Filters








8 Hits in 1.9 sec

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph [article]

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Remi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Medigue, Alexandra Calteau, Stephane Cruveiller, Catherine Matias, Christophe Ambroise (+2 others)
2019 bioRxiv   pre-print
The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative  ...  We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood.  ...  Acknowledgements We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo.  ... 
doi:10.1101/836239 fatcat:utqwlatqkncbleusf2edbx54ei

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise (+3 others)
2020 PLoS Computational Biology  
The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative  ...  We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood.  ...  Acknowledgments We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo.  ... 
doi:10.1371/journal.pcbi.1007732 pmid:32191703 pmcid:PMC7108747 fatcat:ff6ccvwavzcutaxtxcvntfb74e

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

2019 Nucleic Acids Research  
We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs.  ...  Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial  ...  each PPanGGOLiN partition.  ... 
doi:10.1093/nar/gkz926 pmid:31647104 pmcid:PMC7145621 fatcat:dwdxeaytnvar7iq3kudicrcz2q

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome [article]

Stephany Flores Ramos, Silvio D. Brugger, Isabel Fernández Escapa, Chelsey A Skeete, Sean L Cotton, Sara M Eslami, Wei Gao, Lindsey Bomar, Tommy H Tran, Dakota S Jones, Samuel Minot, Richard J Roberts (+2 others)
2021 bioRxiv   pre-print
A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense  ...  To gain insight into D. pigrum's chromosomal structure, pangenome and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years.  ...  (B) This PPanGGOLiN partitioned pangenome graph displays the overall genomic diversity of the 28 D. pigrum genomes.  ... 
doi:10.1101/2021.04.16.440249 fatcat:rhfoq3rwv5d6daaeohmn4whnau

Evidence for selection in a prokaryote pangenome [article]

Fiona Jane Whelan, Rebecca J Hall, James O McInerney
2020 bioRxiv   pre-print
A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection.  ...  Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.  ...  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. Blanchet, F. G., Cazelles, K. & Gravel, D. Co-occurrence is not evidence of ecological interactions.  ... 
doi:10.1101/2020.10.28.359307 fatcat:whzhx6jbefdzbgadrseybhaxki

Construction of a complete set of Neisseria meningitidis defined mutants - the NeMeSys collection - and its use for the phenotypic profiling of the genome of an important human pathogen [article]

Alastair Muir, Ishwori Gurung, Ana Cehovin, Adelme Bazin, David Vallenet, Vladimir Pelicic
2020 bioRxiv   pre-print
The NeMeSys collection is an invaluable resource paving the way for a global phenotypic landscape in a major human bacterial pathogen.  ...  Even in model bacterial species, there is a sizeable proportion of such genes, which has important theoretical and practical consequences.  ...  PPanGGOLiN: Depicting microbial diversity via a partitioned 741 pangenome graph. PLoS Comput. Biol. 16, e1007732 (2020). 742 22. Hutchison, C.A. et al.  ... 
doi:10.1101/2020.08.12.247981 fatcat:oapiryjhkngmhakm7jpoj442rq

Plateforme numérique pour l'antibiorésistance, ABRomics [article]

Claudine Médigue, Philippe Glaser, Consortium ABRomics
2021 Zenodo  
Antibiotic resistance (ABR) is a major public health problem and a threat for the future.  ...  It covers the diversity of ABR research in clinical and fundamental fields, mathematical modeling methods and the whole range of expertise in computer science, bioinformatics, database and computer architecture  ...  The development of the Meta-PanGenomic graph method will be conducted in strong interaction with WP3 of ABROmics, particularly in Task 3.3.1.  ... 
doi:10.5281/zenodo.5230261 fatcat:lhtpmfwdjnddhi6cdilfpccc7q

Evidence for selection in the abundant accessory gene content of a prokaryote pangenome

Fiona J Whelan, Rebecca J Hall, James O McInerney
2021 Molecular biology and evolution  
Keyword: pangenome, microbial genomics, selection.  ...  A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection.  ...  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. 520 PLoS Computational Biology . 521 [Goyal2018] Goyal, A. 2018.  ... 
doi:10.1093/molbev/msab139 pmid:33963386 pmcid:PMC8382901 fatcat:hear75o4wjafralefr47ohe3za