A comprehensive SARS-CoV-2–human protein–protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

(2022) Avi J. Samelson et al.   NATURE CELL BIOLOGY

Review of Ribosome Interactions with SARS-CoV-2 and COVID-19 mRNA Vaccine

(2022) Jiao Wei et al.   Life-Basel

Expanded COVID-19 phenotype definitions reveal distinct patterns of genetic association and protective effects

(2022) Genevieve H. L. Roberts et al.   NATURE GENETICS

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets

(2022) Lipika R. Pal et al.   iScience

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

The Epidemiological and Mechanistic Understanding of the Neurological Manifestations of COVID-19: A Comprehensive Meta-Analysis and a Network Medicine Observation

(2021) Jiayu Shen et al.   Frontiers in Neuroscience

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

(2021) Alexey Stukalov et al.   NATURE

Metoprolol in Critically Ill Patients With COVID-19

(2021) Agustín Clemente-Moragón et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Identification of drugs associated with reduced severity of COVID-19 – a case-control study in a large population

(2021) Ariel Israel et al.   eLife

The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis

(2021) Miao Zou et al.   Frontiers in Immunology

Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes

(2021) Suresh Kumar et al.   CELL

Rare variants in Toll-like receptor 7 results in functional impairment and downregulation of cytokine-mediated signaling in COVID-19 patients

(2021) Stefania Mantovani et al.   GENES AND IMMUNITY

Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets

(2021) Kuoyuan Cheng et al.   Molecular Systems Biology

SARS-CoV-2 spreads through cell-to-cell transmission

(2021) Cong Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SARS-CoV-2 Spike Protein S1-Mediated Endothelial Injury and Pro-Inflammatory State Is Amplified by Dihydrotestosterone and Prevented by Mineralocorticoid Antagonism

(2021) Nitin Kumar et al.   Viruses-Basel

ORF3a Protein of Severe Acute Respiratory Syndrome Coronavirus 2 Inhibits Interferon-Activated Janus Kinase/Signal Transducer and Activator of Transcription Signaling via Elevating Suppressor of Cytokine Signaling 1

(2021) Rong Wang et al.   Frontiers in Microbiology

Evidence for gastrointestinal infection of SARS-CoV-2

(2020) Fei Xiao et al.   GASTROENTEROLOGY

Evidence of SARS-CoV-2 Infection in Returning Travelers from Wuhan, China

(2020) Sebastian Hoehl et al.   NEW ENGLAND JOURNAL OF MEDICINE

Carvedilol and COVID-19: A Potential Role in Reducing Infectivity and Infection Severity

(2020) Charbel Skayem et al.   AMERICAN JOURNAL OF THE MEDICAL SCIENCES

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs

(2020) Sangeun Jeon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2020) Daniel Blanco-Melo et al.   CELL

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

(2020) Bo Shen 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

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

(2020) Alba Grifoni et al.   Cell Host & Microbe

Potential influence of COVID-19/ACE2 on the female reproductive system

(2020) Yan Jing et al.   MOLECULAR HUMAN REPRODUCTION

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

(2020) Denisa Bojkova et al.   NATURE

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

(2020) David E. Gordon et al.   NATURE

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

(2020) Shayne D. Wierbowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SARS-CoV-2 productively infects human gut enterocytes

(2020) Mart M. Lamers et al.   SCIENCE

Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2

(2020) Yadi Zhou et al.   Cell Discovery

Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19

(2020) Yuan Huang et al.   ACTA PHARMACOLOGICA SINICA

Biochemical characterization of SARS-CoV-2 nucleocapsid protein

(2020) Weihong Zeng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The ORF3a protein of SARS-CoV-2 induces apoptosis in cells

(2020) Yujie Ren et al.   Cellular & Molecular Immunology

A proposed role for the SARS‐CoV‐2 nucleocapsid protein in the formation and regulation of biomolecular condensates

(2020) Sean M. Cascarina et al.   FASEB JOURNAL

The Nucleocapsid Protein of SARS–CoV-2: a Target for Vaccine Development

(2020) Noton K. Dutta et al.   JOURNAL OF VIROLOGY

MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures

(2020) Ting Huang et al.   MOLECULAR & CELLULAR PROTEOMICS

A multidimensional precision medicine approach identifies an autism subtype characterized by dyslipidemia

(2020) Yuan Luo et al.   NATURE MEDICINE

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

(2020) Abhik K. Banerjee et al.   CELL

Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2

(2020) William R. Martin et al.   JOURNAL OF PROTEOME RESEARCH

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

(2020) David E. Gordon et al.   SCIENCE

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

Evasion of Type I Interferon by SARS-CoV-2

(2020) Hongjie Xia et al.   Cell Reports

Large-Scale Multi-omic Analysis of COVID-19 Severity

(2020) Katherine A. Overmyer et al.   Cell Systems

Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses

(2020) Eran Mick et al.   Nature Communications

The SARS-CoV-2 RNA–protein interactome in infected human cells

(2020) Nora Schmidt et al.   Nature Microbiology

Network-based prediction of drug combinations

(2019) Feixiong Cheng et al.   Nature Communications

Targeting STT3A-oligosaccharyltransferase with NGI-1 causes herpes simplex virus 1 dysfunction

