An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

Aging and anatomical variations in lung tissue stiffness

(2018) Delphine Sicard et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Automated cell-type classification in intact tissues by single-cell molecular profiling

(2018) Monica Nagendran et al.   eLife

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

The instructive extracellular matrix of the lung: basic composition and alterations in chronic lung disease

(2017) Gerald Burgstaller et al.   EUROPEAN RESPIRATORY JOURNAL

The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop

(2017) GR Scott Budinger et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression

(2017) Michael Wierer et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

The lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors

(2017) Emma Lefrançais et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Stearoyl-CoA desaturase-1 and adaptive stress signaling

(2016) Andreas Koeberle et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Mechanisms of lung aging

(2016) Christina Brandenberger et al.   CELL AND TISSUE RESEARCH

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Diseases of Pulmonary Surfactant Homeostasis

(2015) Jeffrey A. Whitsett et al.   Annual Review of Pathology-Mechanisms of Disease

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Hallmarks of the ageing lung

(2015) Silke Meiners et al.   EUROPEAN RESPIRATORY JOURNAL

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair

(2015) H. B. Schiller et al.   Molecular Systems Biology

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Telomere dysfunction causes alveolar stem cell failure

(2015) Jonathan K. Alder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular composition of the alveolar lining fluid in the aging lung

(2014) Juan I. Moliva et al.   AGE

Aging causes a slowing in ciliary beat frequency, mediated by PKCε

(2014) K. L. Bailey et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Repair and Regeneration of the Respiratory System: Complexity, Plasticity, and Mechanisms of Lung Stem Cell Function

(2014) Brigid L.M. Hogan et al.   Cell Stem Cell

Proteomic Analysis of Altered Extracellular Matrix Turnover in Bleomycin-induced Pulmonary Fibrosis

(2014) Martin L. Decaris et al.   MOLECULAR & CELLULAR PROTEOMICS

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Stretching the boundaries of extracellular matrix research

(2014) Richard O. Hynes   NATURE REVIEWS MOLECULAR CELL BIOLOGY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Flow Cytometric Analysis of Macrophages and Dendritic Cell Subsets in the Mouse Lung

(2013) Alexander V. Misharin et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Activation of Sterol-response Element-binding Proteins (SREBP) in Alveolar Type II Cells Enhances Lipogenesis Causing Pulmonary Lipotoxicity

(2012) Laurent Plantier et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components

(2012) Richard A. Scheltema et al.   JOURNAL OF PROTEOME RESEARCH

Mechanisms of Dysfunction in Senescent Pulmonary Endothelium

(2012) D. Jane-Wit et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

The Collagen Family

(2010) S. Ricard-Blum   Cold Spring Harbor Perspectives in Biology

Molecular Mechanisms of IFN-γ to Up-Regulate MHC Class I Antigen Processing and Presentation

(2009) Fang Zhou   INTERNATIONAL REVIEWS OF IMMUNOLOGY

A CREB-C/EBP  cascade induces M2 macrophage-specific gene expression and promotes muscle injury repair

(2009) D. Ruffell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human innate immunosenescence: causes and consequences for immunity in old age

(2009) Alexander Panda et al.   TRENDS IN IMMUNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY