Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys

(2021) Emily Speranza et al.   Science Translational Medicine

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

(2021) Jessica K. Fiege et al.   PLoS Pathogens

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

(2021) Emanuel Wyler et al.   iScience

A time-resolved proteomic and prognostic map of COVID-19

(2021) Vadim Demichev et al.   Cell Systems

Automated sample preparation with SP 3 for low‐input clinical proteomics

(2020) Torsten Müller et al.   Molecular Systems Biology

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tracing tumorigenesis in a solid tumor model at single-cell resolution

(2020) Samantha D. Praktiknjo et al.   Nature Communications

Pathogenesis of SARS-CoV-2 in transgenic mice expressing human angiotensin-converting enzyme 2

(2020) Ren-Di Jiang et al.   CELL

SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract

(2020) Yixuan J. Hou et al.   CELL

Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals

(2020) Ling Ni et al.   IMMUNITY

Neutrophil-to-lymphocyte ratio and lymphocyte-to-C-reactive protein ratio in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis

(2020) Francisco Alejandro Lagunas-Rangel   JOURNAL OF MEDICAL VIROLOGY

Pathogenesis and transmission of SARS-CoV-2 in golden hamsters

(2020) Sin Fun Sia et al.   NATURE

Virological assessment of hospitalized patients with COVID-2019

(2020) Roman Wölfel et al.   NATURE

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

(2020) Mingfeng Liao et al.   NATURE MEDICINE

Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19

(2020) Maximilian Ackermann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients

(2020) Jing Liu et al.   EBioMedicine

COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure

(2020) Monia Marchetti   ANNALS OF HEMATOLOGY

Neutrophil Extracellular Traps (NETs) Contribute to Immunothrombosis in COVID-19 Acute Respiratory Distress Syndrome

(2020) Elizabeth A Middleton et al.   BLOOD

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

(2020) Jonas Schulte-Schrepping et al.   CELL

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection

(2020) Xuemei Xie et al.   NATURE IMMUNOLOGY

Severe COVID-19 infection associated with endothelial activation

(2020) Robert Escher et al.   THROMBOSIS RESEARCH

The clinical implication of dynamic neutrophil to lymphocyte ratio and D-dimer in COVID-19: A retrospective study in Suzhou China

(2020) Jianhong Fu et al.   THROMBOSIS RESEARCH

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

Standardization of Reporting Criteria for Lung Pathology in SARS-CoV-2 Infected Hamsters – What Matters?

(2020) Achim D Gruber et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model

(2020) Jakob Kreye et al.   CELL

Proteomic characteristics of bronchoalveolar lavage fluid in critical COVID‐19 patients

(2020) Hao‐Long Zeng et al.   FEBS Journal

Animal and translational models of SARS-CoV-2 infection and COVID-19

(2020) M. D. Johansen et al.   Mucosal Immunology

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

(2020) Yanchun Peng et al.   NATURE IMMUNOLOGY

SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function

(2020) Emma S. Winkler et al.   NATURE IMMUNOLOGY

Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters

(2020) Lisa H. Tostanoski et al.   NATURE MEDICINE

Humoral Immune Response to SARS-CoV-2 in Iceland

(2020) Daniel F. Gudbjartsson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Neuropilin-1 is a host factor for SARS-CoV-2 infection

(2020) James L. Daly et al.   SCIENCE

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

(2020) Ludovico Cantuti-Castelvetri et al.   SCIENCE

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Direct visualization of translational GTPase factor pool formed around the archaeal ribosomal P-stalk by high-speed AFM

(2020) Hirotatsu Imai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Roborovski Dwarf Hamster Is A Highly Susceptible Model for a Rapid and Fatal Course of SARS-CoV-2 Infection

(2020) Jakob Trimpert et al.   Cell Reports

CCL7 Is a Negative Regulator of Cutaneous Inflammation Following Leishmania major Infection

(2019) Jill Ford et al.   Frontiers in Immunology

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

(2019) Ilias Angelidis et al.   Nature Communications

CCR5 is a required signaling receptor for macrophage expression of inflammatory genes in response to viral double-stranded RNA

(2019) Zachary R Shaheen et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

(2019) Joanna Zyla et al.   BIOINFORMATICS

Interferon-Stimulated Genes: What Do They All Do?

(2019) John W. Schoggins   Annual Review of Virology

Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells

(2019) Charles-Antoine Dutertre et al.   IMMUNITY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

Monocytes and Monocyte-Derived Antigen-Presenting Cells Have Distinct Gene Signatures in Experimental Model of Multiple Sclerosis

(2019) Kelly L. Monaghan et al.   Frontiers in Immunology

Vascular Niche in Lung Alveolar Development, Homeostasis, and Regeneration

(2019) Akiko Mammoto et al.   Frontiers in Bioengineering and Biotechnology

Single-cell connectomic analysis of adult mammalian lungs

(2019) Micha Sam Brickman Raredon et al.   Science Advances

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells

(2018) Patrick Fernandes Rodrigues et al.   NATURE IMMUNOLOGY

Immune Responses to Middle East Respiratory Syndrome Coronavirus During the Acute and Convalescent Phases of Human Infection

(2018) Hyoung-Shik Shin et al.   CLINICAL INFECTIOUS DISEASES

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Monocyte Subsets: Phenotypes and Function in Tuberculosis Infection

(2018) Pavithra Sampath et al.   Frontiers in Immunology

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Acute Respiratory Distress Syndrome

(2017) B. Taylor Thompson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia

(2017) Kristina Dietert et al.   PLoS One

A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis

(2017) Min-Hyeok Kim et al.   Scientific Reports

Targeting of the pulmonary capillary vascular niche promotes lung alveolar repair and ameliorates fibrosis

(2016) Zhongwei Cao et al.   NATURE MEDICINE

Blood transcriptional signature of recombinant human erythropoietin administration and implications for antidoping strategies

(2016) Jérôme Durussel et al.   PHYSIOLOGICAL GENOMICS

Distinct Transcriptional Programs Control Cross-Priming in Classical and Monocyte-Derived Dendritic Cells

(2016) Carlos G. Briseño et al.   Cell Reports

Crossing the Vascular Wall: Common and Unique Mechanisms Exploited by Different Leukocyte Subsets during Extravasation

(2015) Michael Schnoor et al.   MEDIATORS OF INFLAMMATION

Orphan nuclear receptor NR4A1 regulates transforming growth factor-β signaling and fibrosis

(2015) Katrin Palumbo-Zerr et al.   NATURE MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Animal models for SARS and MERS coronaviruses

(2015) Lisa M Gretebeck et al.   Current Opinion in Virology

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Interferon-Stimulated Genes: A Complex Web of Host Defenses

(2014) William M. Schneider et al.   Annual Review of Immunology

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Heme and erythropoieis: more than a structural role

(2014) D. Chiabrando et al.   HAEMATOLOGICA

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Expression of MS4A and TMEM176 Genes in Human B Lymphocytes

(2013) Jonathan Zuccolo et al.   Frontiers in Immunology

Understanding the T cell immune response in SARS coronavirus infection

(2012) Hsueh-Ling Janice Oh et al.   Emerging Microbes & Infections

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The cytotoxic T lymphocyte protease granzyme A cleaves and inactivates poly(adenosine 5'-diphosphate-ribose) polymerase-1

(2009) P. Zhu et al.   BLOOD

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Red Blood Cells Are the Major Source of Alpha-Synuclein in Blood

(2008) Robin Barbour et al.   Neurodegenerative Diseases