Regenerative lineages and immune-mediated pruning in lung cancer metastasis

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Developmental History Provides a Roadmap for the Emergence of Tumor Plasticity

(2018) Purushothama Rao Tata et al.   DEVELOPMENTAL CELL

Mask R-CNN

(2018) Kaiming He et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Pericyte-like spreading by disseminated cancer cells activates YAP and MRTF for metastatic colonization

(2018) Ekrem Emrah Er et al.   NATURE CELL BIOLOGY

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor

(2018) William J. Zacharias et al.   NATURE

A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers

(2018) Bryan A. Smith et al.   Cell Reports

Calcium-binding protein S100A4 confers mesenchymal progenitor cell fibrogenicity in idiopathic pulmonary fibrosis

(2017) Hong Xia et al.   JOURNAL OF CLINICAL INVESTIGATION

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development

(2017) Yina Du et al.   THORAX

Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT

(2016) Srinivas Malladi et al.   CELL

Regulation and plasticity of intestinal stem cells during homeostasis and regeneration

(2016) Joep Beumer et al.   DEVELOPMENT

The Role of Tumor-Infiltrating Lymphocytes in Development, Progression, and Prognosis of Non–Small Cell Lung Cancer

(2016) Roy M. Bremnes et al.   Journal of Thoracic Oncology

Metastatic colonization by circulating tumour cells

(2016) Joan Massagué et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung: Figure 1

(2015) Yina Du et al.   THORAX

Machine-based method for multiplex in situ molecular characterization of tissues by immunofluorescence detection

(2015) Dmitry Yarilin et al.   Scientific Reports

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

p63+Krt5+ distal airway stem cells are essential for lung regeneration

(2014) Wei Zuo et al.   NATURE

Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury

(2014) Andrew E. Vaughan et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Lung regeneration: mechanisms, applications and emerging stem cell populations

(2014) Darrell N Kotton et al.   NATURE MEDICINE

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer

(2013) Balázs Győrffy et al.   PLoS One

RAE-1 ligands for the NKG2D receptor are regulated by E2F transcription factors, which control cell cycle entry

(2012) Heiyoun Jung et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Neuroepithelial body microenvironment is a niche for a distinct subset of Clara-like precursors in the developing airways

(2012) A. Guha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Distal Airway Stem Cells Yield Alveoli In Vitro and during Lung Regeneration following H1N1 Influenza Infection

(2011) Pooja A. Kumar et al.   CELL

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Suppression of lung adenocarcinoma progression by Nkx2-1

(2011) Monte M. Winslow et al.   NATURE

RGB marking facilitates multicolor clonal cell tracking

(2011) Kristoffer Weber et al.   NATURE MEDICINE

Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

(2011) N. Halko et al.   SIAM REVIEW

Repetitive intratracheal bleomycin models several features of idiopathic pulmonary fibrosis

(2010) Amber L. Degryse et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Preparing for the First Breath: Genetic and Cellular Mechanisms in Lung Development

(2010) Edward E. Morrisey et al.   DEVELOPMENTAL CELL

Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal

(2010) K. K. Niakan et al.   GENES & DEVELOPMENT

S100A4 Regulates Macrophage Chemotaxis

(2010) Zhong-Hua Li et al.   MOLECULAR BIOLOGY OF THE CELL

Contribution of Epithelial-derived Fibroblasts to Bleomycin-induced Lung Fibrosis

(2009) Harikrishna Tanjore et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Targeting distinct tumor-infiltrating myeloid cells by inhibiting CSF-1 receptor: combating tumor evasion of antiangiogenic therapy

(2009) S. J. Priceman et al.   BLOOD

The Id2+ distal tip lung epithelium contains individual multipotent embryonic progenitor cells

(2009) E. L. Rawlins et al.   DEVELOPMENT

Basal cells as stem cells of the mouse trachea and human airway epithelium

(2009) J. R. Rock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development

(2008) Charles E. Murry et al.   CELL

Establishment of Endoderm Progenitors by SOX Transcription Factor Expression in Human Embryonic Stem Cells

(2008) Cheryle A. Séguin et al.   Cell Stem Cell

Negative signaling by inhibitory receptors: the NK cell paradigm

(2008) Eric O. Long   IMMUNOLOGICAL REVIEWS

Generation and Regeneration of Cells of the Liver and Pancreas

(2008) K. S. Zaret et al.   SCIENCE