2]  Mats F. Nilsson,et al.  Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue , 2022, Scientific Reports.

[3]  Evan Z. Macosko,et al.  Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram , 2021, Nature Methods.

[4]  B. Gomperts,et al.  Wnt signaling in lung development, regeneration, and disease progression , 2021, Communications biology.

[5]  Alyssa J Miller,et al.  R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development , 2021, bioRxiv.

[6]  Fabian J Theis,et al.  Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine , 2021, Nature.

[7]  B. Vanderhyden,et al.  Single cell transcriptomic analysis of murine lung development on hyperoxia-induced damage , 2021, Nature Communications.

[8]  A. Tischler,et al.  Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin , 2021, Nature Genetics.

[9]  L. Ostrowski,et al.  Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia. , 2020, American journal of respiratory and critical care medicine.

[10]  Hannah A. Pliner,et al.  A human cell atlas of fetal gene expression , 2020, Science.

[11]  W. Seeger,et al.  SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution , 2020, PLoS biology.

[12]  D. Pe’er,et al.  Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung , 2020, bioRxiv.

[13]  Fabian J. Theis,et al.  CellRank for directed single-cell fate mapping , 2020, Nature Methods.

[14]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[15]  Joseph Bergenstråhle,et al.  Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography , 2020, Communications Biology.

[16]  Sergio Marco Salas,et al.  Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue , 2020, Nucleic acids research.

[17]  S. Di Giovanni,et al.  Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19 , 2020, Nature Reviews Neurology.

[18]  Lihua Zhang,et al.  Inference and analysis of cell-cell communication using CellChat , 2020, Nature Communications.

[19]  J. Lundeberg,et al.  Seamless integration of image and molecular analysis for spatial transcriptomics workflows , 2020, BMC Genomics.

[20]  G. Washko,et al.  Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis , 2020, Science Advances.

[21]  Jaime Fern'andez del R'io,et al.  Array programming with NumPy , 2020, Nature.

[22]  P. Wolters,et al.  Human alveolar Type 2 epithelium transdifferentiates into metaplastic KRT5+ basal cells , 2020, bioRxiv.

[23]  Gabriele Partel,et al.  TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data , 2020, Bioinform..

[24]  Huanming Yang,et al.  An atlas of the protein-coding genes in the human, pig, and mouse brain , 2020, Science.

[25]  Alyssa J. Miller,et al.  In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. , 2020, Developmental cell.

[26]  Y. Saeys,et al.  NicheNet: modeling intercellular communication by linking ligands to target genes , 2019, Nature Methods.

[27]  J. Kim,et al.  Ganglia in the Human Fetal Lung , 2019, Anatomical record.

[28]  Y. Kluger,et al.  Single-cell connectomic analysis of adult mammalian lungs , 2019, Science Advances.

[29]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[30]  T. Lassmann,et al.  Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows , 2019, Genome Biology.

[31]  Fabian J Theis,et al.  Generalizing RNA velocity to transient cell states through dynamical modeling , 2019, Nature Biotechnology.

[32]  K. Harris,et al.  Probabilistic cell typing enables fine mapping of closely related cell types in situ , 2019, Nature Methods.

[33]  M. Krasnow,et al.  Rare Pulmonary Neuroendocrine Cells Are Stem Cells Regulated by Rb, p53, and Notch , 2019, Cell.

[34]  Irving L. Weissman,et al.  A molecular cell atlas of the human lung from single cell RNA sequencing , 2019, Nature.

[35]  Yonghao Yu,et al.  Subtype-specific secretomic characterization of pulmonary neuroendocrine tumor cells , 2019, Nature Communications.

[36]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[37]  G. Castelo-Branco,et al.  An Atlas of Vagal Sensory Neurons and Their Molecular Specialization , 2019, Cell reports.

[38]  Hector Roux de Bézieux,et al.  Trajectory-based differential expression analysis for single-cell sequencing data , 2019, Nature Communications.

[39]  Fabian J Theis,et al.  A cellular census of human lungs identifies novel cell states in health and in asthma , 2019, Nature Medicine.

[40]  W. Richter,et al.  Regulation of WNT5A and WNT11 during MSC in vitro chondrogenesis: WNT inhibition lowers BMP and hedgehog activity, and reduces hypertrophy , 2019, Cellular and Molecular Life Sciences.

[41]  Carina Strell,et al.  Placing RNA in context and space – methods for spatially resolved transcriptomics , 2019, The FEBS journal.

[42]  R. Mirsky,et al.  Schwann Cell Precursors; Multipotent Glial Cells in Embryonic Nerves , 2019, Front. Mol. Neurosci..

[43]  Fabian J Theis,et al.  PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells , 2019, Genome Biology.

[44]  D. Warburton,et al.  Discordant roles for FGF ligands in lung branching morphogenesis between human and mouse , 2018, The Journal of pathology.

[45]  Hui Hu,et al.  AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors , 2018, Nucleic Acids Res..

[46]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[47]  Anne E Carpenter,et al.  CellProfiler 3.0: Next-generation image processing for biology , 2018, PLoS biology.

[48]  Zev J. Gartner,et al.  DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors , 2018, bioRxiv.

[49]  Russell B. Fletcher,et al.  Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics , 2018, BMC Genomics.

[50]  Peter Chen,et al.  Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis , 2018, Cell reports.

[51]  S. Hanash,et al.  β-Catenin maintains lung epithelial progenitors after lung specification , 2018, Development.

[52]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction , 2018, ArXiv.

[53]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[54]  George E. Allen,et al.  Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids , 2017, eLife.

[55]  Y. Cho,et al.  Schwann Cell Precursors from Human Pluripotent Stem Cells as a Potential Therapeutic Target for Myelin Repair , 2017, Stem cell reports.

[56]  K. Garcia,et al.  Intratumoral heterogeneity generated by Notch signaling promotes small cell lung cancer , 2017, Nature.

[57]  S. Kummerfeld,et al.  Transcription factor Etv5 is essential for the maintenance of alveolar type II cells , 2017, Proceedings of the National Academy of Sciences.

[58]  M. Zhang,et al.  GPC5, a novel epigenetically silenced tumor suppressor, inhibits tumor growth by suppressing Wnt/β-catenin signaling in lung adenocarcinoma , 2016, Oncogene.

[59]  R. Deberardinis,et al.  Fatty Acid Oxidation Mediated by Acyl-CoA Synthetase Long Chain 3 Is Required for Mutant KRAS Lung Tumorigenesis. , 2016, Cell reports.

[60]  Luc Girard,et al.  ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs. , 2016, Cell reports.

[61]  Patrik L. Ståhl,et al.  Visualization and analysis of gene expression in tissue sections by spatial transcriptomics , 2016, Science.

[62]  P. Linsley,et al.  MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data , 2015, Genome Biology.

[63]  Christian A. Siltanen,et al.  Therapeutic antibodies reveal Notch control of transdifferentiation in the adult lung , 2015, Nature.

[64]  Ying Zhang,et al.  FGF-Regulated ETV Transcription Factors Control FGF-SHH Feedback Loop in Lung Branching. , 2015, Developmental cell.

[65]  V. Lefebvre,et al.  The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis , 2015, Nucleic acids research.

[66]  Rui B Chang,et al.  Vagal Sensory Neuron Subtypes that Differentially Control Breathing , 2015, Cell.

[67]  Zhenyi Liu,et al.  The intracellular domains of Notch1 and Notch2 are functionally equivalent during development and carcinogenesis , 2015, Development.

[68]  M. Krasnow,et al.  Defining a mesenchymal progenitor niche at single-cell resolution , 2014, Science.

[69]  R. Sandberg,et al.  BMP signaling and its pSMAD1/5 target genes differentially regulate hair follicle stem cell lineages. , 2014, Cell stem cell.

[70]  K. Fried,et al.  Parasympathetic neurons originate from nerve-associated peripheral glial progenitors , 2014, Science.

[71]  E. Coppola,et al.  Parasympathetic ganglia derive from Schwann cell precursors , 2014, Science.

[72]  Qing-Jun Meng,et al.  Gremlin-2 is a BMP antagonist that is regulated by the circadian clock , 2014, Scientific Reports.

[73]  J. Horowitz,et al.  Activated alveolar epithelial cells initiate fibrosis through autocrine and paracrine secretion of connective tissue growth factor. , 2014, American journal of physiology. Lung cellular and molecular physiology.

[74]  Lianyu Shan,et al.  Neuronal chemorepellent Semaphorin 3E inhibits human airway smooth muscle cell proliferation and migration. , 2014, The Journal of allergy and clinical immunology.

[75]  H. Ji,et al.  Lung epithelial branching program antagonizes alveolar differentiation , 2013, Proceedings of the National Academy of Sciences.

[76]  Yan Liu,et al.  Nur77 suppresses pulmonary artery smooth muscle cell proliferation through inhibition of the STAT3/Pim-1/NFAT pathway. , 2013, American journal of respiratory cell and molecular biology.

