Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: pyseer
https://packages.ecosyste.ms/registries/pypi.org/packages/pyseer
Papers Mentioning pyseer 17
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 studyCited 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 phenotypesCited by: 39
Author(s): Morteza M. Saber, B. Jesse Shapiro
Software Mentions: 8
Published: over 4 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 modelCited 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: about 3 years ago
10.1128/mBio.02882-20
Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureusCited 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: almost 4 years ago
10.1128/mSphere.01263-20
Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide ScaleCited 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: over 3 years ago
10.1099/mgen.0.000581
Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium speciesCited 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 markersCited by: 10
Author(s): Julian Libiseller-Egger, Jody Phelan, Susana Campino, Fady Mohareb, Taane G. Clark
Software Mentions: 4
Published: almost 4 years ago
10.3389/fpubh.2020.00451
Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumanniiCited 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: about 4 years ago
10.1099/mgen.0.000469
Hogwash: three methods for genome-wide association studies in bacteriaCited 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 RegressionsCited 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: about 4 years ago
10.1186/s13059-020-02090-4
Producing polished prokaryotic pangenomes with the Panaroo pipelineCited 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 PhylogeniesCited 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 jejuniCited 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 eventsCited by: 129
Author(s): Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix, Laurent Jacob
Software Mentions: 1
Published: almost 6 years ago
10.1093/bioinformatics/bty539
pyseer: a comprehensive tool for microbial pangenome-wide association studiesCited 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 splittingCited 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 institutionsCited 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: almost 5 years ago