(2019) Hua Lu et al.   FASEB JOURNAL

Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin

(2019) J. Patrick Murphy et al.   ANALYTICAL CHEMISTRY

Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer

(2019) Iris Nira Smith et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Uncovering the In Vivo Proxisome Using Proximity‐Tagging Methods

(2019) Yoann G. Santin   BIOESSAYS

A genome-wide positioning systems network algorithm for in silico drug repurposing

(2019) Feixiong Cheng et al.   Nature Communications

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

(2019) Robert Fragoza et al.   Nature Communications

Systematic Comparison of Label-Free, SILAC, and TMT Techniques to Study Early Adaption toward Inhibition of EGFR Signaling in the Colorectal Cancer Cell Line DiFi

(2019) Markus Stepath et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-Wide Evaluation of Two Common Protein Quantification Methods

(2018) Jeremy D. O’Connell et al.   JOURNAL OF PROTEOME RESEARCH

MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells

(2018) Yu Cong et al.   PLoS One

Network-based approach to prediction and population-based validation of in silico drug repurposing

(2018) Feixiong Cheng et al.   Nature Communications

Benchmarking common quantification strategies for large-scale phosphoproteomics

(2018) Alexander Hogrebe et al.   Nature Communications

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Linker Histone in Diseases

(2017) Xin Ye et al.   International Journal of Biological Sciences

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

A Small-Molecule Oligosaccharyltransferase Inhibitor with Pan-flaviviral Activity

(2017) Andreas S. Puschnik et al.   Cell Reports

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human

(2016) Tommy V. Vo et al.   CELL

Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection

(2016) Nicholas S. Heaton et al.   IMMUNITY

MOV10 Provides Antiviral Activity against RNA Viruses by Enhancing RIG-I–MAVS-Independent IFN Induction

(2016) Rolando A. Cuevas et al.   JOURNAL OF IMMUNOLOGY

An inter-species protein-protein interaction network across vast evolutionary distance

(2016) Q. Zhong et al.   Molecular Systems Biology

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

(2016) Caleb D. Marceau et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

(2016) Feixiong Cheng et al.   PLoS Computational Biology

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

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

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

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Dengue virus NS1 triggers endothelial permeability and vascular leak that is prevented by NS1 vaccination

(2015) P. Robert Beatty et al.   Science Translational Medicine

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

(2015) Feixiong Cheng et al.   Oncotarget

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Repurposing of Clinically Developed Drugs for Treatment of Middle East Respiratory Syndrome Coronavirus Infection

(2014) Julie Dyall et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Apremilast is a selective PDE4 inhibitor with regulatory effects on innate immunity

(2014) P.H. Schafer et al.   CELLULAR SIGNALLING

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines

(2013) Dominik A. Megger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

PhosphoNetworks: a database for human phosphorylation networks

(2013) J. Hu et al.   BIOINFORMATICS

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

Epiplakin modifies the motility of the HeLa cells and accumulates at the outer surfaces of 3-D cell clusters

(2013) Hiromitsu Shimada et al.   JOURNAL OF DERMATOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands

(2013) Adam J. Pawson et al.   NUCLEIC ACIDS RESEARCH

Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways

(2013) J. Das et al.   Science Signaling

FDA-Approved Selective Estrogen Receptor Modulators Inhibit Ebola Virus Infection

(2013) L. M. Johansen et al.   Science Translational Medicine

Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era

(2012) Saliha D. Durmuş Tekir et al.   Biotechnology Journal

Anchoring Proteins as Regulators of Signaling Pathways

(2012) Alessia Perino et al.   CIRCULATION RESEARCH

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions

(2012) Anne-Claude Gingras et al.   FEBS LETTERS

Coevolution Reveals a Network of Human Proteins Originating with Multicellularity

(2012) A. Bezginov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

(2012) Orit Rozenblatt-Rosen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

(2012) Cheng-Tsung Lu et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Deficiency of the Cytoskeletal Protein SPECC1L Leads to Oblique Facial Clefting

(2011) Irfan Saadi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Contribution of Sec61α to the Life Cycle of Ebola Virus

(2011) Ayaka Iwasa et al.   JOURNAL OF INFECTIOUS DISEASES

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

(2011) Zhou Li et al.   JOURNAL OF PROTEOME RESEARCH

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Mass spectrometry-based immuno-precipitation proteomics - The user's guide

(2011) Sara ten Have et al.   PROTEOMICS

Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics

(2010) Timothy S. Collier et al.   ANALYTICAL CHEMISTRY

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

Cotranslational and Posttranslational N-Glycosylation of Polypeptides by Distinct Mammalian OST Isoforms

(2009) Catalina Ruiz-Canada et al.   CELL

The completion of the Mammalian Gene Collection (MGC)

(2009) et al.   GENOME RESEARCH

Structural and Functional Diversity of Novel Coronin 1C (CRN2) Isoforms in Muscle

(2009) Charles-Peter Xavier et al.   JOURNAL OF MOLECULAR BIOLOGY

Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support

(2008) Paul A. Harris et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Linker Histones Are Mobilized during Infection with Herpes Simplex Virus Type 1

(2008) K. L. Conn et al.   JOURNAL OF VIROLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen

(2008) John M. Asara et al.   PROTEOMICS

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE