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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jmv.24974openalex-snapshot
Development and application of a real‐time polymerase chain reaction assay for detection of a novel gut bacteriophage (crAssphage)
inferredcites →https://doi.org/10.1002/jmv.25012openalex-snapshot
Quantitative CrAssphage real‐time PCR assay derived from data of multiple geographically distant populations
inferredcites →https://doi.org/10.1016/0967-0653(96)80394-gopenalex-snapshot
10.1016/0967-0653(96)80394-g
inferredcites →https://doi.org/10.1016/j.cell.2016.01.013openalex-snapshot
Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans
inferredcites →https://doi.org/10.1016/j.cell.2016.04.007openalex-snapshot
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
inferredcites →https://doi.org/10.1016/j.cell.2016.05.056openalex-snapshot
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
inferredcites →https://doi.org/10.1016/j.chom.2018.10.002openalex-snapshot
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
inferredcites →https://doi.org/10.1016/j.cmet.2015.10.001openalex-snapshot
Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella
inferredcites →https://doi.org/10.1016/j.watres.2017.12.011openalex-snapshot
Evaluation of the novel crAssphage marker for sewage pollution tracking in storm drain outfalls in Tampa, Florida
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0092-8674(03)00233-2openalex-snapshot
Origins of Highly Mosaic Mycobacteriophage Genomes
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1017/s095026881600176xopenalex-snapshot
crAssphage is not associated with diarrhoea and has high genetic diversity
inferredcites →https://doi.org/10.1021/acs.est.7b02703openalex-snapshot
Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement
inferredcites →https://doi.org/10.1021/ez500266sopenalex-snapshot
Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution
inferredcites →https://doi.org/10.1038/ismej.2015.148openalex-snapshot
The initial state of the human gut microbiome determines its reshaping by antibiotics
inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nature08798openalex-snapshot
Antagonistic coevolution accelerates molecular evolution
inferredcites →https://doi.org/10.1038/nature09199openalex-snapshot
Viruses in the faecal microbiota of monozygotic twins and their mothers
inferredcites →https://doi.org/10.1038/nature11053openalex-snapshot
Human gut microbiome viewed across age and geography
inferredcites →https://doi.org/10.1038/nature12820openalex-snapshot
Diet rapidly and reproducibly alters the human gut microbiome
inferredcites →https://doi.org/10.1038/ncomms5498openalex-snapshot
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
inferredcites →https://doi.org/10.1038/nm.3950openalex-snapshot
Early life dynamics of the human gut virome and bacterial microbiome in infants
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
inferredcites →https://doi.org/10.1038/nmicrobiol.2017.112openalex-snapshot
Bacteriophage evolution differs by host, lifestyle and genome
inferredcites →https://doi.org/10.1038/nrmicro2853openalex-snapshot
Going viral: next-generation sequencing applied to phage populations in the human gut
inferredcites →https://doi.org/10.1038/s41467-018-07225-7openalex-snapshot
ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
inferredcites →https://doi.org/10.1038/s41564-017-0053-yopenalex-snapshot
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
inferredcites →https://doi.org/10.1073/pnas.1005963107openalex-snapshot
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
inferredcites →https://doi.org/10.1073/pnas.1300833110openalex-snapshot
Rapid evolution of the human gut virome
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btm015openalex-snapshot
Assessment of phylogenomic and orthology approaches for phylogenetic inference
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btr595openalex-snapshot
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btx184openalex-snapshot
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive
inferredcites →https://doi.org/10.1093/bioinformatics/btz265openalex-snapshot
PHANOTATE: a novel approach to gene identification in phage genomes
inferredcites →https://doi.org/10.1093/femsle/fnv219openalex-snapshot
Natural mummification of the human gut preserves bacteriophage DNA
inferredcites →https://doi.org/10.1093/femsre/fuv048openalex-snapshot
Computational approaches to predict bacteriophage–host relationships
inferredcites →https://doi.org/10.1093/gbe/evu040openalex-snapshot
The Histone Modification H3K27me3 Is Retained after Gene Duplication and Correlates with Conserved Noncoding Sequences in Arabidopsis
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
inferredcites →https://doi.org/10.1093/molbev/msx302openalex-snapshot
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkw290openalex-snapshot
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/nar/gkx1095openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/sysbio/syz036openalex-snapshot
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
inferredcites →https://doi.org/10.1101/117838openalex-snapshot
Probabilistic recovery of cryptic haplotypes from metagenomic data
inferredcites →https://doi.org/10.1101/gr.122705.111openalex-snapshot
The human gut virome: Inter-individual variation and dynamic response to diet
inferredcites →https://doi.org/10.1101/gr.8.3.175openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
inferredcites →https://doi.org/10.1101/gr.8.3.186openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
inferredcites →https://doi.org/10.1109/mcse.2014.80openalex-snapshot
XSEDE: Accelerating Scientific Discovery
inferredcites →https://doi.org/10.1111/1751-7915.12841openalex-snapshot
Determination of crAssphage in water samples and applicability for tracking human faecal pollution
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.aad2545openalex-snapshot
The 5300-year-old Helicobacter pylori genome of the Iceman
inferredcites →https://doi.org/10.1126/science.aad3369openalex-snapshot
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
inferredcites →https://doi.org/10.1126/science.aaf3951openalex-snapshot
Cospeciation of gut microbiota with hominids
inferredcites →https://doi.org/10.1126/scitranslmed.3000322openalex-snapshot
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
inferredcites →https://doi.org/10.1128/aem.70.3.1633-1640.2004openalex-snapshot
Phage Community Dynamics in Hot Springs
inferredcites →https://doi.org/10.1128/mbio.01874-17openalex-snapshot
Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers
inferredcites →https://doi.org/10.1136/bmjopen-2014-006772openalex-snapshot
Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics
inferredcites →https://doi.org/10.1177/0148607116658762openalex-snapshot
Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
inferredcites →https://doi.org/10.1186/s12967-017-1175-yopenalex-snapshot
Influence of diet on the gut microbiome and implications for human health
inferredcites →https://doi.org/10.3354/meps072205openalex-snapshot
Production and decay of viruses in aquatic environments
inferredcites →https://doi.org/10.3354/meps131287openalex-snapshot
Abundance and production of bacteria and viruses in the Bering and Chukchi Seas
inferredcites →https://doi.org/10.3390/v9040070openalex-snapshot
How to Name and Classify Your Phage: An Informal Guide
inferredcites →https://doi.org/10.5281/zenodo.1043561openalex-snapshot
linsalrob/SearchSRA: Alpha Release
inferredcites →https://doi.org/10.5281/zenodo.1069672openalex-snapshot
linsalrob/crAssphage: Cirulated to collaborators
inferredcites →https://doi.org/10.6084/m9.figshare.3475406openalex-snapshot
SOP - DNA Isolation QIAamp Fast DNA Stool Modified
inferredcites →https://doi.org/10.7287/peerj.preprints.27553openalex-snapshot
PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets
inferredcites →https://doi.org/10.7287/peerj.preprints.27553v1openalex-snapshot
PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/s12560-024-09584-5openalex-snapshot
CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker
inferred← citeshttps://doi.org/10.1016/j.envint.2021.106620openalex-snapshot
Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China
inferred← citeshttps://doi.org/10.1016/j.watres.2020.116161openalex-snapshot
CrAssphage abundance and correlation with molecular viral markers in Italian wastewater
inferred← citeshttps://doi.org/10.1021/acs.estlett.9b00130openalex-snapshot
Co-Occurrence of crAssphage with Antibiotic Resistance Genes in an Impacted Urban Watershed
inferred← citeshttps://doi.org/10.1038/s41396-021-01090-xopenalex-snapshot
Phages in the infant gut: a framework for virome development during early life
inferred← citeshttps://doi.org/10.1038/s41423-020-00532-4openalex-snapshot
Phages and their potential to modulate the microbiome and immunity
inferred← citeshttps://doi.org/10.1038/s41467-019-14103-3openalex-snapshot
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
