Master Regulator Analysis of the SARS-CoV-2/Human Interactome

Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China

(2020) Zunyou Wu et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Coronavirus Infections—More Than Just the Common Cold

(2020) Catharine I. Paules et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV

(2020) Rui Li et al.   JOURNAL OF INFECTION

Genomic variance of the 2019‐nCoV coronavirus

(2020) Carmine Ceraolo et al.   JOURNAL OF MEDICAL VIROLOGY

Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS

(2020) Yushun Wan et al.   JOURNAL OF VIROLOGY

Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury

(2020) Clark D Russell et al.   LANCET

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Therapeutic options for the 2019 novel coronavirus (2019-nCoV)

(2020) Guangdi Li et al.   NATURE REVIEWS DRUG DISCOVERY

A Novel Coronavirus from Patients with Pneumonia in China, 2019

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

High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa

(2020) Hao Xu et al.   International Journal of Oral Science

Coronavirus: covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate

(2020) Elisabeth Mahase   BMJ-British Medical Journal

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

(2020) B. Coutard et al.   ANTIVIRAL RESEARCH

corto: a lightweight R package for gene network inference and master regulator analysis

(2020) Daniele Mercatelli et al.   BIOINFORMATICS

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

Soluble angiotensin-converting enzyme 2: a potential approach for coronavirus infection therapy?

(2020) Daniel Batlle et al.   CLINICAL SCIENCE

Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

(2020) Tao Zhang et al.   CURRENT BIOLOGY

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

(2020) Fei Zhou et al.   LANCET

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19

(2020) Bin Cao et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

(2020) Suhas Srinivasan et al.   Viruses-Basel

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

(2020) Yadi Zhou et al.   Cell Discovery

Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression

(2019) Daniele Mercatelli et al.   Frontiers in Genetics

Gene regulatory network inference resources: A practical overview

(2019) Daniele Mercatelli et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

(2019) Ping Liu et al.   Viruses-Basel

Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors

(2019) Young-Jun Park et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2

(2018) Wenfei Song et al.   PLoS Pathogens

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China

(2017) Zhi-Qi Zeng et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Computational methods in drug discovery

(2016) Sumudu P Leelananda et al.   Beilstein Journal of Organic Chemistry

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

E3 ubiquitin ligase RNF128 promotes innate antiviral immunity through K63-linked ubiquitination of TBK1

(2016) Guanhua Song et al.   NATURE IMMUNOLOGY

Critical role of eukaryotic elongation factor 1 alpha 1 (EEF1A1) in avian reovirus sigma-C-induced apoptosis and inhibition of viral growth

(2015) Zhiqiang Zhang et al.   ARCHIVES OF VIROLOGY

Transcriptional master regulator analysis in breast cancer genetic networks

(2015) Hugo Tovar et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

(2015) Christian Selinger et al.   BMC GENOMICS

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information

(2014) Federico M. Giorgi et al.   PLoS One

Downregulation of angiotensin-converting enzyme 2 by the neuraminidase protein of influenza A (H1N1) virus

(2014) Xin Liu et al.   VIRUS RESEARCH

Coronavirus infection, ER stress, apoptosis and innate immunity

(2014) To S. Fung et al.   Frontiers in Microbiology

The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR

(2013) Chen Li et al.   ANTIVIRAL RESEARCH

Mitochondrial permeability transition pore is a potential drug target for neurodegeneration

(2013) Valasani Koteswara Rao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes

(2012) Aleksandar Vasilevski et al.   Molecular BioSystems

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

(2012) Ali M. Zaki et al.   NEW ENGLAND JOURNAL OF MEDICINE

Up-Regulation of Mcl-1 and Bak by Coronavirus Infection of Human, Avian and Animal Cells Modulates Apoptosis and Viral Replication

(2012) Yanxin Zhong et al.   PLoS One

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Algorithm-driven Artifacts in median polish summarization of Microarray data

(2010) Federico M Giorgi et al.   BMC BIOINFORMATICS

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Dynamic Innate Immune Responses of Human Bronchial Epithelial Cells to Severe Acute Respiratory Syndrome-Associated Coronavirus Infection

(2010) Tomoki Yoshikawa et al.   PLoS One

Quantitative proteomic analysis of A549 cells infected with human respiratory syncytial virus subgroup B using SILAC coupled to LC-MS/MS

(2010) Diane C. Munday et al.   PROTEOMICS

Coronavirus Genomics and Bioinformatics Analysis

(2010) Patrick C. Y. Woo et al.   Viruses-Basel

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Differential Downregulation of ACE2 by the Spike Proteins of Severe Acute Respiratory Syndrome Coronavirus and Human Coronavirus NL63

(2009) I. Glowacka et al.   JOURNAL OF VIROLOGY

The hepatitis delta virus RNA genome interacts with eEF1A1, p54nrb, hnRNP-L, GAPDH and ASF/SF2

(2009) Dorota Sikora et al.   VIROLOGY

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS