pypi: NanoFilt | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.1371/journal.ppat.1009418

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity
Cited by: 10
Author(s): Cédric Lood, Charlotte Peeters, Quentin Lamy-Besnier, Jeroen Wagemans, Daniël De Vos, Marijke Proesmans, Jean‐Paul Pirnay, Fedoua Echahidi, Denis Piérard, M Thimmesch, Anca Boeras, Katrien Lagrou, Evelien De Canck, Elke De Wachter, Vera van Noort, Rob Lavigne, Peter Vandamme
Software Mentions: 7
Published: over 3 years ago

10.1186/s40104-021-00601-2

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets
Cited by: 13
Author(s): Yan Hui, Paulina Tamez-Hidalgo, Tomasz Cieplak, Gizaw Dabessa Satessa, Witold Kot, Søren Kjærulff, Mette Olaf Nielsen, Dennis Sandris Nielsen, Łukasz Krych
Software Mentions: 7
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

10.1186/s12864-020-07183-9

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Cited by: 7
Author(s): Sophie Dhorne–Pollet, Éric Barrey, Nicolas Pollet
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-61158-0

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
Cited by: 46
Author(s): Bas Berbers, Assia Saltykova, Cristina Garcı́a-Graells, Patrick Philipp, F Arella, Kathleen Marchal, Raf Winand, Kevin Vanneste, Nancy Roosens, Sigrid C. J. De Keersmaecker
Software Mentions: 5
Published: over 4 years ago

10.1093/gbe/evab148

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains
Cited by: 2
Author(s): Kun Wu, Zhou‐Hua Cheng, Emily Williams, Nathan T Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dongfeng Liu, Michael Lynch, Hongan Long
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giaa067

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish
Cited by: 10
Author(s): Lisa K. Johnson, Ruta Sahasrabudhe, James Anthony Gill, Jennifer L. Roach, Lutz Froenicke, C. Titus Brown, Andrew Whitehead
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-52832-z

New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies
Cited by: 14
Author(s): Weihong Qi, Andrea Colarusso, Miriam Olombrada, Ermenegilda Parrilli, Andrea Patrignani, Maria Luisa Tutino, Macarena Toll‐Riera
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms9040841

A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
Cited by: 29
Author(s): Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan Kreuze, Marie Lefebvre, Gonçalo Silva, Martha Malapi‐Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoît Remenant, Jean-Sébastien Reynard, Johan Rollin, M. Rott, Olivier Schumpp, Sébastien Massart, Annelies Haegeman
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-97158-x

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
Cited by: 3
Author(s): Zack Saud, Matthew D. Hitchings, Tariq M. Butt
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.42535

An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
Cited by: 77
Author(s): Sergio A. Muñoz-Gómez, Sebastian Hess, Gertraud Burger, B. Franz Lang, Edward Susko, Claudio H. Slamovits, Andrew J. Roger
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.00496

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
Cited by: 55
Author(s): HueyTyng Lee, Harmeet Singh Chawla, Christian Obermeier, Felix Dreyer, Amine Abbadi, Rod J. Snowdon
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-021-07491-8

A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis
Cited by: 8
Author(s): Zofia Bakuła, Paweł Siedlecki, Robert Gromadka, Jan Gawor, Agnieszka Gromadka, Jan J. Pomorski, Hanna Panagiotopoulou, Tomasz Jagielski
Software Mentions: 4
Published: over 3 years ago

10.3389/fpubh.2021.710985

Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
Cited by: 16
Author(s): Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva‐Rocha, María-Eugenia Guazzaroni
Software Mentions: 4
Published: about 3 years ago

10.1534/g3.120.401059

A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly
Cited by: 8
Author(s): Graham B. Wiley, Matthew J. Miller
Software Mentions: 4
Published: over 4 years ago

10.1002/ece3.7146

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data
Cited by: 22
Author(s): Kristoffer Sahlin, Marisa Lim, Stefan Prost
Software Mentions: 4
Published: almost 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: almost 4 years ago

10.1007/s00253-021-11133-0

Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains
Cited by: 5
Author(s): Małgorzata Ryngajłło, Tomasz Boruta, Marcin Bizukojć
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41597-019-0311-3

Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
Cited by: 21
Author(s): Robert Nowak, J Jastrzebski, Wiktor Kuśmirek, Rusłan Sałamatin, Małgorzata Rydzanicz, Agnieszka Sobczyk-Kopcioł, Anna Sulima-Celińska, Łukasz Paukszto, Karol G Makowczenko, Rafał Płoski, Vasyl V. Tkach, Katarzyna Basałaj, Daniel Młocicki
Software Mentions: 3
Published: almost 5 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: over 4 years ago

10.1186/s13104-021-05484-0

Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA
Cited by: 3
Author(s): Iskandar Z. Siregar, Fifi Gus Dwiyanti, Rahadian Pratama, Deden Derajat Matra, Muhammad Majiidu
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: over 5 years ago

10.1186/s43008-020-00041-z

The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM): introducing a new repository of barcoded Chytridiomyceta and Blastocladiomycota cultures
Cited by: 17
Author(s): D. Rabern Simmons, Anne E. Bonds, Buck T. Castillo, Rebecca A. Clemons, Alexander D. Glasco, Jillian M. Myers, Natasha Thapa, Peter M. Letcher, Martha J. Powell, Joyce E. Longcore, Timothy Y. James
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

10.1093/g3journal/jkab211

Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex
Cited by: 2
Author(s): Sara J. Hanson, Eoin Ó Cinnéide, Letal I. Salzberg, Kenneth H. Wolfe, Jamie McGowan, David A. Fitzpatrick, Kate Matlin
Software Mentions: 3
Published: over 3 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

10.3389/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: about 4 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: about 4 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

10.3389/fimmu.2021.650621

Delayed Gut Colonization Shapes Future Allergic Responses in a Murine Model of Atopic Dermatitis
Cited by: 6
Author(s): Amalie W. Arildsen, Line Fisker Zachariassen, Łukasz Krych, Axel Kornerup Hansen, Camilla Hartmann Friis Hansen
Software Mentions: 3
Published: over 3 years ago

10.1042/ETLS20200287

Nanopore sequencing in non-human forensic genetics
Cited by: 4
Author(s): Rob Ogden, Nina Vasiljevic, Stefan Prost
Software Mentions: 3
Published: over 3 years ago

10.1128/MRA.00891-20

Complete Genome Sequences of Methicillin-Resistant Staphylococcus aureus Strains 110900 and 128254, Two Representatives of the CRISPR-Cas-Carrying Sequence Type 630/ spa Type t4549 Lineage
Cited by: 5
Author(s): Raphael N. Sieber, Søren Overballe‐Petersen, Hülya Kaya, Anders Rhod Larsen, Andreas Petersen
Software Mentions: 3
Published: about 4 years ago

10.1128/MRA.00814-20

Complete Genome Sequence of Nitrogen-Fixing Paenibacillus sp. Strain URB8-2, Isolated from the Rhizosphere of Wild Grass
Cited by: 1
Author(s): Kyosuke Kita, Shu Ishikawa, Kenichi Yoshida
Software Mentions: 2
Published: about 4 years ago

10.1128/MRA.00215-21

Complete Genome Sequence of Arcanobacterium phocisimile Strain DSM 26142, Isolated from a Harbor Seal
Cited by: 1
Author(s): Maria Blettner, Mazen Alssahen, Burkhard Malorny, Christoph Lämmler, Ursula Siebert, Madeleine Plötz, Amir Abdulmawjood
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.00761-21

Draft Genome Sequence of a Diploid and Hybrid Candida Strain, Candida sanyaensis UCD423, Isolated from Compost in Ireland
Cited by: 1
Author(s): Adam P. Ryan, Eoin Ó Cinnéide, Sean A Bergin, Ghozlan Alhajeri, Hawraa Almotawaa, Isabelle Daly, Sophia Heneghan, Kellie Horan, Roslyn Kavanagh, C. J. Keane, A. M. Martin, Ada McDonagh, Julia O'Leary, Matthieu Osborne, Emma Watson, Kevin Byrne, Kenneth H. Wolfe, Geraldine Butler
Software Mentions: 2
Published: about 3 years ago

10.1128/MRA.00253-20

Complete Genome Sequence of Novel Psychrotolerant Legionella Strain TUM19329, Isolated from Antarctic Lake Sediment
Cited by: 5
Author(s): Shunsuke Shimada, Ryosuke Nakai, Kotaro Aoki, Norifumi Shimoeda, Giichiro Ohno, Yasunari Miyazaki, Sakae Kudoh, Satoru Imura, Kouichi Watanabe, Yoshikazu Ishii, Kazuhiro Tateda
Software Mentions: 2
Published: over 4 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: about 4 years ago

10.3390/v13060959

Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay
Cited by: 7
Author(s): Katrine Wacenius Skov Alanin, Laura Milena Forero‐Junco, Jacob Bruun Jørgensen, Tue Kjærgaard Nielsen, Morten Arendt Rasmussen, Witold Kot, Lars Hestbjerg Hansen
Software Mentions: 2
Published: over 3 years ago

10.3390/v13081510

Severe SARS-CoV-2 Infection in a Cat with Hypertrophic Cardiomyopathy
Cited by: 28
Author(s): Francisco R. Carvallo, Mathias Martins, Lok R. Joshi, Leonardo Cardia Caserta, Patrick K. Mitchell, Thomas E. Cecere, Sandy Hancock, Erin L. Goodrich, Julia Murphy, Diego G. Diel
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0226234

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing
Cited by: 27
Author(s): Agnes Scheunert, Marco Dorfner, Thomas Lingl, Christoph Oberprieler
Software Mentions: 2
Published: over 4 years ago

10.1093/dnares/dsab015

Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome
Cited by: 4
Author(s): Cheng-Yi Tang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07390-y

Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
Cited by: 5
Author(s): Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis, Tariq M. Butt
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcimb.2021.696669

Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm
Cited by: 13
Author(s): Jinming Wang, Kai Chen, Qiaoyun Ren, Ying Zhang, Junlong Liu, Guangying Wang, Aihong Liu, Youquan Li, Guangyuan Liu, Jianxun Luo, Wei Miao, Jie Xiong, Hong Yin, Guiquan Guan
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.743230

Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence Capture
Cited by: 8
Author(s): Valentina Grosso, Luca Marcolungo, Simone Maestri, Massimiliano Alfano, Denise Lavezzari, Barbara Iadarola, Alessandro Salviati, Barbara Mariotti, Annalisa Botta, Maria Rosaria D’Apice, Giuseppe Novelli, Massimo Delledonne, Marzia Rossato
Software Mentions: 2
Published: about 3 years ago

10.3389/fgene.2021.620009

Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing
Cited by: 9
Author(s): Mu Zhou, Yarong Wu, Timothy Kudinha, Peng Jia, Lei Wang, Yingchun Xu
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.00021-19

Complete Genome Sequence of Caldicellulosiruptor changbaiensis CBS-Z, an Extremely Thermophilic, Cellulolytic Bacterium Isolated from a Hot Spring in China
Cited by: 4
Author(s): Carl Mendoza, Sara E. Blumer-Schuette
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.515319

Genomic and Functional Characterization of Enterococcus faecalis Isolates Recovered From the International Space Station and Their Potential for Pathogenicity
Cited by: 9
Author(s): Noelle C. Bryan, François Lebreton, Michael S. Gilmore, Gary Ruvkun, M. T. Zuber, Christopher E. Carr
Software Mentions: 2
Published: almost 4 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

10.3389/fpls.2020.00624

A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing
Cited by: 9
Author(s): Spencer P. Hunt, David E. Jarvis, Dallas J. Larsen, Sergei L. Mosyakin, Bożena Kolano, Eric W. Jackson, Sara L. Martin, Eric N. Jellen, Peter J. Maughan
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.120.401361

Completed Genomic Sequence ofBacillus thuringiensisHER1410 Reveals aCry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage
Cited by: 15
Author(s): Ana Lechuga, Cédric Lood, Margarita Salas, Vera van Noort, Rob Lavigne, Modesto Redrejo-Rodríguez
Software Mentions: 2
Published: about 4 years ago

10.3390/genes10110858

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions
Cited by: 58
Author(s): Henrik Krehenwinkel, Aaron Pomerantz, Stefan Prost
Software Mentions: 2
Published: about 5 years ago

10.1093/gigascience/giz160

The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies
Cited by: 38
Author(s): Weiwen Wang, Ashutosh Das, David Kainer, Miriam Schalamun, Alejandro Morales-Suarez, Benjamin Schwessinger, Robert Lanfear
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-018-28180-9

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
Cited by: 57
Author(s): Sebastiaan Theuns, Bert Vanmechelen, Quinten Bernaert, Ward Deboutte, Marilou Vandenhole, Leen Beller, Jelle Matthijnssens, Piet Maes, Hans Nauwynck
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56763-7

Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations
Cited by: 36
Author(s): Kira Kondratyeva, Mali Salmon‐Divon, Shiri Navon-Venezia
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-70769-6

Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing
Cited by: 14
Author(s): Samuel S. Slattery, Helen Wang, Daniel J. Giguere, Csanad Kocsis, Bradley L. Urquhart, Bogumil J. Karas, David R. Edgell
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-94011-z

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe
Cited by: 25
Author(s): Jack M. Crook, Ivana Murphy, Dan Carter, Steven T. Pullan, Miles W. Carroll, Richard Vipond, Andrew A. Cunningham, Diana Bell
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21239177

A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings
Cited by: 13
Author(s): Simone Maestri, Maria Giovanna Maturo, Emanuela Cosentino, Luca Marcolungo, Barbara Iadarola, Elisabetta Fortunati, Marzia Rossato, Massimo Delledonne
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22084144

Antarctic Rahnella inusitata: A Producer of Cold-Stable β-Galactosidase Enzymes
Cited by: 7
Author(s): Kattia Núñez-Montero, Rodrigo Salazar, Andrés Santos, Olman Gómez-Espinoza, Scandar Farah, Claudia Troncoso, Catalina Hoffmann, Damaris Melivilu, Felipe Scott, Leticia Barrientos
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.01228-19

Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain JP-H-1, Isolated from an Equine Abortion Case in Japan
Cited by: 0
Author(s): Yuta Kinoshita, Hidekazu Niwa, Eri Uchida‐Fujii, Toshio Nukada
Software Mentions: 2
Published: almost 5 years ago

10.1128/MRA.00042-21

Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5419, Representative of Australian Genospecies L
Cited by: 0
Author(s): Christine Oger-Desfeux, Jérôme Briolay, Philippe Oger, Bénédicte Lafay
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.01213-20

Genome Sequence of the Fungus Nannizziopsis barbatae, an Emerging Reptile Pathogen
Cited by: 1
Author(s): Daniel Powell, Ashley Jones, Nicola Kent, Parwinder Kaur, Ido Bar, Benjamin Schwessinger, Céline Frère
Software Mentions: 2
Published: almost 4 years ago

10.1128/MRA.00057-20

Complete Genome Sequence of Mycoplasma felis Strain Myco-2, Isolated from an Equine Tracheal Wash Sample in Japan
Cited by: 2
Author(s): Yuta Kinoshita, Hidekazu Niwa, Eri Uchida‐Fujii, Toshio Nukada
Software Mentions: 2
Published: over 4 years ago

10.3390/md18090442

Nostoc edaphicum CCNP1411 from the Baltic Sea—A New Producer of Nostocyclopeptides
Cited by: 6
Author(s): Anna Fidor, Michał Grabski, Jan Gawor, Robert Gromadka, Grzegorz Węgrzyn, Hanna Mazur‐Marzec
Software Mentions: 2
Published: about 4 years ago

10.1099/mgen.0.000507

Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes
Cited by: 7
Author(s): Chloe D. Goldsmith, Damien Cohen, A. Dubois, María del Carmen Jiménez Martínez, Kilian Petitjean, Anne Corlu, Barbara Testoni, Héctor Hernandez-Vargas, Isabelle Chemin
Software Mentions: 2
Published: over 3 years ago

10.1186/s40478-020-00963-0

A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma
Cited by: 23
Author(s): Thidathip Wongsurawat, Piroon Jenjaroenpun, Annick De Loose, Duah Alkam, David W. Ussery, Intawat Nookaew, Yuet-Kin Leung, Shuk‐Mei Ho, John D. Day, Analiz Rodriguez
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.01435-20

Complete and Circularized Genome Assembly of a Human Isolate of Vibrio navarrensis Biotype pommerensis with MiSeq and MinION Sequence Data
Cited by: 2
Author(s): Keike Schwartz, Maria Blettner, Carlus Deneke, Veronika Balau, Claudia Metelmann, Eckhard Strauch
Software Mentions: 2
Published: almost 4 years ago

10.3390/antibiotics9080503

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination
Cited by: 9
Author(s): Bas Berbers, Pieter‐Jan Ceyssens, Pierre Bogaerts, Kevin Vanneste, Nancy Roosens, Kathleen Marchal, Sigrid C. J. De Keersmaecker
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.01257-20

Whole-Genome Shotgun Sequence of Bacillus mycoides Strain U53, a Psychrotolerant Bacterium Isolated from the Sakhalin Region in Russia
Cited by: 1
Author(s): Ha My T. Phan, М. Л. Сидоренко, Po Chun Tsai, Shir Ly Huang
Software Mentions: 2
Published: almost 4 years ago

10.1128/MRA.00567-21

Complete Genome Sequence of the Highly Adhesive Bacterium Acinetobacter sp. Strain Tol 5
Cited by: 1
Author(s): Masahito Ishikawa, Katsutoshi Hori
Software Mentions: 1
Published: about 3 years ago

10.1128/MRA.01069-20

Complete Genome Sequence of a Japanese Clinical Isolate of Haemophilus influenzae Type a Strain TAMBA230
Cited by: 0
Author(s): Mayumi Kubota, Tsuyoshi Kenri, Yuko Sasaki, Keigo Shibayama, Kosuke Takayanagi, Tsuneaki Kenzaka
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.01156-20

Complete Genome Sequence of Sphingomonas paucimobilis Strain Kira, Isolated from Human Neuroblastoma SH-SY5Y Cell Cultures Supplemented with Retinoic Acid
Cited by: 2
Author(s): Kohei Nishimura, Mirai Ikarashi, Yuji Yasuda, Mayu Sato, Marta Cano Guerrero, Josephine Galipon, Kazuharu Arakawa
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00339-20

Complete Genome Sequence of Geobacillus sp. Strain E55-1, Isolated from Mine Geyser in Japan
Cited by: 0
Author(s): Kentaro Miyazaki, Erina Hase, Natsuko Tokito
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00135-20

Complete Genome Sequence of Flavonifractor plautii JCM 32125 T
Cited by: 1
Author(s): Dieter M. Tourlousse, Mitsuo Sakamoto, Takamasa Miura, Koji Narita, Akiko Ohashi, Yuichi Uchino, Atsushi Yamazoe, Keishi Kameyama, Jun Terauchi, Moriya Ohkuma, Hiroko Kawasaki, Yuji Sekiguchi
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01277-19

Complete Genome Sequence of Alteromonas sp. Strain I4, Isolated from the Japan Sea
Cited by: 0
Author(s): Kentaro Miyazaki, Kouki Izumi
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00281-21

Complete Genome Sequence of an mcr-9 -Possessing Enterobacter asburiae Strain Isolated from a Cat in Japan
Cited by: 2
Author(s): Toyotaka Sato, Masaru Usui, Kazuki Harada, Yukari Fukushima, Chie Nakajima, Yasuhiko Suzuki, Shinichi Yokota
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01475-19

Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan
Cited by: 0
Author(s): Natsuki Tomariguchi, Kentaro Miyazaki
Software Mentions: 1
Published: almost 5 years ago

10.1128/MRA.00797-21

Complete Genome Sequences of Three of the Earliest Community-Associated Methicillin-Resistant Staphylococcus aureus Strains Isolated in Remote Western Australia
Cited by: 0
Author(s): Nicola M. Karakatsanis, Elena Colombi, Shakeel Mowlaboccus, Julie Pearson, Geoffrey W. Coombs, Joshua P. Ramsay
Software Mentions: 1
Published: about 3 years ago

10.1128/MRA.00820-19

Complete Genome Sequences of Thermus thermophilus Strains AA2-20 and AA2-29, Isolated from Arima Onsen in Japan
Cited by: 8
Author(s): Kentaro Miyazaki, Natsuki Tomariguchi
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00013-21

Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater
Cited by: 0
Author(s): Kentaro Miyazaki, Hikaru Suenaga, Mamoru Oshiki, Shuichi Kawano, Toshikazu Fukushima
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00696-19

Complete Genome Sequence of Staphylococcus arlettae Strain P2, Isolated from a Laboratory Environment
Cited by: 4
Author(s): Hiroki Yu, Makoto Taniguchi, Kazuma Uesaka, Apirak Wiseschart, Kusol Pootanakit, Yoko Nishitani, Yota Murakami, Koichiro Ishimori, Kentaro Miyazaki, Kei Kitahara
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00075-21

Complete Genome Sequence of Pseudoalteromonas sp. Strain LC2018020214, a Bacterium Isolated from Natural Seawater
Cited by: 0
Author(s): Pish Wattanadilokchatkun, Pattanapon Kayansamruaj, Jiao Pan
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01239-20

