Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19

(2020) Hin Chu et al.   CLINICAL INFECTIOUS DISEASES

Abnormal pulmonary function in COVID-19 patients at time of hospital discharge

(2020) Xiaoneng Mo et al.   EUROPEAN RESPIRATORY JOURNAL

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

(2020) Denisa Bojkova et al.   NATURE

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

(2020) Tran Thi Nhu Thao et al.   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy

(2020) Peter M George et al.   Lancet Respiratory Medicine

Statin therapy in COVID-19 infection

(2020) Vincenzo Castiglione et al.   European Heart Journal-Cardiovascular Pharmacotherapy

Antiviral activities of type I interferons to SARS-CoV-2 infection

(2020) Emily Mantlo et al.   ANTIVIRAL RESEARCH

Immunothrombotic Dysregulation in COVID-19 Pneumonia is Associated with Respiratory Failure and Coagulopathy

(2020) Leo Nicolai et al.   CIRCULATION

Vimentin as a Multifaceted Player and Potential Therapeutic Target in Viral Infections

(2020) Irene Ramos et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication

(2020) Kevin Klann et al.   MOLECULAR CELL

Single-cell landscape of immunological responses in patients with COVID-19

(2020) Ji-Yuan Zhang et al.   NATURE IMMUNOLOGY

Genomewide Association Study of Severe Covid-19 with Respiratory Failure

(2020) David Ellinghaus et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Cholesterol in Relation to COVID-19: Should We Care about It?

(2020) Dina Radenkovic et al.   Journal of Clinical Medicine

High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2

(2020) Luca Zinzula et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification of required host factors for SARS-CoV-2 infection in human cells

(2020) Zharko Daniloski et al.   CELL

SARS-CoV-2 Infection of Pluripotent Stem Cell-Derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response

(2020) Jessie Huang et al.   Cell Stem Cell

Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses

(2020) Eleni Gavriilaki et al.   CURRENT HYPERTENSION REPORTS

Distinct and early increase in circulating MMP-9 in COVID-19 patients with respiratory failure

(2020) T Ueland et al.   JOURNAL OF INFECTION

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

(2020) David E. Gordon et al.   SCIENCE

A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape

(2019) Philipp Hubel et al.   NATURE IMMUNOLOGY

Clinical development of targeted and immune based anti-cancer therapies

(2019) N. A. Seebacher et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy

(2019) Jin-Mi Heo et al.   Science Advances

Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway

(2019) Justin S. A. Perry et al.   NATURE CELL BIOLOGY

The alternative cap-binding complex is required for antiviral defense in vivo

(2019) Anna Gebhardt et al.   PLoS Pathogens

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Contribution of EDF1 to PPARγ Transcriptional Activation in VEGF-Treated Human Endothelial Cells

(2018) Alessandra Cazzaniga et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An orthogonal proteomic survey uncovers novel Zika virus host factors

(2018) Pietro Scaturro et al.   NATURE

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

(2018) Birgit H M Meldal et al.   NUCLEIC ACIDS RESEARCH

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

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

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics

(2017) Nils A. Kulak et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

PTEN modulates EGFR late endocytic trafficking and degradation by dephosphorylating Rab7

(2016) Swapnil Rohidas Shinde et al.   Nature Communications

Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics

(2015) Ludger J. E. Goeminne et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Vimentin regulates activation of the NLRP3 inflammasome

(2015) Gimena dos Santos et al.   Nature Communications

Role of MMP2 and MMP9 in TRPV4-induced lung injury

(2014) Patricia C. Villalta et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Coronavirus NSP6 restricts autophagosome expansion

(2014) Eleanor M Cottam et al.   Autophagy

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications

(2014) Andreas Warnecke et al.   BMC BIOINFORMATICS

SARS-Coronavirus Open Reading Frame-9b Suppresses Innate Immunity by Targeting Mitochondria and the MAVS/TRAF3/TRAF6 Signalosome

(2014) Chong-Shan Shi et al.   JOURNAL OF IMMUNOLOGY

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

(2014) Nils A Kulak et al.   NATURE METHODS

Janus kinase inhibitors in autoimmune diseases

(2013) John J O'Shea et al.   ANNALS OF THE RHEUMATIC DISEASES

Large-scale identification of ubiquitination sites by mass spectrometry

(2013) Namrata D Udeshi et al.   Nature Protocols

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

ACE/ACE2 Ratio and MMP-9 Activity as Potential Biomarkers in Tuberculous Pleural Effusions

(2012) Wen-Yeh Hsieh et al.   International Journal of Biological Sciences

ERBB Receptor Activation Is Required for Profibrotic Responses to Transforming Growth Factor  

(2010) M. Andrianifahanana et al.   CANCER RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

The p38 MAPK inhibitors for the treatment of inflammatory diseases and cancer

(2009) Hae-Young Yong et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 2 Interacts with a Host Protein Complex Involved in Mitochondrial Biogenesis and Intracellular Signaling

(2009) C. T. Cornillez-Ty et al.   JOURNAL OF VIROLOGY

The Interferon Antagonist ML Protein of Thogoto Virus Targets General Transcription Factor IIB

(2008) C. Vogt et al.   JOURNAL OF VIROLOGY

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

(2008) Sunhwan Jo et al.   NUCLEIC ACIDS RESEARCH