Jean Cury
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View article: Ancient genomic insights into <i>Salmonella enterica</i> Paratyphi C from Central Mexico
Ancient genomic insights into <i>Salmonella enterica</i> Paratyphi C from Central Mexico Open
Salmonella enterica is a widespread pathogen of major global health relevance, with over 2,500 serovars classified into non-typhoidal and typhoidal groups. Within the typhoidal group, S. enterica Paratyphi C causes paratyphoid fever in hum…
View article: A human homolog of SIR2 antiphage proteins mediates immunity via the Toll-like receptor pathway
A human homolog of SIR2 antiphage proteins mediates immunity via the Toll-like receptor pathway Open
Key actors of mammalian immunity originated from bacterial antiphage systems. The full extent of immune system conservation between bacteria and eukaryotes is unknown. Here, we show that the silent information regulator 2 (SIR2) protein do…
View article: Protein and genomic language models chart a vast landscape of antiphage defenses
Protein and genomic language models chart a vast landscape of antiphage defenses Open
The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted. In this study, we developed language models to predict novel antiphage proteins in two ways: first via fine-tuning ESM2, …
View article: The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae Open
Bacterial genomes contain a plethora of secondary replicons of divergent size. Circular replicons must carry a system for resolving dimeric forms, resulting from recombination between sister copies. These systems use site-specific recombin…
View article: A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases Open
In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021…
View article: A human homolog of SIR2 antiphage proteins mediates immunity via the TLR pathway
A human homolog of SIR2 antiphage proteins mediates immunity via the TLR pathway Open
The full extent of immune system conservation between prokaryotes and eukaryotes is unknown. However, recent research supports that a subset of bacterial antiphage proteins is conserved in eukaryotes and likely gave rise to key actors of m…
View article: Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements
Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements Open
The co-evolution of prokaryotes, phages, and mobile genetic elements (MGEs) over the past billions of years has driven the emergence and diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse function…
View article: The immune modules conserved across the tree of life: Towards a definition of ancestral immunity
The immune modules conserved across the tree of life: Towards a definition of ancestral immunity Open
Immune defence mechanisms exist across the tree of life in such diversity that prokaryotic antiviral responses have historically been considered unrelated to eukaryotic immunity. Mechanisms of defence in divergent eukaryotes were similarly…
View article: Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons
Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons Open
Transposase genes are ubiquitous in all domains of life and provide a rich reservoir for the evolution of novel protein functions. Here we report deep evolutionary links between bacterial IS110 transposases, which catalyze RNA-guided DNA r…
View article: The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae Open
Bacterial genomes contain a plethora of secondary replicons of divergent size. Circular replicons must carry a system for resolving dimeric forms, resulting from recombination between sister copies. These systems use site-specific recombin…
View article: A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.
A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases. Open
In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021…
View article: Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold
Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold Open
Evolutionary arms races between cells and viruses drive the rapid diversification of antiviral genes in diverse life forms. Recent discoveries have revealed the existence of shared immune genes between prokaryotes and eukaryotes, showing m…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Full text Figures and data Side by side Abstract eLife assessment Introduction Data availability References Peer review Author response Article and author information Metrics Abstract Simulation is a key tool in population genetics for bot…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulati…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulati…
View article: Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences Open
Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny s…
View article: Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans
Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans Open
Viral infection is a common threat to prokaryotic and eukaryotic life, which has resulted in the evolution of a myriad of antiviral systems. Some of these eukaryotic systems are thought to have evolved from prokaryotic antiphage proteins, …
View article: <tt>dnadna</tt>: a deep learning framework for population genetics inference
dnadna: a deep learning framework for population genetics inference Open
Motivation We present dnadna, a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural netw…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: A new route for integron cassette dissemination among bacterial genomes
A new route for integron cassette dissemination among bacterial genomes Open
Integrons are genetic elements involved in bacterial adaptation. They can capture, shuffle and express adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination betwee…
View article: Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences Open
Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This c…
View article: IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella
IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella Open
Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic …