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: chewBBACA

https://packages.ecosyste.ms/registries/pypi.org/packages/chewBBACA

A complete suite for gene-by-gene schema creation and strain identification.
35 versions
Latest release: about 1 year ago
63 downloads last month

Papers Mentioning chewBBACA 22

10.1099/mgen.0.000552

Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Cited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.1099/mgen.0.000491

Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes
Cited by: 10
Author(s): Stefanie Lüth, Carlus Deneke, Sylvia Kleta, Sascha Al Dahouk
Software Mentions: 9
Published: almost 4 years ago

10.3389/fcimb.2020.608020

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes
Cited by: 12
Author(s): Morgane Nennig, Ann-Katrin Llarena, Malte Herold, Joël Mossong, Christian Penny, Serge Losch, Odile Tresse, Catherine Ragimbeau
Software Mentions: 4
Published: almost 4 years ago

10.1186/s42522-020-0010-1

Typing methods based on whole genome sequencing data
Cited by: 72
Author(s): Laura Uelze, Josephine Grützke, Maria Blettner, Jens A. Hammerl, Katharina Juraschek, Carlus Deneke, Simon H. Tausch, Burkhard Malorny
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9091911

What WGS Reveals about Salmonella enterica subsp. enterica in Wildlife in Germany
Cited by: 8
Author(s): Laura Uelze, Angelina Bloch, Maria Blettner, Mirjam Grobbel, Carlus Deneke, Matthias Fischer, Burkhard Malorny, Michael Pietsch, Sandra Simon, István Szabó, Simon H. Tausch, Jennie Fischer
Software Mentions: 2
Published: about 3 years ago

10.1155/2019/1860275

Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal
Cited by: 8
Author(s): Leonor Silveira, Miguel Pinto, Joana Isidro, Ângela Pista, Patrícia Themudo, Luı́s Vieira, Jorge Machado, João Paulo Gomes
Software Mentions: 2
Published: almost 5 years ago

10.1128/AEM.02910-18

Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk
Cited by: 16
Author(s): Anniina Jaakkonen, Hanna Castro, Saija Hallanvuo, Jukka Ranta, Mirko Rossi, Joana Isidro, Miia Lindström, Marjaana Hakkinen
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2020.00260

Tracing Back the Evolutionary Route of Enteroinvasive Escherichia coli (EIEC) and Shigella Through the Example of the Highly Pathogenic O96:H19 EIEC Clone
Cited by: 6
Author(s): Valeria Michelacci, Rosangela Tozzoli, Silvia Arancia, Alfio D'Angelo, Arianna Boni, Arnold Knijn, Gianni Prosseda, David R. Greig, Claire Jenkins, Teresa Camou, Alfredo Sirok, Alexandre Guida Navarro, Felipé Schelotto, Gustavo Varela, Stefano Morabito
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.573972

German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing
Cited by: 10
Author(s): Laura Uelze, Maria Blettner, Markus Bönn, Erik Brinks, Carlus Deneke, Thomas Hankeln, Sylvia Kleta, Larissa Murr, Kerstin Stingl, Kathrin Szabo, Simon H. Tausch, Anne Wöhlke, Burkhard Malorny
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.626941

Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
Cited by: 14
Author(s): Laura Uelze, Natalie Becker, Maria Blettner, Ulrich Busch, Alexandra Dangel, Carlus Deneke, Jennie Fischer, Antje Flieger, Sabrina Hepner, Ingrid Huber, Ulrich Methner, Jörg Linde, Michael Pietsch, Sandra Simon, Andreas Sing, Simon H. Tausch, István Szabó, Burkhard Malorny
Software Mentions: 2
Published: over 3 years ago

10.1099/mgen.0.000166

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Cited by: 162
Author(s): Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Susana Santos, Mário Ramirez, João André Carriço
Software Mentions: 2
Published: over 6 years ago

10.3390/pathogens10050591

A Nosocomial Outbreak of Invasive Listeriosis in An Italian Hospital: Epidemiological and Genomic Features
Cited by: 12
Author(s): Valeria Russini, Martina Spaziante, T. Zottola, Anna Giovanna Fermani, Gina Di Giampietro, Giovanni Blanco, Paolo Fabietti, Riccardo Marrone, Roberta Parisella, Sergio Parrocchia, Teresa Bossù, Stefano Bilei, Maria Laura De Marchis
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-020-06817-2

The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis
Cited by: 8
Author(s): Áron Botond Kovács, Zsuzsa Kreizinger, Barbara Forró, Dénes Grózner, Alexa Mitter, Szilvia Marton, Krisztina Bali, Anna Sawicka, Grzegorz Tomczyk, Krisztián Bànyai, Miklós Gyuranecz
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8060900

Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans
Cited by: 4
Author(s): Gema Carrasco, Sara Monzón, María San Segundo, E García, Noelia Garrido, María José Medina, Pilar Villalón, Ana S. Ramírez, Pilar Jiménez, Isabel Cuesta, Sylvia Valdezate
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms7050113

Nontuberculous Mycobacteria Persistence in a Cell Model Mimicking Alveolar Macrophages
Cited by: 10
Author(s): Susana Sousa, Vítor Borges, Inês João, João Paulo Gomes, Luísa Jordão
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens9110868

Human Campylobacteriosis Cases Traceable to Chicken Meat—Evidence for Disseminated Outbreaks in Finland
Cited by: 3
Author(s): Ann-Katrin Llarena, Rauni Kivistö
Software Mentions: 1
Published: about 4 years ago

10.3390/pathogens9050363

Identification of Transmission Routes of Campylobacter and On-Farm Measures to Reduce Campylobacter in Chicken
Cited by: 22
Author(s): Sara Frosth, Oskar Karlsson Lindsjö, Adnan Niazi, Lise-Lotte Fernström, Ingrid Hansson
Software Mentions: 1
Published: over 4 years ago

10.3390/antibiotics10030304

Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA
Cited by: 6
Author(s): Sylvia Valdezate, Fernando Cobo, Sara Monzón, María José Medina, Ángel Zaballos, Isabel Cuesta, Pilar Villalón
Software Mentions: 1
Published: over 3 years ago

10.1038/s41396-020-00819-4

Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
Cited by: 59
Author(s): Fabienne Benz, Jana S. Huisman, Erik Bakkeren, Joana Anuschka Herter, Tanja Stadler, Martin Ackermann, Médéric Diard, Adrian Egli, Alex R. Hall, Wolf‐Dietrich Hardt, Sebastian Bonhoeffer
Software Mentions: 1
Published: about 4 years ago

10.1155/2021/6636138

Retrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247
Cited by: 5
Author(s): Mihkel Mäesaar, Rafael Mamede, Terje Elias, Mati Roasto
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms21249419

Whole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland
Cited by: 16
Author(s): Kinga Wieczorek, Arkadiusz Bomba, Jacek Osek
Software Mentions: 1
Published: almost 4 years ago