[77]  R. Loddenkemper,et al.  Respiratory health and disease in Europe: the new European Lung White Book , 2013, European Respiratory Journal.

[78]  R. Muñoz-Chápuli,et al.  Wt1-expressing progenitors contribute to multiple tissues in the developing lung. , 2013, American journal of physiology. Lung cellular and molecular physiology.

[79]  Carolina Wählby,et al.  In situ sequencing for RNA analysis in preserved tissue and cells , 2013, Nature Methods.

[80]  Zhenyi Liu,et al.  The extracellular domain of Notch2 increases its cell-surface abundance and ligand responsiveness during kidney development. , 2013, Developmental cell.

[81]  R. Mallampalli,et al.  Surfactant phospholipid metabolism. , 2013, Biochimica et biophysica acta.

[82]  J. Davie,et al.  Myogenin Recruits the Histone Chaperone Facilitates Chromatin Transcription (FACT) to Promote Nucleosome Disassembly at Muscle-specific Genes* , 2013, The Journal of Biological Chemistry.

[83]  N. Molina-Frechero,et al.  Comparison of the value of PCNA and Ki-67 as markers of cell proliferation in ameloblastic tumor , 2012, Medicina oral, patologia oral y cirugia bucal.

[84]  T. Sauka-Spengler,et al.  Dynamic and Differential Regulation of Stem Cell Factor FoxD3 in the Neural Crest Is Encrypted in the Genome , 2012, PLoS genetics.

[85]  D. Sahoo,et al.  Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs, and their vasculature , 2012, Nature Cell Biology.

[86]  M. Krasnow,et al.  Radial construction of an arterial wall. , 2012, Developmental Cell.

[87]  O. Delattre,et al.  PHOX2B Immunolabeling: A Novel Tool for the Diagnosis of Undifferentiated Neuroblastomas Among Childhood Small Round Blue-cell Tumors , 2012, The American journal of surgical pathology.

[88]  C. Godoy-Guzmán,et al.  Proteoglycan and collagen expression during human air conducting system development , 2012, European journal of histochemistry : EJH.

[89]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[90]  Daniel Müllner,et al.  Modern hierarchical, agglomerative clustering algorithms , 2011, ArXiv.

[91]  E. Morrisey,et al.  Wnt2 signaling is necessary and sufficient to activate the airway smooth muscle program in the lung by regulating myocardin/Mrtf-B and Fgf10 expression. , 2011, Developmental biology.

[92]  E. Kremmer,et al.  Notch inhibition by the ligand DELTA-LIKE 3 defines the mechanism of abnormal vertebral segmentation in spondylocostal dysostosis. , 2011, Human molecular genetics.

[93]  H. Yeger,et al.  The role of hypoxia and neurogenic genes (Mash-1 and Prox-1) in the developmental programming and maturation of pulmonary neuroendocrine cells in fetal mouse lung , 2010, Laboratory Investigation.

[94]  Wei Liu,et al.  Differentiation of adipose-derived stem cells into contractile smooth muscle cells induced by transforming growth factor-beta1 and bone morphogenetic protein-4. , 2010, Tissue engineering. Part A.

[95]  T. Reh,et al.  Acheate‐scute like 1 (Ascl1) is required for normal delta‐like (Dll) gene expression and notch signaling during retinal development , 2009, Developmental dynamics : an official publication of the American Association of Anatomists.

[96]  Peter Lloyd Jones,et al.  Wnt signaling regulates smooth muscle precursor development in the mouse lung via a tenascin C/PDGFR pathway. , 2009, The Journal of clinical investigation.

[97]  P. Tsao,et al.  Notch signaling controls the balance of ciliated and secretory cell fates in developing airways , 2009, Development.

[98]  F. Guillemot,et al.  Notch controls embryonic Schwann cell differentiation, postnatal myelination and adult plasticity , 2009, Nature Neuroscience.

[99]  Jing Chen,et al.  ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..

[100]  R. M. Henke,et al.  Ascl1 and Neurog2 form novel complexes and regulate Delta-like3 (Dll3) expression in the neural tube. , 2009, Developmental biology.

[101]  Stephan Saalfeld,et al.  Globally optimal stitching of tiled 3D microscopic image acquisitions , 2009, Bioinform..

[102]  K. Nave,et al.  Neuregulin‐1, a key axonal signal that drives Schwann cell growth and differentiation , 2008, Glia.

[103]  Scott H Randell,et al.  Resident cellular components of the human lung: current knowledge and goals for research on cell phenotyping and function. , 2008, Proceedings of the American Thoracic Society.

[104]  B. Kablar,et al.  Pulmonary hypoplasia in the connective tissue growth factor (Ctgf) null mouse , 2008, Developmental dynamics : an official publication of the American Association of Anatomists.

[105]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[106]  Hiroki Matsui,et al.  Jagged1-selective Notch Signaling Induces Smooth Muscle Differentiation via a RBP-Jκ-dependent Pathway* , 2006, Journal of Biological Chemistry.

[107]  J. Vermylen,et al.  The TUBB1 Q43P functional polymorphism reduces the risk of cardiovascular disease in men by modulating platelet function and structure. , 2005, Blood.

[108]  J. Boulter,et al.  The divergent DSL ligand Dll3 does not activate Notch signaling but cell autonomously attenuates signaling induced by other DSL ligands , 2005, The Journal of cell biology.

[109]  R. Mirsky,et al.  The origin and development of glial cells in peripheral nerves , 2005, Nature Reviews Neuroscience.

[110]  S. Chin,et al.  A Pathogenic Peripherin Gene Mutation in a Patient with Amyotrophic Lateral Sclerosis , 2004, Brain pathology.

[111]  B. Gomperts,et al.  Foxj1 regulates basal body anchoring to the cytoskeleton of ciliated pulmonary epithelial cells , 2004, Journal of Cell Science.

[112]  M. Hermiston,et al.  CD45: a critical regulator of signaling thresholds in immune cells. , 2003, Annual review of immunology.

[113]  David J. Anderson,et al.  SOX10 Maintains Multipotency and Inhibits Neuronal Differentiation of Neural Crest Stem Cells , 2003, Neuron.

[114]  B. Stripp,et al.  Secretoglobins SCGB3A1 and SCGB3A2 define secretory cell subsets in mouse and human airways. , 2002, American journal of respiratory and critical care medicine.

[115]  M. Detmar,et al.  An essential role for Prox1 in the induction of the lymphatic endothelial cell phenotype , 2002, The EMBO journal.

[116]  C. Plopper,et al.  CELLULAR AND MOLECULAR CHARACTERISTICS OF BASAL CELLS IN AIRWAY EPITHELIUM , 2001, Experimental lung research.

[117]  J. Thiery,et al.  Evidence that SPROUTY2 functions as an inhibitor of mouse embryonic lung growth and morphogenesis , 2001, Mechanisms of Development.

[118]  R. Blakely,et al.  Molecular cloning of a human, hemicholinium-3-sensitive choline transporter. , 2000, Biochemical and biophysical research communications.

[119]  H. Rohrer,et al.  The expression of dopamine β-hydroxylase, tyrosine hydroxylase, and Phox2 transcription factors in sympathetic neurons: evidence for common regulation during noradrenergic induction and diverging regulation later in development , 2000, Mechanisms of Development.

[120]  G. Mardon,et al.  Synergistic regulation of vertebrate muscle development by Dach2, Eya2, and Six1, homologs of genes required for Drosophila eye formation. , 1999, Genes & development.

[121]  G. Oliver,et al.  Prox1 Function Is Required for the Development of the Murine Lymphatic System , 1999, Cell.

[122]  Pao-Tien Chuang,et al.  Vertebrate Hedgehog signalling modulated by induction of a Hedgehog-binding protein , 1999, Nature.

[123]  B. Hogan,et al.  Fibroblast growth factor 10 (FGF10) and branching morphogenesis in the embryonic mouse lung. , 1997, Development.

[124]  V. Lefebvre,et al.  Parallel expression of Sox9 and Col2a1 in cells undergoing chondrogenesis , 1997, Developmental dynamics : an official publication of the American Association of Anatomists.

[125]  S. Baylin,et al.  An achaete-scute homologue essential for neuroendocrine differentiation in the lung , 1997, Nature.

[126]  K. Andersson,et al.  Nitric oxide synthase-containing neurons in rat parasympathetic, sympathetic and sensory ganglia: a comparative study , 1995, The Histochemical Journal.

[127]  R. Verheijen,et al.  Assignment of the gene(s) involved in the expression of the proliferation-related Ki-67 antigen to human chromosome 10 , 1989, Human Genetics.

[128]  K. Sullivan,et al.  Identification of conserved isotype-defining variable region sequences for four vertebrate beta tubulin polypeptide classes. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[129]  E. Crelin Atlas of Human Anatomy , 1965, The Yale Journal of Biology and Medicine.

[130]  Mark Peterson,et al.  Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching , 2015 .

[131]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[132]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[133]  N. Bandeira,et al.  Bioinformatics Applications Note Databases and Ontologies Neuropedia: Neuropeptide Database and Spectral Library , 2022 .