OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Microbiology is 80. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)

Article	Citations
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	2136
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans	1020
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	683
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets	598
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	530
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies	527
The continued threat of emerging flaviviruses	523
Community-led, integrated, reproducible multi-omics with anvi’o	356
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	350
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	307
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	307
Diversity, ecology and evolution of Archaea	259
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes	256
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	251
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	245
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens	236
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	234
The SARS-CoV-2 RNA–protein interactome in infected human cells	230
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	207
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	206
A standardized archaeal taxonomy for the Genome Taxonomy Database	192
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	191
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks	191
COVID-19-associated fungal infections	184
Quantitative image analysis of microbial communities with BiofilmQ	179

Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	175
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan	164
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems	161
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome	158
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	153
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	153
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	152
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	150
LY6E impairs coronavirus fusion and confers immune control of viral disease	149
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses	145
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	141
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters	137
SARS-CoV-2 detection in patients with influenza-like illness	134
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	132
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus	132
Cellular host factors for SARS-CoV-2 infection	127
Structures of the stator complex that drives rotation of the bacterial flagellum	127
Species- and site-specific genome editing in complex bacterial communities	123
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	117
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity	112
Roadmap for naming uncultivated Archaea and Bacteria	112
Moving from probiotics to precision probiotics	110
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome	109
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes	108
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	107
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	106
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria	105
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	105
The Syntrophy hypothesis for the origin of eukaryotes revisited	105
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation	104
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	102
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing	102
Fungal taxonomy and sequence-based nomenclature	101
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission	100
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection	99
Trace gas oxidizers are widespread and active members of soil microbial communities	99
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	98
Towards a deeper understanding of the vaginal microbiota	96
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal	95
Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol	94
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	93
Reduction of microbial diversity in grassland soil is driven by long-term climate warming	92
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	91
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome	91
Fetal meconium does not have a detectable microbiota before birth	90
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance	88
Genetic circuit design automation for yeast	88
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses	87
SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities	85
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	85

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	84
Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity	84
Metagenomics-enabled microbial surveillance	83
A bottom-up view of antimicrobial resistance transmission in developing countries	81
Escherichia coli is engineered to grow on CO2 and formic acid	80
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland	80
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA	80