Cargando…

Genome-wide epistasis and co-selection study using mutual information

Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pensar, Johan, Puranen, Santeri, Arnold, Brian, MacAlasdair, Neil, Kuronen, Juri, Tonkin-Hill, Gerry, Pesonen, Maiju, Xu, Yingying, Sipola, Aleksi, Sánchez-Busó, Leonor, Lees, John A, Chewapreecha, Claire, Bentley, Stephen D, Harris, Simon R, Parkhill, Julian, Croucher, Nicholas J, Corander, Jukka
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2019
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765119/ https://www.ncbi.nlm.nih.gov/pubmed/31361894 http://dx.doi.org/10.1093/nar/gkz656

Ejemplares similares

SuperDCA for genome-wide epistasis analysis
por: Puranen, Santeri, et al.
Publicado: (2018)

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
por: Skwark, Marcin J., et al.
Publicado: (2017)

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium
por: Top, Janetta, et al.
Publicado: (2020)

The effect of recombination on the evolution of a population of Neisseria meningitidis
por: MacAlasdair, Neil, et al.
Publicado: (2021)

Producing polished prokaryotic pangenomes with the Panaroo pipeline
por: Tonkin-Hill, Gerry, et al.
Publicado: (2020)

Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment
por: Chewapreecha, Claire, et al.
Publicado: (2021)

Probabilistic Prediction of Contacts in Protein-Ligand Complexes
por: Hakulinen, Riku, et al.
Publicado: (2012)

Challenges in prokaryote pangenomics
por: Tonkin-Hill, Gerry, et al.
Publicado: (2023)

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets
por: Pessia, Alberto, et al.
Publicado: (2015)

Causal discovery for the microbiome
por: Corander, Jukka, et al.
Publicado: (2022)

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
por: Lees, John A., et al.
Publicado: (2016)

The impact of antimicrobials on gonococcal evolution
por: Sánchez-Busó, Leonor, et al.
Publicado: (2019)

Two-phase importance sampling for inference about transmission trees
por: Numminen, Elina, et al.
Publicado: (2014)

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS
por: Tonkin-Hill, Gerry, et al.
Publicado: (2018)

Fast hierarchical Bayesian analysis of population structure
por: Tonkin-Hill, Gerry, et al.
Publicado: (2019)

Fast and flexible bacterial genomic epidemiology with PopPUNK
por: Lees, John A., et al.
Publicado: (2019)

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era
por: Pöntinen, Anna K., et al.
Publicado: (2021)

Pneumococcal within-host diversity during colonization, transmission and treatment
por: Tonkin-Hill, Gerry, et al.
Publicado: (2022)

Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation
por: Lees, John A., et al.
Publicado: (2022)

Climate induces seasonality in pneumococcal transmission
por: Numminen, Elina, et al.
Publicado: (2015)

Corrigendum: Climate induces seasonality in pneumococcal transmission
por: Numminen, Elina, et al.
Publicado: (2016)

Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae
por: Mallawaarachchi, Sudaraka, et al.
Publicado: (2022)

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium
por: Arredondo-Alonso, S., et al.
Publicado: (2020)

Dense genomic sampling identifies highways of pneumococcal recombination
por: Chewapreecha, Claire, et al.
Publicado: (2014)

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
por: Tonkin-Hill, Gerry, et al.
Publicado: (2023)

pyseer: a comprehensive tool for microbial pangenome-wide association studies
por: Lees, John A, et al.
Publicado: (2018)

PANINI: Pangenome Neighbour Identification for Bacterial Populations
por: Abudahab, Khalil, et al.
Publicado: (2018)

PYLFIRE: Python implementation of likelihood-free inference by ratio estimation
por: Kokko, Jan, et al.
Publicado: (2019)

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions
por: Lees, John A., et al.
Publicado: (2020)

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
por: Harrow, Gabrielle L., et al.
Publicado: (2021)

Detection of recombination events in bacterial genomes from large population samples
por: Marttinen, Pekka, et al.
Publicado: (2012)

Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach
por: Everett, Dean B., et al.
Publicado: (2012)

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae
por: Lehtinen, Sonja, et al.
Publicado: (2020)

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics
por: Corander, Jukka, et al.
Publicado: (2017)

Epistasis and Entropy
por: Crona, Kristina
Publicado: (2016)

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection
por: McNally, Alan, et al.
Publicado: (2019)

Identification, variation and transcription of pneumococcal repeat sequences
por: Croucher, Nicholas J, et al.
Publicado: (2011)

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
por: Lees, John A, et al.
Publicado: (2017)

Recombination produces coherent bacterial species clusters in both core and accessory genomes
por: Marttinen, Pekka, et al.
Publicado: (2015)

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci
por: Kremer, Philip H.C., et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_ba3d4lju68h1ilmk4hd1j1d0rt