Coronavirus genomes carry the signatures of their habitats

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges

(2020) Chih-Cheng Lai et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Molecular Mechanism of RNA Recognition by Zinc-Finger Antiviral Protein

(2020) Xiu Luo et al.   Cell Reports

CpG-Recoding in Zika Virus Genome Causes Host-Age-Dependent Attenuation of Infection With Protection Against Lethal Heterologous Challenge in Mice

(2020) Ivan Trus et al.   Frontiers in Immunology

Pathological evidence for residual SARS-CoV-2 in pulmonary tissues of a ready-for-discharge patient

(2020) Xiao-Hong Yao et al.   CELL RESEARCH

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

SARS-CoV-2 productively infects human gut enterocytes

(2020) Mart M. Lamers et al.   SCIENCE

SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

(2020) Nina Le Bert et al.   NATURE

Intra-genome variability in the dinucleotide composition of SARS-CoV-2

(2020) Paul Digard et al.   Virus Evolution

SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans

(2020) Rayhane Nchioua et al.   mBio

The role of ZAP and OAS3/RNAseL pathways in the attenuation of an RNA virus with elevated frequencies of CpG and UpA dinucleotides

(2019) Valerie Odon et al.   NUCLEIC ACIDS RESEARCH

Conservation, acquisition, and functional impact of sex-biased gene expression in mammals

(2019) Sahin Naqvi et al.   SCIENCE

Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences

(2019) Jennifer L. Meagher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure

(2019) Yumeng Z McDaniel et al.   NUCLEIC ACIDS RESEARCH

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

(2018) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity

(2018) Joshua A Hayward et al.   MOLECULAR BIOLOGY AND EVOLUTION

A-to-I RNA editing — immune protector and transcriptome diversifier

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

Influence of the DNA sequence/length and pH on deaminase activity, as well as the roles of the amino acid residues around the catalytic center of APOBEC3F

(2018) Li Wan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions

(2018) Tania V. Silvas et al.   Scientific Reports

APOBEC3-mediated restriction of RNA virus replication

(2018) Aleksandra Milewska et al.   Scientific Reports

Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

(2018) Kristof Theys et al.   PLoS Genetics

Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates

(2018) Madison B. Adolph et al.   ACS Infectious Diseases

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

CG dinucleotide suppression enables antiviral defence targeting non-self RNA

(2017) Matthew A. Takata et al.   NATURE

Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

(2017) Madison B. Adolph et al.   NUCLEIC ACIDS RESEARCH

Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication

(2017) Irati Antzin-Anduetza et al.   Retrovirology

The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression

(2017) Mishi Kaushal Wasson et al.   Scientific Reports

The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes

(2017) Jeffrey Chen et al.   PLoS Computational Biology

CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry

(2017) Jelke Jan Fros et al.   eLife

The Lair: a resource for exploratory analysis of published RNA-Seq data

(2016) Harold Pimentel et al.   BMC BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

APOBEC3 proteins can copackage and comutate HIV-1 genomes

(2016) Belete A. Desimmie et al.   NUCLEIC ACIDS RESEARCH

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide identification of zero nucleotide recursive splicing in Drosophila

(2015) Michael O. Duff et al.   NATURE

Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities

(2015) Mithun Mitra et al.   Retrovirology

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

APOBECs and virus restriction

(2015) Reuben S. Harris et al.   VIROLOGY

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages

(2015) Shraddha Sharma et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication

(2014) Nicky J. Atkinson et al.   NUCLEIC ACIDS RESEARCH

Insights into the Motif Preference of APOBEC3 Enzymes

(2014) Diako Ebrahimi et al.   PLoS One

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch et al.   eLife

Suppression of APOBEC3-mediated restriction of HIV-1 by Vif

(2014) Yuqing Feng et al.   Frontiers in Microbiology

HIV-1 Vif Adaptation to Human APOBEC3H Haplotypes

(2013) Marcel Ooms et al.   Cell Host & Microbe

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure

(2013) Colleen M. Holtz et al.   NUCLEIC ACIDS RESEARCH

Efficient Deamination of 5-Methylcytidine and 5-Substituted Cytidine Residues in DNA by Human APOBEC3A Cytidine Deaminase

(2013) Rodolphe Suspène et al.   PLoS One

Quasispecies structure, cornerstone of hepatitis B virus infection: Mass sequencing approach

(2013) Francisco Rodriguez-Frias   WORLD JOURNAL OF GASTROENTEROLOGY

Coronaviruses Lacking Exoribonuclease Activity Are Susceptible to Lethal Mutagenesis: Evidence for Proofreading and Potential Therapeutics

(2013) Everett Clinton Smith et al.   PLoS Pathogens

Suppression of HIV-1 Infection by APOBEC3 Proteins in Primary Human CD4+T Cells Is Associated with Inhibition of Processive Reverse Transcription as Well as Excessive Cytidine Deamination

(2012) Kieran Gillick et al.   JOURNAL OF VIROLOGY

Human and Rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H Demonstrate a Conserved Capacity To Restrict Vif-Deficient HIV-1

(2011) J. F. Hultquist et al.   JOURNAL OF VIROLOGY

A Compendium of Canine Normal Tissue Gene Expression

(2011) Joseph Briggs et al.   PLoS One

Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation

(2011) Y. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

APOBEC3 Proteins Expressed in Mammary Epithelial Cells Are Packaged into Retroviruses and Can Restrict Transmission of Milk-Borne Virions

(2010) Chioma M. Okeoma et al.   Cell Host & Microbe

Double-Stranded RNA Adenosine Deaminase ADAR-1-Induced Hypermutated Genomes among Inactivated Seasonal Influenza and Live Attenuated Measles Virus Vaccines

(2010) R. Suspene et al.   JOURNAL OF VIROLOGY

APOBEC3G Contributes to HIV-1 Variation through Sublethal Mutagenesis

(2010) H. A. Sadler et al.   JOURNAL OF VIROLOGY

Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction

(2010) Eric W. Refsland et al.   NUCLEIC ACIDS RESEARCH

RNA editing enzyme adenosine deaminase is a restriction factor for controlling measles virus replication that also is required for embryogenesis

(2010) S. V. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

(2010) Lance D. Eckerle et al.   PLoS Pathogens

A Portable Hot Spot Recognition Loop Transfers Sequence Preferences from APOBEC Family Members to Activation-induced Cytidine Deaminase

(2009) Rahul M. Kohli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons

(2009) C. C. Burns et al.   JOURNAL OF VIROLOGY

Defining APOBEC3 Expression Patterns in Human Tissues and Hematopoietic Cell Subsets

(2009) F. A. Koning et al.   JOURNAL OF VIROLOGY

Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System

(2009) Benjamin D. Greenbaum et al.   PLoS One

APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein

(2009) Shui-Mei Wang et al.   VIROLOGY

The APOBEC3 Cytidine Deaminases: An Innate Defensive Network Opposing Exogenous Retroviruses and Endogenous Retroelements

(2008) Ya-Lin Chiu et al.   Annual Review of Immunology

Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences

(2008) A. E. Armitage et al.   JOURNAL OF VIROLOGY

Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H

(2008) A. Harari et al.   JOURNAL OF VIROLOGY

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

(2008) Benjamin D. Greenbaum et al.   PLoS Pathogens