pypi: qcat | Projects | Ecosyste.ms: Papers

10.1128/mSphere.00743-20

Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: over 3 years ago

10.3390/ijms22189824

Species-Specific Humoral Immune Responses in Sheep and Goats upon Small Ruminant Lentivirus Infections Inversely Correlate with Protection against Virus Replication and Pathological Lesions
Cited by: 2
Author(s): Rodolphe Michiels, Stefan Roels, Nick Vereecke, Élisabeth Mathijs, Laurent Mostin, Nick De Regge
Software Mentions: 6
Published: about 3 years ago

10.3390/genes11040445

MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples
Cited by: 25
Author(s): Adeline Seah, Marisa Lim, Denise McAloose, Stefan Prost, Tracie A. Seimon
Software Mentions: 5
Published: over 4 years ago

10.3390/genes12010106

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing
Cited by: 37
Author(s): Sarah Stahl-Rommel, Miten Jain, Hang N. Nguyen, Richard R. Arnold, Serena M. Auñón-Chancellor, Gretta Marie Sharp, C. L. Castro, Kristen K. John, Sissel Juul, Daniel J. Turner, David Stoddart, Benedict Paten, Mark Akeson, Aaron S. Burton, Sarah L. Castro-Wallace
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.01022

Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions
Cited by: 14
Author(s): Elizabeth A. Savory, Alexandra J. Weisberg, Danielle M. Stevens, Allison Creason, Skylar L Fuller, Emma M Pearce, Jeff H. Chang
Software Mentions: 4
Published: over 4 years ago

10.1128/MRA.01288-19

Chromosome-Scale Genome Assembly of Two Australian Nannochloropsis oceanica Isolates Exhibiting Superior Lipid Characteristics
Cited by: 10
Author(s): Reuben B. Brown, Taylor J. Wass, Skye R. Thomas‐Hall, Peer M. Schenk
Software Mentions: 3
Published: almost 5 years ago

10.3390/vaccines9060594

Comparison of Primary Virus Isolation in Pulmonary Alveolar Macrophages and Four Different Continuous Cell Lines for Type 1 and Type 2 Porcine Reproductive and Respiratory Syndrome Virus
Cited by: 3
Author(s): Jiexiong Xie, Nick Vereecke, Sebastiaan Theuns, Dayoung Oh, Nathalie Vanderheijden, Ivan Trus, Jannes Sauer, Philip Vyt, Caroline Bonckaert, Christian Lalonde, Chantale Provost, Carl A. Gagnon, Hans Nauwynck
Software Mentions: 3
Published: over 3 years ago

10.1007/s00253-019-10021-y

A deletion in the STA1 promoter determines maltotriose and starch utilization in STA1+ Saccharomyces cerevisiae strains
Cited by: 29
Author(s): Kristoffer Krogerus, Frederico Magalhães, Joosu Kuivanen, Brian Gibson
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-020-03856-0

High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
Cited by: 33
Author(s): Nick Vereecke, Jade Bokma, Freddy Haesebrouck, Hans Nauwynck, Filip Boyen, Bart Pardon, Sebastiaan Theuns
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-021-07767-z

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
Cited by: 20
Author(s): Valentine Murigneux, Leah W. Roberts, Brian M. Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam Irwin, Patrick N A Harris, David L. Paterson, Mark A. Schembri, David M. Whiley, Scott A. Beatson
Software Mentions: 3
Published: about 3 years ago

10.1099/mgen.0.000428

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
Cited 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

10.1128/MRA.00333-21

Genome Sequences of Equine Herpesvirus 1 Strains from a European Outbreak of Neurological Disorders Linked to a Horse Gathering in Valencia, Spain, in 2021
Cited by: 10
Author(s): Nick Vereecke, Flora Carnet, Stéphane Pronost, Katleen Vanschandevijl, Sebastiaan Theuns, Hans Nauwynck
Software Mentions: 3
Published: over 3 years ago

10.3390/v12080801

Determining the Suitability of MinION’s Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification
Cited by: 10
Author(s): Deborah M. Leigh, Christopher Schefer, Carolina Cornejo
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2020.596626

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
Cited by: 3
Author(s): Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard Ø. Palsson, M. N. Parenteau
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2021.647565

Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting
Cited by: 6
Author(s): Meshack O Juma, Arun Sankaradoss, Redcliff Ndombi, Patrick Mwaura, Tina Damodar, Junaid Nazir, Awadhesh Pandit, Rupsy Khurana, Moses Masika, Ruth Chirchir, John Gachie, Sudhir Krishna, Ramanathan Sowdhamini, Omu Anzala, Iyer Meenakshi
Software Mentions: 3
Published: about 3 years ago

10.1128/JVI.01869-20

The Human Adenovirus 2 Transcriptome: an Amazing Complexity of Alternatively Spliced mRNAs
Cited by: 11
Author(s): Amanda Westergren Jakobsson, Bo Segerman, Ola Wallerman, Sara Bergström Lind, Hongxing Zhao, Carl-Johan Rubin, Ulf Pettersson, Göran Akusjärvi
Software Mentions: 3
Published: over 3 years ago

10.3390/pathogens10070896

West Nile Virus in Brazil
Cited by: 15
Author(s): Érica Azevedo Costa, Marta Giovanetti, Lilian Silva Catenacci, Vagner Fonseca, Flávia Figueira Aburjaile, Flávia Löwen Levy Chalhoub, Joilson Xavier, Felipe Campos de Melo Iani, Marcelo Adriano da Cunha e Silva Vieira, Danielle Freitas Henriques, Daniele Barbosa de Almeida Medeiros, Maria Isabel Maldonado Coelho Guedes, Beatriz Senra Álvares da Silva Santos, Aila Solimar Gonçalves Silva, Renata de Pino Albuquerque Maranhão, Nieli Rodrigues da Costa Faria, Renata Farinelli de Siqueira, Túlio de Oliveira, Karina Ribeiro Leite Jardim Cavalcante, Noely Fabiana Oliveira de Moura, Alessandro Romano, Carlos Frederico Campelo de Albuquerque, Lauro César Soares Feitosa, José Joffre Martins Bayeux, Raffaella Bertoni Cavalcanti Teixeira, Osmaikon Lisboa Lobato, Silvokleio da Costa Silva, Ana María Bispo de Filippis, Rivaldo Venâncio da Cunha, José Lourenço, Luíz Carlos Júnior Alcântara
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pntd.0009591

Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil
Cited by: 11
Author(s): Stephane Tosta, Marta Giovanetti, Vanessa Brandão Nardy, Luciana Reboredo de Oliveira da Silva, Marcela Gómez, Jaqueline Gomes Lima, Cristiane Wanderley Cardoso, Tarcisio Oliveira Silva, Márcia São Pedro Leal Souza, Pedro Henrique Presta Dia, Vagner Fonseca, Túlio de Oliveira, José Lourenço, Luiz Carlos Júnior Alcântara, Felicidade Mota Pereira, Ana Leal
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0253403

A CRISPR-based assay for the study of eukaryotic DNA repair onboard the International Space Station
Cited by: 5
Author(s): Sarah Stahl-Rommel, David Li, Michelle Sung, Rebecca Li, Aarthi Vijayakumar, Kutay Deniz Atabay, G. Guy Bushkin, C. L. Castro, Kevin Foley, D. Scott Copeland, Sarah L. Castro-Wallace, Ezequiel Alvarez Saavedra, Emily Gleason, Sebastian Kraves
Software Mentions: 2
Published: about 3 years ago

10.3390/microorganisms9040834

Presence of Broad-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Zoo Mammals
Cited by: 7
Author(s): Chloë De Witte, Nick Vereecke, Sebastiaan Theuns, Claudia De Ruyck, Francis Vercammen, Tim Bouts, Filip Boyen, Hans Nauwynck, Freddy Haesebrouck
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.637771

Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing
Cited by: 5
Author(s): Xinqi Wu, Hao Luo, Feng Xu, Chongtao Ge, Shaoting Li, Xiangyu Deng, Martin Wiedmann, R. C. Baker, Abigail E. Stevenson, Guangtao Zhang, Silin Tang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.725414

Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers
Cited by: 19
Author(s): Fiona Valerie Franklin-Alming, Håkon Kaspersen, Marit Andrea Klokkhammer Hetland, Ragna-Johanne Bakksjø, Live L. Nesse, Thongpan Leangapichart, Iren Høyland Löhr, Amar A. Telke, Marianne Sunde
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2020.00844

The Application of Nanopore Sequencing Technology to the Study of Dinoflagellates: A Proof of Concept Study for Rapid Sequence-Based Discrimination of Potentially Harmful Algae
Cited by: 19
Author(s): Robert G. Hatfield, Frederico M. Batista, Timothy Bean, Vera G. Fonseca, Andrés Santos, Andrew D. Turner, Adam M. Lewis, Karl Dean, Jaime Martínez-Urtaza
Software Mentions: 2
Published: over 4 years ago

10.3390/genes10080578

Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)
Cited by: 17
Author(s): Samir V. Deshpande, Timothy M Reed, Raymond F. Sullivan, Lee J. Kerkhof, Keith M Beigel, Mary Margaret Wade
Software Mentions: 2
Published: about 5 years ago

10.1186/s13567-020-00848-z

Phylogenomic analysis of Mycoplasma bovis from Belgian veal, dairy and beef herds
Cited by: 15
Author(s): Jade Bokma, Nick Vereecke, Koen De Bleecker, Jozefien Callens, Stefaan Ribbens, Hans Nauwynck, Freddy Haesebrouck, Sebastiaan Theuns, Filip Boyen, Bart Pardon
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.10778

Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis
Cited by: 13
Author(s): Liying Low, Pablo Fuentes-Utrilla, James Hodson, John D. O’Neil, Amanda E. Rossiter, Ghazala Begum, Kusy Suleiman, Philip I. Murray, Graham R. Wallace, Nicholas J. Loman, Saaeha Rauz
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pntd.0009290

Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas
Cited by: 14
Author(s): Elaine Cristina de Oliveira, Vagner Fonseca, Joilson Xavier, Talita Adelino, Ingra Morales Claro, Allison Fabri, Eduardo Marques Macário, Ana Elisa Viniski, Cláudio Luís Campos Souza, Evanil Sebastiana Gomes da Costa, Claudia Soares de Sousa, Flávia Guimarães Dias Duarte, Arnaldo Correia de Medeiros, Carlos Frederico Campelo de Albuquerque, Rivaldo Venâncio da Cunha, Noely Fabiana Oliveira de Moura, Ana María Bispo de Filippis, Túlio de Oliveira, José Lourenço, André Luiz de Abreu, Luiz Carlos Júnior Alcântara, Marta Giovanetti
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00141-21

Complete Genome Sequencing of Mycobacterium heckeshornense Strain JMUB5695, Isolated from Necrotizing Granulomatous Lesions
Cited by: 0
Author(s): Katsuyuki Katahira, Shinya Watanabe, Kentaro Wakamatsu, Zenzo Nagasawa, Masayuki Kawasaki, Longzhu Cui
Software Mentions: 1
Published: about 3 years ago

10.1080/22221751.2020.1803146

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing
Cited by: 40
Author(s): Joilson Xavier, Marta Giovanetti, Talita Adelino, Vagner Fonseca, Alana Vitor Barbosa da Costa, Adriana Aparecida Ribeiro, Katlin Nascimento Felicio, Clara Guerra-Duarte, Marcos Vinícius Ferreira Silva, Álvaro Salgado, Maurício Lima, Ronaldo de Jesus, Allison Fabri, Cristiane Franco Soares Zoboli, Thales Gutemberg Souza Santos, Felipe Campos de Melo Iani, Massimo Ciccozzi, Ana María Bispo de Filippis, Marilda Agudo Mendonça Teixeira de Siqueira, André Luiz de Abreu, Vasco Azevedo, Dario Brock Ramalho, Carlos Frederico Campelo de Albuquerque, Túlio de Oliveira, Edward C. Holmes, José Lourenço, Luiz Carlos Júnior Alcântara, Marluce Aparecida Assunção Oliveira
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2020.02007

Nanopore MinION Sequencing Reveals Possible Transfer of blaKPC–2 Plasmid Across Bacterial Species in Two Healthcare Facilities
Cited by: 20
Author(s): Catharine Prussing, Emily Snavely, Navjot Singh, Pascal Lapierre, Erica Lasek‐Nesselquist, Kara Mitchell, Wolfgang Haas, Rita Owsiak, Elizabeth Nazarian, Kimberlee A. Musser
Software Mentions: 1
Published: about 4 years ago

10.3390/pathogens9120984

Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil
Cited by: 12
Author(s): Allison Fabri, Cintia Damasceno dos Santos Rodrigues, Carolina Cardoso dos Santos, Flávia Löwen Levy Chalhoub, Simone Alves Sampaio, Nieli Rodrigues da Costa Faria, María Celeste Torres, Vagner Fonseca, Patrícia Brasil, Guilherme Amaral Calvet, Luíz Carlos Júnior Alcântara, Ana María Bispo de Filippis, Marta Giovanetti, Fernanda de Bruycker-Nogueira
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00230-20

Genome Sequences of Chikungunya Virus Isolates from Bolivia
Cited by: 0
Author(s): Caio Martinelle B. França, Roxana Loayza, Yelin Roca, Ana Maria Montaño Arias, Freddy Tinajeros, José R. Loaiza, Anshule Takyar, Robert H. Gilman, Matthew J. Miller
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01174-20

Complete Genome Sequence of a Pseudomonas Species Isolated from Tailings Pond Water in Alberta, Canada
Cited by: 0
Author(s): Steven M. Shideler, John V. Headley, Jeff Gauthier, Iréna Kukavica-Ibrulj, Roger C. Levesque, Shawn Lewenza
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00394-21

Complete Genome Sequences of Three Human Oral Treponema parvum Isolates
Cited by: 1
Author(s): Huihui Zeng, RM Watt
Software Mentions: 1
Published: about 3 years ago

Ecosyste.ms: Papers

Projects: pypi: qcat

Papers Mentioning qcat 34