Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

(2020) Aiping Wu et al.   Cell Host & Microbe

Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

(2020) Dawei Wang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

(2020) Jasper Fuk-Woo Chan et al.   LANCET

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

(2020) Nanshan Chen et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

A novel coronavirus outbreak of global health concern

(2020) Chen Wang et al.   LANCET

Clinical Characteristics of Coronavirus Disease 2019 in China

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

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Lysosome biology in autophagy

(2020) Willa Wen-You Yim et al.   Cell Discovery

Coronaviruses and SARS-CoV-2

(2020) Stephan Ludwig et al.   ANESTHESIA AND ANALGESIA

Mitochondrial hyperfusion: a friend or a foe

(2020) Rajdeep Das et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls 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

Clinical and immunological features of severe and moderate coronavirus disease 2019

(2020) Guang Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

COVID-19 and Thrombotic or Thromboembolic Disease: Implications for Prevention, Antithrombotic Therapy, and Follow-up

(2020) Behnood Bikdeli et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Cutaneous manifestations in COVID‐19: the experiences of Barcelona and Rome

(2020) A. Tammaro et al.   JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY

COVID-19: consider cytokine storm syndromes and immunosuppression

(2020) Puja Mehta et al.   LANCET

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

SARS-CoV-2 and COVID-19: The most important research questions

(2020) Kit-San Yuen et al.   Cell and Bioscience

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes

(2020) Ruochen Zang et al.   Science Immunology

Viral dynamics in mild and severe cases of COVID-19

(2020) Yang Liu et al.   LANCET INFECTIOUS DISEASES

Immune Response, Inflammation, and the Clinical Spectrum of COVID-19

(2020) Luis F. García   Frontiers in Immunology

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

(2020) James L. Daly et al.   SCIENCE

β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway

(2020) Sourish Ghosh et al.   CELL

TMPRSS2 contributes to virus spread and immunopathology in the airways of murine models after coronavirus infection

(2019) Naoko Iwata-Yoshikawa et al.   JOURNAL OF VIROLOGY

Modulation of Autophagy for Controlling Immunity

(2019) Young Jin Jang et al.   Cells

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease

(2019) Herbert B Schiller et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

SKP2 attenuates autophagy through Beclin1-ubiquitination and its inhibition reduces MERS-Coronavirus infection

(2019) Nils C. Gassen et al.   Nature Communications

Basal Cells in Lung Development and Repair

(2018) Edward E. Morrisey   DEVELOPMENTAL CELL

mTORC1 and Nutrient Homeostasis: The Central Role of the Lysosome

(2018) et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

GeneMANIA update 2018

(2018) Max Franz et al.   NUCLEIC ACIDS RESEARCH

Enteroviral Infection Inhibits Autophagic Flux via Disruption of the SNARE Complex to Enhance Viral Replication

(2018) Yasir Mohamud et al.   Cell Reports

Blockade of the C5a–C5aR axis alleviates lung damage in hDPP4-transgenic mice infected with MERS-CoV

(2018) Yuting Jiang et al.   Emerging Microbes & Infections

Diverse Roles of Mitochondria in Immune Responses: Novel Insights Into Immuno-Metabolism

(2018) Anusha Angajala et al.   Frontiers in Immunology

LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step

(2018) Katrina B. Mar et al.   Nature Communications

Calu-3 epithelial cells exhibit different immune and epithelial barrier responses from freshly isolated primary nasal epithelial cells in vitro

(2018) Katleen Martens et al.   Clinical and Translational Allergy

Released Tryptophanyl-tRNA Synthetase Stimulates Innate Immune Responses against Viral Infection

(2018) Hyun-Cheol Lee et al.   JOURNAL OF VIROLOGY

Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection

(2017) Marie L Landry et al.   JOURNAL OF INFECTIOUS DISEASES

mTOR Controls Mitochondrial Dynamics and Cell Survival via MTFP1

(2017) Masahiro Morita et al.   MOLECULAR CELL

Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology

(2017) Rudragouda Channappanavar et al.   Seminars in Immunopathology

Dengue virus induces mitochondrial elongation through impairment of Drp1-triggered mitochondrial fission

