Ecosyste.ms: Papers

10.1371/journal.pgen.1009065

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago

10.1099/mgen.0.000337

Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes
Cited by: 39
Author(s): Morteza M. Saber, B. Jesse Shapiro
Software Mentions: 8
Published: almost 5 years ago

10.1186/s40168-021-01108-8

Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model
Cited by: 13
Author(s): Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Hao Zhang, Ruifu Yang, Colin Hill, Yu‐Jun Cui, Qixiao Zhai
Software Mentions: 6
Published: over 3 years ago

10.1128/mBio.02882-20

Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus
Cited by: 23
Author(s): Stefano Giulieri, Romain Guérillot, Jason C Kwong, Ian R. Monk, Ashleigh S Hayes, Diane Daniel, Sarah L. Baines, Norelle L Sherry, Natasha E Holmes, Peter Ward, Wei Gao, Torsten Seemann, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 5
Published: about 4 years ago

10.1128/mSphere.01263-20

Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale
Cited by: 17
Author(s): Abraham G Moller, Kyle Winston, Sang Yong Ji, Junting Wang, Michelle N. Hargita Davis, Claudia Solís-Lemus, Timothy D. Read
Software Mentions: 5
Published: almost 4 years ago

10.1099/mgen.0.000581

Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species
Cited by: 13
Author(s): Yue Xiao, Jianxin Zhao, Hao Zhang, Qixiao Zhai
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1008518

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers
Cited by: 10
Author(s): Julian Libiseller-Egger, Jody Phelan, Susana Campino, Fady Mohareb, Taane G. Clark
Software Mentions: 4
Published: about 4 years ago

10.3389/fpubh.2020.00451

Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii
Cited by: 6
Author(s): Chandler C. Roe, Charles H. D. Williamson, Adam J. Vazquez, Kristen Kyger, Michael Valentine, Jolene R. Bowers, P.D. Phillips, Veronica Harrison, Elizabeth M. Driebe, David M. Engelthaler, Jason W. Sahl
Software Mentions: 4
Published: over 4 years ago

10.1099/mgen.0.000469

Hogwash: three methods for genome-wide association studies in bacteria
Cited by: 11
Author(s): Katie Saund, Evan S. Snitkin
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.01344-20

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions
Cited by: 57
Author(s): John A. Lees, The Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel Horsfield, Julian Parkhill, Jukka Corander
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-020-02090-4

Producing polished prokaryotic pangenomes with the Panaroo pipeline
Cited by: 327
Author(s): Gerry Tonkin‐Hill, Neil MacAlasdair, Christopher Ruis, Aaron Weimann, Gal Horesh, John A. Lees, Rebecca A. Gladstone, Stephanie Lo, Christopher Beaudoin, R. Andres Floto, Simon D. W. Frost, Jukka Corander, Stephen D. Bentley, Julian Parkhill
Software Mentions: 3
Published: over 4 years ago

10.1089/cmb.2020.0375

Estimating Genetic Similarity Matrices Using Phylogenies
Cited by: 3
Author(s): Shijia Wang, Shufei Ge, Caroline Colijn, Priscila Biller, Liangliang Wang, Lloyd T. Elliott
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-89683-6

Genome-wide insights into population structure and host specificity of Campylobacter jejuni
Cited by: 17
Author(s): Lennard Epping, Birgit Walther, Rosario M. Piro, Marie-Theres Knüver, Charlotte Huber, Andrea Thürmer, Antje Flieger, Angelika Fruth, Nicol Janecko, Lothar H. Wieler, Kerstin Stingl, Torsten Semmler
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1007758

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
Cited by: 129
Author(s): Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix, Laurent Jacob
Software Mentions: 1
Published: about 6 years ago

10.1093/bioinformatics/bty539

pyseer: a comprehensive tool for microbial pangenome-wide association studies
Cited by: 175
Author(s): John A. Lees, Marco Galardini, Stephen D. Bentley, Jeffrey N. Weiser, Jukka Corander
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-021-04079-7

Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting
Cited by: 5
Author(s): Paul Turner, Jukka Corander
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-55086-x

Genome investigations show host adaptation and transmission of LA-MRSA CC398 from pigs into Danish healthcare institutions
Cited by: 44
Author(s): Raphael N. Sieber, Anders Rhod Larsen, Tinna Ravnholt Urth, Søren Iversen, Camilla Holten Møller, Robert Skov, Jesper Larsen, Marc Stegger
Software Mentions: 1
Published: about 5 years ago