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: pyani

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

pyani provides a package and script for calculation of genome-scale average nucleotide identity.
18 versions
Latest release: over 2 years ago
1 dependent package
610 downloads last month

Papers Mentioning pyani 120

Corynebacterium rouxii, a recently described member of the C. diphtheriae group isolated from three dogs with ulcerative skin lesions
Cited by: 4
Author(s): Karen Schlez, Tobias Eisenberg, Jörg Rau, Sabine Dubielzig, Matthias Kornmayer, Georg Wolf, Anja Berger, Alexandra Dangel, Christiane Hoffmann, Christa Ewers, Andreas Sing
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.664810

Isolation and Characterization of a Novel Salmonella Phage vB_SalP_TR2
Cited by: 28
Author(s): Yuting Shang, Qifan Sun, Hanfang Chen, Qingping Wu, Moutong Chen, Shuanghong Yang, Mingzhu Du, Fei Zha, Qinghua Ye, Jumei Zhang
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00485-20

Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery
Cited by: 8
Author(s): Alex J. Mullins, Jones Ca, Matthew Bull, Gordon Webster, Julian Parkhill, Thomas R. Connor, James A. H. Murray, Gregory L. Challis, Eshwar Mahenthiralingam
Software Mentions: 1
Published: about 4 years ago

10.1128/mSphere.00971-19

To Dereplicate or Not To Dereplicate?
Cited by: 15
Author(s): Jacob T. Evans, Vincent J. Denef
Software Mentions: 1
Published: over 4 years ago

10.1002/mbo3.938

Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway
Cited by: 13
Author(s): Alfonso Esposito, Sabrina Tamburini, Luca Triboli, Luca Ambrosino, Maria Luisa Chiusano, Olivier Jousson
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2021.732969

Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine
Cited by: 9
Author(s): Vanina Guernier, Julian Trachsel, Joel J. Maki, Jing Qi, Matthew J. Sylte, Zahra Hanafy, Sophia Kathariou, Torey Looft
Software Mentions: 1
Published: about 3 years ago

10.1186/s42523-019-0015-1

Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis
Cited by: 28
Author(s): Raymond Kiu, Joseph Brown, Harley Bedwell, Charlotte Leclaire, Shabhonam Caim, Derek Pickard, Gordon Dougan, Ronald Dixon, Lindsay J. Hall
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2020.01535

First Genome Sequences of Two Multidrug-Resistant Candida haemulonii var. vulnera Isolates From Pediatric Patients With Candidemia
Cited by: 6
Author(s): Luiza Souza Rodrigues, Rajesh Kumar Gazara, Hemanoel Passarelli‐Araujo, Andressa Eloisa Valengo, Paula Veronesi Marinho Pontes, Rodrigo Nunes da Fonseca, Robson Francisco de Souza, Thiago M. Venâncio, Líbera Maria Dalla-Costa
Software Mentions: 1
Published: over 4 years ago

10.1007/s10482-021-01637-0

Characterization of clinical Ralstonia strains and their taxonomic position
Cited by: 14
Author(s): Ad C. Fluit, Jumamurat R. Bayjanov, María Díez Aguilar, Rafael Cantón, Michael Tunney, J.S. Elborn, Mireille van Westreenen, Miquel B. Ekkelenkamp
Software Mentions: 1
Published: about 3 years ago

10.3389/fvets.2019.00128

First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China
Cited by: 4
Author(s): Dekang Zhu, Jianbang Wan, Zhishuang Yang, Jinge Xu, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Xiaoyue Chen, Anchun Cheng
Software Mentions: 1
Published: over 5 years ago

10.3390/genes11091104

Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance
Cited by: 6
Author(s): Eva Müller, Mostafa Y. Abdel-Glil, Helmut Hotzel, Ingrid Hänel, Herbert Tomaso
Software Mentions: 1
Published: about 4 years ago

10.1128/genomeA.01280-17

Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere
Cited by: 2
Author(s): Víctor Manuel Ruíz-Valdiviezo, Marco Antonio Rogel-Hernández, Gabriela Guerrero, Clara Ivette Rincón-Molina, Luis Galdino García-Perez, Federico Antonio Gutiérrez-Miceli, Juan José Villalobos-Maldonado, Aline López-López, Esperanza Martı́nez-Romero, Reiner Rincón-Rosales
Software Mentions: 1
Published: about 7 years ago

10.1186/s12866-021-02140-2

Molecular characterisation of Mycobacterium avium subsp. paratuberculosis in Australia
Cited by: 3
Author(s): Rachel Hodgeman, Rachel Mann, Keith W. Savin, Noel Djitro, Simone Rochfort, Brendan Rodoni
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-019-5982-9

Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts
Cited by: 13
Author(s): Helisson Faoro, Willian K. Oliveira, Vinícius Almir Weiss, Michelle Z. Tadra-Sfeir, Rodrigo Luis Alves Cardoso, Eduardo Balsanelli, Liziane Cristina Campos Brusamarello-Santos, Doumit Camilios-Neto, Leonardo M. Cruz, Roberto Tadeu Raittz, Ana C. Marques, John J. LiPuma, Geraldo Picheth, Emanuel Maltempi de Souza, Fábio O. Pedrosa
Software Mentions: 1
Published: over 5 years ago

10.1111/mpp.12925

Genome‐wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors
Cited by: 52
Author(s): Shree Prasad Thapa, Agustina De Francesco, Jessica Trinh, Fatta B. Gurung, Zhe Pang, Georgios Vidalakis, Nian Wang, Veronica Ancona, Wenbo Ma, Gitta Coaker
Software Mentions: 1
Published: over 4 years ago

10.3390/v12060601

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia
Cited by: 6
Author(s): Rebecca Weiser, Zhong Ling Yap, Ashley Otter, Brian V. Jones, Jonathan P. Salvage, Julian Parkhill, Eshwar Mahenthiralingam
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8081166

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene
Cited by: 14
Author(s): Léa Girard, Cédric Lood, Hassan Rokni‐Zadeh, Vera van Noort, Rob Lavigne, René De Mot
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms9010146

Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
Cited by: 17
Author(s): Caroline Öhrman, Jason W. Sahl, Andreas Sjödin, Ingrid Uneklint, Rebecca Ballard, Linda Karlsson, Ryelan F. McDonough, David Sundell, Kathleen Soria, Stina Bäckman, Kitty Chase, Björn Brindefalk, Shanmuga Sozhamannan, Adriana Vallesi, Emil Hägglund, José Gustavo Ramírez‐Paredes, Johanna Thelaus, Duncan J. Colquhoun, Kerstin Myrtennäs, Dawn N. Birdsell, Anders Johansson, David M. Wagner, Mats Forsman
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.9151

Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov
Cited by: 48
Author(s): Debra A. Brock, Suegene Noh, Alicia N.M. Hubert, Tamara S. Haselkorn, Susanne DiSalvo, Melanie K Suess, Alexander S. Bradley, Mahboubeh Tavakoli-Nezhad, Katherine S Geist, David C. Queller, Joan E. Strassmann
Software Mentions: 1
Published: over 4 years ago

10.1186/s40168-018-0579-0

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea
Cited by: 17
Author(s): Quanyin Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin Pham, Zhi Jiang, Herbert L. DuPont, Sarah K. Highlander
Software Mentions: 1
Published: about 6 years ago