Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes
暂无分享,去创建一个
[1] P. François,et al. Co-Carriage of Metal and Antibiotic Resistance Genes in Sewage Associated Staphylococci , 2021, Genes.
[2] J. McInerney,et al. Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility , 2021, bioRxiv.
[3] E. Snitkin,et al. Hogwash: three methods for genome-wide association studies in bacteria , 2020, bioRxiv.
[4] B. Shapiro,et al. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes , 2020, Microbial genomics.
[5] Christopher Beaudoin,et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline , 2020, Genome Biology.
[6] J. McInerney,et al. Coinfinder: detecting significant associations and dissociations in pangenomes , 2019, bioRxiv.
[7] Xavier Didelot,et al. Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel , 2019, bioRxiv.
[8] J. Corander,et al. Genome-wide epistasis and co-selection study using mutual information , 2019, bioRxiv.
[9] Hong Gu,et al. Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions , 2018, Genome biology and evolution.
[10] Robert A Petit,et al. Staphylococcus aureus viewed from the perspective of 40,000+ genomes , 2018, PeerJ.
[11] Jukka Corander,et al. pyseer: a comprehensive tool for microbial pangenome-wide association studies , 2018, bioRxiv.
[12] Jukka Corander,et al. SuperDCA for genome-wide epistasis analysis , 2017, bioRxiv.
[13] Xavier Didelot,et al. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination , 2017, bioRxiv.
[14] M. Gutmann,et al. Weak Epistasis May Drive Adaptation in Recombining Bacteria , 2017, Genetics.
[15] Jacqueline A. Keane,et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.
[16] Lonneke Scheffer,et al. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary , 2016, Genome Biology.
[17] Tulio de Oliveira,et al. Microbial genome-wide association studies: lessons from human GWAS , 2016, Nature Reviews Genetics.
[18] D. Pillay,et al. Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance , 2016, bioRxiv.
[19] Jukka Corander,et al. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes , 2016, Nature Communications.
[20] Brian D. Ondov,et al. Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.
[21] David A. Clifton,et al. Identifying lineage effects when controlling for population structure improves power in bacterial association studies , 2015, Nature Microbiology.
[22] Peter E. Chen,et al. The advent of genome-wide association studies for bacteria , 2015, bioRxiv.
[23] T. Read,et al. Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology , 2014, Genome Medicine.
[24] W. Hanage,et al. Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes , 2014, PLoS genetics.
[25] Daniel J. Wilson,et al. Predicting the virulence of MRSA from its genome sequence , 2014, Genome research.
[26] Barry G. Hall,et al. SNP-Associations and Phenotype Predictions from Hundreds of Microbial Genomes without Genome Alignments , 2014, PloS one.
[27] Peggy Hall,et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..
[28] T. Mackay. Epistasis and quantitative traits: using model organisms to study gene–gene interactions , 2013, Nature Reviews Genetics.
[29] Razvan Sultana,et al. Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug Resistant Mycobacterium tuberculosis , 2013, Nature Genetics.
[30] Keith A. Jolley,et al. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter , 2013, Proceedings of the National Academy of Sciences.
[31] Tal Pupko,et al. CoPAP: Coevolution of Presence–Absence Patterns , 2013, Nucleic Acids Res..
[32] Tal Pupko,et al. Uncovering the co-evolutionary network among prokaryotic genes , 2012, Bioinform..
[33] J. Lindsay,et al. The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated , 2012, BMC Microbiology.
[34] Andy Purvis,et al. Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits , 2010, Conservation biology : the journal of the Society for Conservation Biology.
[35] Torsten Seemann,et al. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[36] P. Phillips. Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems , 2008, Nature Reviews Genetics.
[37] Manuel A. R. Ferreira,et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.
[38] J. Ott,et al. Complement Factor H Polymorphism in Age-Related Macular Degeneration , 2005, Science.
[39] P. Donnelly,et al. Case-control studies of association in structured or admixed populations. , 2001, Theoretical population biology.
[40] W. Maddison,et al. Testing character correlation using pairwise comparisons on a phylogeny. , 2000, Journal of theoretical biology.
[41] M. Pagel. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.