inferred← citeshttps://doi.org/10.1038/s41467-020-18236-8openalex-snapshot
Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems
inferred← citeshttps://doi.org/10.1038/s41467-020-18281-3openalex-snapshot
A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase
inferred← citeshttps://doi.org/10.1038/s41467-021-27917-xopenalex-snapshot
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
inferred← citeshttps://doi.org/10.1038/s41467-022-31390-5openalex-snapshot
Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome
inferred← citeshttps://doi.org/10.1038/s41545-019-0032-3openalex-snapshot
Metagenomics and the development of viral water quality tools
inferred← citeshttps://doi.org/10.1038/s41576-025-00871-wopenalex-snapshot
Viromics approaches for the study of viral diversity and ecology in microbiomes
inferred← citeshttps://doi.org/10.1038/s41579-021-00536-5openalex-snapshot
The human virome: assembly, composition and host interactions
inferred← citeshttps://doi.org/10.1038/s41579-021-00602-yopenalex-snapshot
Interactions between bacterial and phage communities in natural environments
inferred← citeshttps://doi.org/10.1038/s41579-022-00755-4openalex-snapshot
Mutualistic interplay between bacteriophages and bacteria in the human gut
inferred← citeshttps://doi.org/10.1038/s41579-024-01107-0openalex-snapshot
Examining the healthy human microbiome concept
inferred← citeshttps://doi.org/10.1038/s41586-023-06019-2openalex-snapshot
Structural atlas of a human gut crassvirus
inferred← citeshttps://doi.org/10.1038/s41586-024-08485-8openalex-snapshot
Expanding the human gut microbiome atlas of Africa
inferred← citeshttps://doi.org/10.1038/s41587-025-02570-7openalex-snapshot
Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage
inferred← citeshttps://doi.org/10.1097/phh.0000000000001797openalex-snapshot
Establishing a Statewide Wastewater Surveillance System in Response to the COVID-19 Pandemic: A Reliable Model for Continuous and Emerging Public Health Threats
inferred← citeshttps://doi.org/10.1101/2020.07.06.186817openalex-snapshot
The human oral phageome is highly diverse and rich in jumbo phages
inferred← citeshttps://doi.org/10.1101/585067openalex-snapshot
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
inferred← citeshttps://doi.org/10.1111/mec.17801openalex-snapshot
Intestivirid Acquisition Increases Across Infancy in a Wild Primate Population
inferred← citeshttps://doi.org/10.1128/aem.01470-24openalex-snapshot
CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing
inferred← citeshttps://doi.org/10.1186/s12866-020-01891-8openalex-snapshot
Efficacy of phage cocktail AB-SA01 therapy in diabetic mouse wound infections caused by multidrug-resistant Staphylococcus aureus
inferred← citeshttps://doi.org/10.1186/s40168-021-01036-7openalex-snapshot
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens
inferred← citeshttps://doi.org/10.1371/journal.pone.0226930openalex-snapshot
Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion
inferred← citeshttps://doi.org/10.1371/journal.pone.0231864openalex-snapshot
Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples
inferred← citeshttps://doi.org/10.14309/ctg.0000000000000659openalex-snapshot
Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1077771/v1openalex-snapshot
Diet, microbes, and cancer across the tree of life: a systematic review
inferred← citeshttps://doi.org/10.21203/rs.3.rs-273865/v1openalex-snapshot
A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue
inferred← citeshttps://doi.org/10.31219/osf.io/s9px2openalex-snapshot
The human gut virome: Composition, colonisation, interactions, and impacts on human health
inferred← citeshttps://doi.org/10.33540/111openalex-snapshot
On uncovering and understanding interactions between bacteriophages and bacteria
inferred← citeshttps://doi.org/10.33696/signaling.4.100openalex-snapshot
The Human Gut Phageome: Identification and Roles in the Diseases
inferred← citeshttps://doi.org/10.3390/books978-3-03928-569-3openalex-snapshot
Enteric Viruses in Aquatic Environments
inferred← citeshttps://doi.org/10.51415/10321/5151openalex-snapshot
Assessment of biomarkers for normalization of SARS-CoV-2 concentrations in wastewater
inferred← citeshttps://doi.org/10.7287/peerj.11950v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11950v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11950v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.11950v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies (v0.2)"
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