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: HierCC
https://packages.ecosyste.ms/registries/pypi.org/packages/HierCC
Hierarchical Clustering of cgMLST profiles
8 versions
Latest release: over 3 years ago
37 downloads last month
Papers Mentioning HierCC 15
10.3389/fmicb.2021.649517
Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLSTCited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pgen.1009820
Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into natureCited by: 7
Author(s): Mark Achtman, Frederik Van den Broeck, Kerry K. Cooper, Philippe Lemey, Craig T. Parker, Zhemin Zhou
Software Mentions: 5
Published: about 3 years ago
10.1099/mgen.0.000484
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the GambiaCited by: 14
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Nicholas M. Thomson, Sheikh Jarju, Brenda Kwambana-Adams, Arss Secka, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: almost 4 years ago
10.1099/mgen.0.000428
Genomic diversity of Escherichia coli isolates from non-human primates in the GambiaCited by: 11
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Gaëtan Thilliez, Nicholas M. Thomson, David Baker, Gemma L. Kay, Jennifer Danzy Cramer, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pgen.1008850
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptationCited by: 37
Author(s): Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E. Wheeler, Liljana Petrovska, Timothy J. Dallman, Evelien M. Adriaenssens, Neil Hall, Robert A. Kingsley
Software Mentions: 3
Published: over 4 years ago
10.12688/wellcomeopenres.16291.2
Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes projectCited by: 34
Author(s): Mark Achtman, Zhemin Zhou, Nabil-Fareed Alikhan, William Tyne, Julian Parkhill, Martin Cormican, Chien-Shun Chiou, Mia Torpdahl, Eva Litrup, Deirdre M. Prendergast, John E. Moore, Sam Strain, Christian Kornschober, Richard J. Meinersmann, Alexandra Uesbeck, François‐Xavier Weill, Aidan Coffey, Helene Andrews‐Polymenis, Roy Curtiss, Séamus Fanning
Software Mentions: 2
Published: almost 4 years ago
10.7717/peerj.10256
Genomic characterization and phylogenetic analysis of <i>Salmonella enterica</i> serovar JavianaCited by: 3
Author(s): Lauren K. Hudson, Lisha Constantine-Renna, Linda S Thomas, Charles A. Moore, Xiaorong Qian, Katie Garman, John R. Dunn, Thomas G. Denes
Software Mentions: 2
Published: about 4 years ago
10.3390/ani11010029
Epidemiological and Bacteriological Investigations Using Whole-Genome Sequencing in a Recurrent Outbreak of Pullorum Disease on a Quail Farm in FranceCited by: 5
Author(s): Sophie Le Bouquin, Laetitia Bonifait, Amandine Thépault, Thomas Ledein, François Guillon, Sandra Rouxel, Rozenn Souillard, Marianne Chemaly
Software Mentions: 1
Published: almost 4 years ago
10.3390/antibiotics10091041
Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin SelectionCited by: 5
Author(s): Guerrino Macori, Scott V. Nguyen, Ankita Naithani, Daniel Hurley, Li Bai, Farid El Garch, Frédérique Woehrlé, Christine Miossec, Benjamin Roques, Peadar Ó’Gaora, James L. Bono, Séamus Fanning
Software Mentions: 1
Published: about 3 years ago
10.1186/s12864-019-6260-6
WGS based study of the population structure of Salmonella enterica serovar InfantisCited by: 44
Author(s): Pernille Gymoese, Kristoffer Kiil, Mia Torpdahl, Mark T. Østerlund, Gitte Sørensen, John Elmerdahl Olsen, Eva Møller Nielsen, Eva Litrup
Software Mentions: 1
Published: about 5 years ago
10.3390/antibiotics9040192
Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic SamplesCited by: 24
Author(s): Dafne Díaz-Jiménez, Isidro García-Meniño, Alexandra Herrera, Vanesa García, Ana María López-Beceiro, Marı́a Pilar Alonso, Jorge Blanco, Azucena Mora
Software Mentions: 1
Published: over 4 years ago
10.1017/S0950268820000904
Outbreak of <i>Salmonella</i> Newport associated with internationally distributed raw goats' milk cheese, France, 2018Cited by: 25
Author(s): Eve Robinson, M Travanut, Laëtitia Fabre, S. Larréché, L. Ramelli, Laurence Pascal, A. Guinard, N. Vincent, Clémentine Calba, Laure Meurice, Ma. Le Thien, E. Fourgere, Gabrielle Jones, Nelly Fournet, Alison Smith‐Palmer, D. J. F. Brown, Simon Le Hello, María Pardos de la Gándara, François‐Xavier Weill, N. Jourdan-Da Silva
Software Mentions: 1
Published: almost 5 years ago
10.2807/1560-7917.ES.2020.25.20.1900519
Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogensCited by: 11
Author(s): Michael Payne, Sandeep Kaur, Qinning Wang, Daneeta Hennessy, Lijuan Luo, Sophie Octavia, Mark M. Tanaka, Vitali Sintchenko, Ruiting Lan
Software Mentions: 1
Published: over 4 years ago
10.3389/fcimb.2021.681588
Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From EgyptCited by: 16
Author(s): Hazem Ramadan, Ahmed M. Soliman, Lari M. Hiott, Mohammed Elbediwi, Tiffanie A. Woodley, Marie Anne Chattaway, Claire Jenkins, Jonathan G. Frye, Charlene R. Jackson
Software Mentions: 1
Published: over 3 years ago
10.1099/mgen.0.000410
A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemicsCited by: 19
Author(s): Martinique Frentrup, Zhemin Zhou, Matthias Steglich, Jan P. Meier‐Kolthoff, Markus Göker, Thomas Riedel, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Marion Blaschitz, Alexander Indra, Lutz von Müller, Thomas A. Kohl, Stefan Niemann, Christian Seyboldt, Frank Klawonn, Nitin Kumar, Trevor D. Lawley, Sergio García‐Fernández, Rafael Cantón, Rosa del Campo, Ortrud Zimmermann, Uwe Groß, Mark Achtman, Ulrich Nübel
Software Mentions: 1
Published: over 4 years ago