(2017) Vincent Barbier et al.   VIROLOGY

Essential control of mitochondrial morphology and function by chaperone-mediated autophagy through degradation of PARK7

(2016) Bao Wang et al.   Autophagy

Unraveling the complexity of mitochondrial complex I assembly: A dynamic process

(2016) Laura Sánchez-Caballero et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Knockdown of GSK3  increases basal autophagy and AMPK signalling in nutrient-laden human aortic endothelial cells

(2016) K. A. Weikel et al.   BIOSCIENCE REPORTS

SARS and MERS: recent insights into emerging coronaviruses

(2016) Emmie de Wit et al.   NATURE REVIEWS MICROBIOLOGY

Inhibition of glycogen synthase kinase 3β promotes autophagy to protect mice from acute liver failure mediated by peroxisome proliferator-activated receptor α

(2016) F Ren et al.   Cell Death & Disease

mTOR coordinates protein synthesis, mitochondrial activity and proliferation

(2015) Masahiro Morita et al.   CELL CYCLE

Rotenone-induced Impairment of Mitochondrial Electron Transport Chain Confers a Selective Priming Signal for NLRP3 Inflammasome Activation

(2015) Ji-Hee Won et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Glycogen Synthase Kinase-3 (GSK3) Inhibition Induces Prosurvival Autophagic Signals in Human Pancreatic Cancer Cells

(2015) Benoît Marchand et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dengue Virus Inhibition of Autophagic Flux and Dependency of Viral Replication on Proteasomal Degradation of the Autophagy Receptor p62

(2015) Philippe Metz et al.   JOURNAL OF VIROLOGY

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

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

CTRP6 is an endogenous complement regulator that can effectively treat induced arthritis

(2015) Masanori A. Murayama et al.   Nature Communications

The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney

(2015) Zach K. O’Brown et al.   PLoS Genetics

ADAP2 Is an Interferon Stimulated Gene That Restricts RNA Virus Entry

(2015) Qian Shu et al.   PLoS Pathogens

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

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

(2014) Charity W Law et al.   GENOME BIOLOGY

mTOR inhibition increases cell viability via autophagy induction during endoplasmic reticulum stress - An experimental and modeling study

(2014) Orsolya Kapuy et al.   FEBS Open Bio

mTORC1 Controls Mitochondrial Activity and Biogenesis through 4E-BP-Dependent Translational Regulation

(2013) Masahiro Morita et al.   Cell Metabolism

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Suppressor of cytokine signaling 6 (SOCS6) promotes mitochondrial fission via regulating DRP1 translocation

(2012) H-Y Lin et al.   CELL DEATH AND DIFFERENTIATION

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Superoxide Dismutases: Role in Redox Signaling, Vascular Function, and Diseases

(2011) Tohru Fukai et al.   ANTIOXIDANTS & REDOX SIGNALING

Mechanisms of mitochondria and autophagy crosstalk

(2011) Angelika S. Rambold et al.   CELL CYCLE

Mitochondria regulate autophagy by conserved signalling pathways

(2011) Martin Graef et al.   EMBO JOURNAL

Interactions between coagulation and complement—their role in inflammation

(2011) Katerina Oikonomopoulou et al.   Seminars in Immunopathology

TRIM5 Acts as More Than a Retroviral Restriction Factor

(2011) Suresh De Silva et al.   Viruses-Basel

The many faces of the mitochondrial TIM23 complex

(2010) Dejana Mokranjac et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

C1q induces a rapid up-regulation of P-selectin and modulates collagen- and collagen-related peptide-triggered activation in human platelets

(2010) Caroline Skoglund et al.   IMMUNOBIOLOGY

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

(2010) Daniele Merico et al.   PLoS One

The role of Interleukin 6 in the pathophysiology of rheumatoid arthritis

(2010) Srinivasan Srirangan et al.   Therapeutic Advances in Musculoskeletal Disease

Mitochondrial Complex I decrease is responsible for bioenergetic dysfunction in K-ras transformed cells

(2009) Alessandra Baracca et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The Interferon Response Inhibits HIV Particle Production by Induction of TRIM22

(2008) Stephen D. Barr et al.   PLoS Pathogens

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY