Evolution of enhanced innate immune evasion by SARS-CoV-2

Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption

(2021) Marcos V. P. Gondim et al.   Science Translational Medicine

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

(2021) Jennifer Gribble et al.   PLoS Pathogens

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

(2021) Summer E. Galloway et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Infection sustained by lineage B.1.1.7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs

(2021) Paolo Calistri et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Nicholas G. Davies et al.   SCIENCE

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

(2021) Seiya Ozono et al.   Nature Communications

SARS-CoV-2 Nucleocapsid Protein Targets RIG-I-Like Receptor Pathways to Inhibit the Induction of Interferon Response

(2021) Soo Jin Oh et al.   Cells

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

(2021) Nicholas G. Davies et al.   NATURE

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Erik Volz et al.   NATURE

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

(2021) Irwin Jungreis et al.   Nature Communications

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

(2021) Mariana G. Ferrarini et al.   Communications Biology

SARS‐CoV‐2 sensing by RIG‐I and MDA5 links epithelial infection to macrophage inflammation

(2021) Lucy G Thorne et al.   EMBO JOURNAL

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

(2021) Delphine Planas et al.   NATURE

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

(2021) Irwin Jungreis et al.   VIROLOGY

Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation

(2021) Akatsuki Saito 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

Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors

(2020) Matthew Hackbart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

(2020) Mehdi Bouhaddou et al.   CELL

SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70

(2020) He-wei Jiang et al.   Cellular & Molecular Immunology

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

(2020) Luke W Meredith et al.   LANCET INFECTIOUS DISEASES

Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model

(2020) Thomas F. Rogers et al.   SCIENCE

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling

(2020) Lisa Miorin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) David E. Gordon et al.   SCIENCE

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

(2020) Qian Zhang et al.   SCIENCE

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

(2020) Paul Bastard et al.   SCIENCE

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

(2020) Erik Volz et al.   CELL

Genetic mechanisms of critical illness in Covid-19

(2020) Erola Pairo-Castineira et al.   NATURE

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss

(2018) Huayang Liu et al.   NATURE MEDICINE

RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway

(2018) J.-M. Heo et al.   Science Advances

Are Evolution and the Intracellular Innate Immune System Key Determinants in HIV Transmission?

(2017) Rebecca P. Sumner et al.   Frontiers in Immunology

Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction

(2016) Toshana L. Foster et al.   Cell Host & Microbe

An atlas of human kinase regulation

(2016) David Ochoa et al.   Molecular Systems Biology

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

(2016) Mariano J Alvarez et al.   NATURE GENETICS

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Tom70 mediates activation of interferon regulatory factor 3 on mitochondria

(2010) Xin-Yi Liu et al.   CELL RESEARCH

Use of the Pharmacological Inhibitor BX795 to Study the Regulation and Physiological Roles of TBK1 and IκB Kinase ϵ

(2009) Kristopher Clark et al.   JOURNAL OF BIOLOGICAL CHEMISTRY