Complete Genome Sequence of Streptococcus mitis Strain Nm-65, Isolated from a Patient with Kawasaki Disease
Cited by: 1
Author(s): Atsushi Tabata, Hisashi Ohkuni, Yasuhiko Itoh, Yoshitaka Fukunaga, Toshifumi Tomoyasu, Hideaki Nagamune
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.01050-20

Complete Genome Sequences of Francisella marina Strains E95-16 and E103-15, Isolated from Maricultured Spotted Rose Snapper ( Lutjanus guttatus ) on the Pacific Coast of Central America
Cited by: 0
Author(s): Hasan C. Tekedar, Matt J. Griffin, Larry A. Hanson, Geoffrey C. Waldbieser, Esteban Soto
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01434-20

Closed Genome Sequences of Clinical Listeria monocytogenes PCR Serogroup IVb Isolates Associated with Two Recent Large Listeriosis Outbreaks in Germany
Cited by: 0
Author(s): Sven Halbedel, Martin Fischer, Andrea Thürmer, Antje Flieger
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00700-20

Complete Genome Sequences of Seven Uropathogenic Escherichia coli Strains Isolated from Postmenopausal Women with Recurrent Urinary Tract Infection
Cited by: 2
Author(s): Belle M. Sharon, Amber Nguyen, Amanda P. Arute, Neha V. Hulyalkar, Vivian Nguyen, Philippe E. Zimmern, Nicole J. De Nisco
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00322-20

Complete Genome Sequence of Athalassotoga saccharophila Strain NAS-01, a Deep-Branching Thermophilic Lineage in the Phylum Thermotogae
Cited by: 3
Author(s): Shingo Kato, Takashi Itoh, Moriya Ohkuma
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00818-19

Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan
Cited by: 2
Author(s): Natsuki Tomariguchi, Kentaro Miyazaki
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00073-21

Complete Genome Sequences of Three Uropathogenic Klebsiella quasipneumoniae Strains Isolated from Postmenopausal Women with Recurrent Urinary Tract Infection
Cited by: 4
Author(s): Sundharamani Venkitapathi, Belle M. Sharon, Tahira A. Ratna, Amanda P. Arute, Philippe E. Zimmern, Nicole J. De Nisco
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00195-20

Complete Genome Sequence of Bacillus cereus Strain PL1, Isolated from Soil in Japan
Cited by: 1
Author(s): Kentaro Miyazaki, Erina Hase, Tomomasa Maruya
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00039-21

Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan
Cited by: 5
Author(s): Kentaro Miyazaki, Toshiyuki Moriya, Norio Nemoto, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01022-20

Complete Genome Sequence of Multidrug-Resistant Strain Nocardia wallacei FMUON74, Isolated from a Sputum Culture
Cited by: 2
Author(s): Masahiro Toyokawa, Makoto Taniguchi, Kazuma Uesaka, Keiko Nishimura
Software Mentions: 1
Published: about 4 years ago

10.1128/MRA.00279-21

Complete Genome Sequence of Veillonella nakazawae JCM 33966 T (=CCUG 74597 T ), Isolated from the Oral Cavity of Japanese Children
Cited by: 2
Author(s): Izumi Mashima, Fumio Nakazawa, Riyoko Tamai, Yusuke Kiyoura
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00303-21

Complete Genome Sequences of Three Clinical Listeria monocytogenes Sequence Type 8 Strains from Recent German Listeriosis Outbreaks
Cited by: 3
Author(s): Martin Fischer, Andrea Thürmer, Antje Flieger, Sven Halbedel
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00134-20

Complete Genome Sequence of Collinsella aerofaciens JCM 10188 T
Cited by: 1
Author(s): Dieter M. Tourlousse, Mitsuo Sakamoto, Takamasa Miura, Koji Narita, Akiko Ohashi, Yuichi Uchino, Atsushi Yamazoe, Keishi Kameyama, Jun Terauchi, Moriya Ohkuma, Hiroko Kawasaki, Yuji Sekiguchi
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01447-20

Complete Genome Sequences of Staphylococcus argenteus Tokyo13064 and Tokyo13069, Isolated from Specimens Obtained during a Food Poisoning Outbreak in Tokyo, Japan
Cited by: 1
Author(s): Yasunori Suzuki, Hiroaki Kubota, Tsutomu Kakuda, Shinji Takaı̈, Kenji Sadamasu
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: NanoFilt

Papers Mentioning NanoFilt 124