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High-resolution sweep metagenomics using fast probabilistic inference

https://doi.org/10.1101/332544
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Condorcet's jury theorem, dependency among jurors
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Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species
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Advances in neural information processing systems 7
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Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study
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Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
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Optimal enzymes for amplifying sequencing libraries
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Metagenomic microbial community profiling using unique clade-specific marker genes
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Microbiota-mediated colonization resistance against intestinal pathogens
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Escherichia coliStrains Belonging to Phylogenetic Group B2 Have Superior Capacity to Persist in the Intestinal Microflora of Infants
inferredcites →https://doi.org/10.1086/597402openalex-snapshot
Campylobacter Genotyping to Determine the Source of Human Infection
inferredcites →https://doi.org/10.1093/bioinformatics/bts260openalex-snapshot
Identifying differentially expressed transcripts from RNA-seq data with biological variation
inferredcites →https://doi.org/10.1093/bioinformatics/btv483openalex-snapshot
Fast and accurate approximate inference of transcript expression from RNA-seq data
inferredcites →https://doi.org/10.1093/bioinformatics/btx106openalex-snapshot
Pseudoalignment for metagenomic read assignment
inferredcites →https://doi.org/10.1093/gbe/evv066openalex-snapshot
Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis
inferredcites →https://doi.org/10.1093/molbev/mst028openalex-snapshot
Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software
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Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism
inferredcites →https://doi.org/10.1099/mgen.0.000075openalex-snapshot
Bayesian identification of bacterial strains from sequencing data
inferredcites →https://doi.org/10.1099/mgen.0.000131openalex-snapshot
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
inferredcites →https://doi.org/10.1101/gr.201863.115openalex-snapshot
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
inferredcites →https://doi.org/10.1101/gr.216242.116openalex-snapshot
Microbial strain-level population structure and genetic diversity from metagenomes
inferredcites →https://doi.org/10.1101/gr.216606.116openalex-snapshot
Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
inferredcites →https://doi.org/10.1111/1462-2920.13628openalex-snapshot
Genome‐wide association of functional traits linked with C ampylobacter jejuni survival from farm to fork
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05179.xopenalex-snapshot
Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species
inferredcites →https://doi.org/10.1111/j.1469-0691.2011.03570.xopenalex-snapshot
Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance
inferredcites →https://doi.org/10.1128/aem.00078-16openalex-snapshot
Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain
inferredcites →https://doi.org/10.1128/aem.00428-11openalex-snapshot
Temporal Variation and Host Association in the Campylobacter Population in a Longitudinal Ruminant Farm Study
inferredcites →https://doi.org/10.1128/aem.69.11.6816-6824.2003openalex-snapshot
Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken
inferredcites →https://doi.org/10.1128/mbio.00489-17openalex-snapshot
Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307
inferredcites →https://doi.org/10.1186/s13073-017-0397-1openalex-snapshot
Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae
inferredcites →https://doi.org/10.1371/journal.pbio.2001457openalex-snapshot
Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli
inferredcites →https://doi.org/10.1371/journal.pone.0022825openalex-snapshot
The Prevalence of Campylobacter amongst a Free-Range Broiler Breeder Flock Was Primarily Affected by Flock Age
inferredcites →https://doi.org/10.1371/journal.pone.0099290openalex-snapshot
Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples
inferredcites →https://doi.org/10.2307/2529131openalex-snapshot
Maximum Likelihood Estimation for the Beta-Binomial Distribution and an Application to the Household Distribution of the Total Number of Cases of a Disease
inferredcites →https://doi.org/10.3389/fmicb.2016.01475openalex-snapshot
Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota
inferredcites →https://doi.org/10.4137/mbi.s25800openalex-snapshot
Phenotypic and Genotypic Characteristics of Small Colony Variants and Their Role in Chronic Infection

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf234openalex-snapshot
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment
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