Sean Benler
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View article: Modularity and diversity of target selectors in Tn7 transposons
Modularity and diversity of target selectors in Tn7 transposons Open
View article: Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes
Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes Open
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly p…
View article: Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox
Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox Open
Significance Bacteriophages, the most widespread reproducing biological entity on Earth, employ two strategies of virus–host interaction: lysis of the host cell and lysogeny whereby the virus genome integrates into the host genome and prop…
View article: Erratum for Benler et al., “Cargo Genes of Tn <i>7</i> -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes”
Erratum for Benler et al., “Cargo Genes of Tn <i>7</i> -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes” Open
View article: Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes
Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes Open
Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding ge…
View article: Three-Dimensional Molecular Cartography of the Caribbean Reef-Building Coral Orbicella faveolata
Three-Dimensional Molecular Cartography of the Caribbean Reef-Building Coral Orbicella faveolata Open
All organisms host a diversity of associated viruses, bacteria, and protists, collectively defined as the holobiont. While scientific advancements have enhanced the understanding of the functional roles played by various components of the …
View article: Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
View article: Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo’s Paradox
Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo’s Paradox Open
Temperate bacteriophages lyse or lysogenize the host cells depending on various parameters of infection, a key one being the host population density. However, the effect of different propensities of phages for lysis and lysogeny on phage f…
View article: Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features Open
CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze …
View article: Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Background: Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant on…
View article: Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" Open
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)
View article: Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" Open
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)
View article: Additional file 3 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Additional file 3 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Additional file 2. Taxonomic information for 1,886 representative phage genomes. Each taxonomically classified phage genome was scored by ViralVerify, Seeker and vcontact2 and the assignments are provided in columns 9-10, 11 and 12-13, res…
View article: Additional file 6 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Additional file 6 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Additional file 5. Candidate anti-CRISPR (Acr) proteins encoded on each phage genome. Proteins predicted to be an Acr with high confidence (score > 0.9) and meeting all other heuristic criteria are listed along with their inferred host. Fo…
View article: Additional file 5 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Additional file 5 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Additional file 4. Host ranges inferred from CRISPR-spacer matches. The nucleotide coordinates of the protospacer are provided in columns 2 and 3. The sequence of the CRISPR spacer and protospacer are provided in columns 4 and 5. The taxon…
View article: Additional file 2 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Additional file 2 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Additional file 1. Clustering information for 3,378 gut phages identified in the study. Phage genomes were dereplicated at 95% identity over 80% of the contig length. The GenBank accession codes for each phage and the representative sequen…
View article: The Missing Tailed Phages: Prediction of Small Capsid Candidates
The Missing Tailed Phages: Prediction of Small Capsid Candidates Open
Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common ic…
View article: Phage lysis‐lysogeny switches and programmed cell death: Danse macabre
Phage lysis‐lysogeny switches and programmed cell death: Danse macabre Open
Exploration of immune systems in prokaryotes, such as restriction‐modification or CRISPR‐Cas, shows that both innate and adaptive systems possess programmed cell death (PCD) potential. The key outstanding question is how the immune systems…
View article: The Missing Tailed Phages: Prediction of Small Capsid Candidates
The Missing Tailed Phages: Prediction of Small Capsid Candidates Open
Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common ic…
View article: Thousands of Previously Unknown Phages Discovered in Whole-community Human Gut Metagenomes
Thousands of Previously Unknown Phages Discovered in Whole-community Human Gut Metagenomes Open
Background: Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut phageome is far from being fully characterized, and additional groups of phages, including highly abundant …
View article: Thousands of previously unknown phages discovered in whole-community human gut metagenomes
Thousands of previously unknown phages discovered in whole-community human gut metagenomes Open
Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut phageome is far from being fully characterized, and additional groups of phages, including highly abundant o…
View article: Seeker: alignment-free identification of bacteriophage genomes by deep learning
Seeker: alignment-free identification of bacteriophage genomes by deep learning Open
Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in…
View article: Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Seeker: Alignment-free identification of bacteriophage genomes by deep learning Open
Training and testing data.
View article: Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Seeker: Alignment-free identification of bacteriophage genomes by deep learning Open
Training and testing data.
View article: A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes Open
To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture me…
View article: Unique genomic features of crAss-like phages, the dominant component of the human gut virome
Unique genomic features of crAss-like phages, the dominant component of the human gut virome Open
CrAssphage is the most abundant virus identified in the human gut virome and the founding member of a large group of bacteriophages that infect bacteria of the phylum Bacteroidetes and have been discovered by metagenomics of both animal-as…
View article: Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Seeker: Alignment-free identification of bacteriophage genomes by deep learning Open
Summary Advances in metagenomics enable massive discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequen…
View article: Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes
Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes Open
View article: A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes
A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes Open
An imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in the microbiome field is to identify factors produced by normal microbiome bacteria th…
View article: Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information Open
Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate tre…