OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Microbiology is 79. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-10-01 to 2023-10-01.)

Article	Citations
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2	4809
Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses	2275
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	1998
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans	969
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	640
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets	557
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies	492
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	468
The continued threat of emerging flaviviruses	428
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	284
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	278
Community-led, integrated, reproducible multi-omics with anvi’o	259
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	245
Safety of bacteriophage therapy in severe Staphylococcus aureus infection	225
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes	209
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	208
Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth	207
The SARS-CoV-2 RNA–protein interactome in infected human cells	206
Diversity, ecology and evolution of Archaea	203
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	195
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	190
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens	190
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	185
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	185
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks	171

ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	164
Quantitative image analysis of microbial communities with BiofilmQ	152
A standardized archaeal taxonomy for the Genome Taxonomy Database	150
N6-methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I	145
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan	143
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	139
LY6E impairs coronavirus fusion and confers immune control of viral disease	133
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology	133
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems	132
SARS-CoV-2 detection in patients with influenza-like illness	132
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	131
Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection	131
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome	129
Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection	126
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	126
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses	126
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters	126
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	124
We shouldn’t worry when a virus mutates during disease outbreaks	122
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus	117
Control of nitrogen fixation in bacteria that associate with cereals	117
COVID-19-associated fungal infections	114
Spatial metabolomics of in situ host–microbe interactions at the micrometre scale	114
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	110
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	110
Structures of the stator complex that drives rotation of the bacterial flagellum	107
Roadmap for naming uncultivated Archaea and Bacteria	104
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity	103
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance	100
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	98
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens	96
Species- and site-specific genome editing in complex bacterial communities	94
Cellular host factors for SARS-CoV-2 infection	94
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	93
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	93
Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra	92
Moving from probiotics to precision probiotics	89
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria	89
The Syntrophy hypothesis for the origin of eukaryotes revisited	88
Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets	88
Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol	88
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal	88
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation	87
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	87
The microbiota programs DNA methylation to control intestinal homeostasis and inflammation	87
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	87
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission	86
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	85
Envelope stress responses defend against type six secretion system attacks independently of immunity proteins	83
Cyclophilin A protects HIV-1 from restriction by human TRIM5α	82

Fungal taxonomy and sequence-based nomenclature	82
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing	80
Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex	80
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation	79