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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

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What this work says

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

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Appendix D: Quadratic Equation for the Odds Ratio

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A solution to the problem of separation in logistic regression

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From Theory to Practice: Plug and Play with Succinct Data Structures

inferredcites →https://doi.org/10.1007/978-3-642-33122-0_35openalex-snapshot

Distributed String Mining for High-Throughput Sequencing Data

inferredcites →https://doi.org/10.1016/j.mib.2015.03.002openalex-snapshot

The advent of genome-wide association studies for bacteria

inferredcites →https://doi.org/10.1016/j.tim.2009.03.002openalex-snapshot

A modular master on the move: the Tn916 family of mobile genetic elements

inferredcites →https://doi.org/10.1038/ncomms7740openalex-snapshot

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

inferredcites →https://doi.org/10.1038/ncomms8272openalex-snapshot

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

inferredcites →https://doi.org/10.1038/ng.2656openalex-snapshot

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

inferredcites →https://doi.org/10.1038/ng.2747openalex-snapshot

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1038/ng.2895openalex-snapshot

Dense genomic sampling identifies highways of pneumococcal recombination

inferredcites →https://doi.org/10.1038/nrg3472openalex-snapshot

Meta-analysis methods for genome-wide association studies and beyond

inferredcites →https://doi.org/10.1073/pnas.1305559110openalex-snapshot

Genome-wide association study identifies vitamin B 5 biosynthesis as a host specificity factor in Campylobacter

inferredcites →https://doi.org/10.1093/bioinformatics/bth471openalex-snapshot

DWE: Discriminating Word Enumerator

inferredcites →https://doi.org/10.1093/bioinformatics/bti1200openalex-snapshot

DNA assembly with gaps (Dawg): simulating sequence evolution

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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pIRS: Profile-based Illumina pair-end reads simulator

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DSK: k -mer counting with very low memory usage

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Exploration and retrieval of whole-metagenome sequencing samples

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Strategies for fine-mapping complex traits

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An Empirical Codon Model for Protein Sequence Evolution

inferredcites →https://doi.org/10.1093/molbev/msp063openalex-snapshot

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

inferredcites →https://doi.org/10.1093/molbev/msr268openalex-snapshot

ALF—A Simulation Framework for Genome Evolution

inferredcites →https://doi.org/10.1093/molbev/mst028openalex-snapshot

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

inferredcites →https://doi.org/10.1093/nar/gkg509openalex-snapshot

SIFT: predicting amino acid changes that affect protein function

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1101/gr.165415.113openalex-snapshot

Predicting the virulence of MRSA from its genome sequence

inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot

BLAT —The BLAST -Like Alignment Tool

inferredcites →https://doi.org/10.1109/bigdata.2014.7004291openalex-snapshot

Random projection based clustering for population genomics

inferredcites →https://doi.org/10.1126/science.1198545openalex-snapshot

Rapid Pneumococcal Evolution in Response to Clinical Interventions

inferredcites →https://doi.org/10.1128/aac.45.4.1104-1108.2001openalex-snapshot

Multiple Mutations Modulate the Function of Dihydrofolate Reductase in Trimethoprim-Resistant Streptococcus pneumoniae

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Analysis of immunoglobulin G-binding-protein expression by invasive isolates of Streptococcus pyogenes

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Association between expression of immunoglobulin G-binding proteins by group A streptococci and virulence in a mouse skin infection model

inferredcites →https://doi.org/10.1128/jb.01343-08openalex-snapshot

Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic CloneStreptococcus pneumoniaeSpain23FST81

inferredcites →https://doi.org/10.1146/annurev.micro.53.1.217openalex-snapshot

DNA Uptake in Bacteria

inferredcites →https://doi.org/10.1186/gb-2007-8-5-r71openalex-snapshot

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

inferredcites →https://doi.org/10.1371/journal.pgen.1004547openalex-snapshot

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

inferredcites →https://doi.org/10.3201/eid2202.151358openalex-snapshot

Invasive Group AStreptococcusInfection among Children, Rural Kenya

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

inferredcites →https://doi.org/10.5555/1577069.1755843openalex-snapshot

Dlib-ml: A Machine Learning Toolkit

What points at this work

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

inferred← citeshttps://doi.org/10.1007/13836_2017_3openalex-snapshot

Computational Methods in Microbial Population Genomics

inferred← citeshttps://doi.org/10.1038/nmicrobiol.2016.59openalex-snapshot

Bacterial genomics: Microbial GWAS coming of age

inferred← citeshttps://doi.org/10.1038/s41467-019-10110-6openalex-snapshot

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions

inferred← citeshttps://doi.org/10.1038/s41538-025-00527-3openalex-snapshot

Advancing microbial risk assessment: perspectives from the evolution of detection technologies

inferred← citeshttps://doi.org/10.1038/s41564-022-01238-1openalex-snapshot

Pneumococcal within-host diversity during colonization, transmission and treatment

inferred← citeshttps://doi.org/10.1038/s41588-018-0343-1openalex-snapshot

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

inferred← citeshttps://doi.org/10.1038/s41588-019-0417-8openalex-snapshot

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

inferred← citeshttps://doi.org/10.1038/s41588-020-0612-7openalex-snapshot

Identifying genetic variants underlying phenotypic variation in plants without complete genomes

inferred← citeshttps://doi.org/10.1038/s42003-022-03194-2openalex-snapshot

PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies

inferred← citeshttps://doi.org/10.1093/nar/gkx702openalex-snapshot

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations

inferred← citeshttps://doi.org/10.1101/2022.05.16.492091openalex-snapshot

Combined reference-free and multi-reference approaches uncover cryptic variation underlying rapid adaptation in microbial pathogens

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Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation

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Understanding the Population Structure Correction Regression

inferred← citeshttps://doi.org/10.1186/s12864-020-6555-7openalex-snapshot

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

inferred← citeshttps://doi.org/10.1186/s13059-021-02473-1openalex-snapshot

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008518openalex-snapshot

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers

inferred← citeshttps://doi.org/10.1371/journal.pgen.1006508openalex-snapshot

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

inferred← citeshttps://doi.org/10.1371/journal.pone.0240834openalex-snapshot

In silico characterisation of stand-alone response regulators of Streptococcus pyogenes

inferred← citeshttps://doi.org/10.21203/rs.3.rs-200227/v1openalex-snapshot

Boosting Heritability: Estimating the Genetic Component of Phenotypic Variation With Multiple Sample Splitting

inferred← citeshttps://doi.org/10.22215/etd/2019-13815openalex-snapshot

Genome-wide association study of Pseudomonas aeruginosa adaptations to the cystic fibrosis lung

inferred← citeshttps://doi.org/10.33540/778openalex-snapshot

Genomic dynamics of antimicrobial resistance in canine and human derived Staphylococcus pseudintermedius

inferred← citeshttps://doi.org/10.3389/fmicb.2019.00809openalex-snapshot

Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin

inferred← citeshttps://doi.org/10.7554/elife.69244openalex-snapshot

Pneumococcal genetic variability in age-dependent bacterial carriage

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