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: NanoFilt
https://packages.ecosyste.ms/registries/pypi.org/packages/NanoFilt
Filtering and trimming of Oxford Nanopore Sequencing data
34 versions
Latest release: over 3 years ago
368 downloads last month
Papers Mentioning NanoFilt 124
10.1093/bioinformatics/bty149
NanoPack: visualizing and processing long-read sequencing dataCited 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 diversityCited 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 pigletsCited 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 LesionsCited 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 SamplesCited 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 variantsCited by: 7
Author(s): Sophie Dhorne–Pollet, Éric Barrey, Nicolas Pollet
Software Mentions: 5
Published: almost 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 BacillusCited 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 StrainsCited 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 killifishCited 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 technologiesCited by: 14
Author(s): Weihong Qi, Andrea Colarusso, Miriam Olombrada, Ermenegilda Parrilli, Andrea Patrignani, Maria Luisa Tutino, Macarena Toll‐Riera
Software Mentions: 4
Published: almost 5 years ago
10.3390/microorganisms9040841
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant VirusesCited 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 peptidesCited 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 originsCited 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 napusCited 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 protothecosisCited 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 UnitsCited 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 (<i>Melanerpes aurifrons</i>) via Hybrid Oxford Nanopore and Short Read AssemblyCited 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 dataCited 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 SequencingCited 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 strainsCited 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 diminutaCited 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 IdentificationCited 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 DNACited 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 strainsCited 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 culturesCited 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 2021Cited 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 <i>Ogataea polymorpha</i> species complexCited 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 CharacteristicsCited 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 AssembliesCited 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
10.1186/s12859-020-03856-0
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencingCited 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
10.3390/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 VirusCited 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 DermatitisCited 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 geneticsCited 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/ <i>spa</i> Type t4549 LineageCited 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 <i>Paenibacillus</i> sp. Strain URB8-2, Isolated from the Rhizosphere of Wild GrassCited 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 SealCited 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 <i>Candida</i> Strain, <i>Candida sanyaensis</i> UCD423, Isolated from Compost in IrelandCited 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 <i>Legionella</i> Strain TUM19329, Isolated from Antarctic Lake SedimentCited 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 herdsCited 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 AssayCited 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 CardiomyopathyCited 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 sequencingCited 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 <i>O</i>-acyltransferases by a reliable <i>Lithospermum erythrorhizon</i> genomeCited by: 4
Author(s): Cheng-Yi Tang
Software Mentions: 2
Published: about 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 pipelineCited 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 PiroplasmCited 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: about 3 years ago
10.3389/fgene.2021.743230
Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence CaptureCited 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 SequencingCited 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 ChinaCited 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 PathogenicityCited 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 AlgaeCited 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 SequencingCited 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 of<i>Bacillus thuringiensis</i>HER1410 Reveals a<i>Cry</i>-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial ProphageCited 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 DirectionsCited 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 assembliesCited 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 virusCited 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 AssociationsCited 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 editingCited 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: about 4 years ago
10.1038/s41598-021-94011-z
Metagenomic identification of a new sarbecovirus from horseshoe bats in EuropeCited 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 SettingsCited 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 EnzymesCited 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 JapanCited 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 LCited 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 PathogenCited 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 JapanCited 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 NostocyclopeptidesCited 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 genomesCited 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 gliomaCited 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 <i>pommerensis</i> with MiSeq and MinION Sequence DataCited 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 DisseminationCited 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: about 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 RussiaCited 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 5Cited 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 TAMBA230Cited 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 AcidCited by: 2
Author(s): Kohei Nishimura, Mirai Ikarashi, Yuji Yasuda, Mayu Sato, Marta Cano Guerrero, Josephine Galipon, Kazuharu Arakawa
Software Mentions: 1
Published: over 3 years ago
10.1128/MRA.00339-20
Complete Genome Sequence of Geobacillus sp. Strain E55-1, Isolated from Mine Geyser in JapanCited 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 <sup>T</sup>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 SeaCited by: 0
Author(s): Kentaro Miyazaki, Kouki Izumi
Software Mentions: 1
Published: almost 5 years ago
10.1128/MRA.00281-21
Complete Genome Sequence of an mcr-9 -Possessing Enterobacter asburiae Strain Isolated from a Cat in JapanCited 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 JapanCited 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 AustraliaCited 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 JapanCited 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 WastewaterCited by: 0
Author(s): Kentaro Miyazaki, Hikaru Suenaga, Mamoru Oshiki, Shuichi Kawano, Toshikazu Fukushima
Software Mentions: 1
Published: over 3 years ago
10.1128/MRA.00696-19
Complete Genome Sequence of Staphylococcus arlettae Strain P2, Isolated from a Laboratory EnvironmentCited 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: almost 5 years ago
10.1128/MRA.00075-21
Complete Genome Sequence of Pseudoalteromonas sp. Strain LC2018020214, a Bacterium Isolated from Natural SeawaterCited 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 DiseaseCited 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 AmericaCited 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 GermanyCited 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 InfectionCited 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: about 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 <i>Thermotogae</i>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 JapanCited by: 2
Author(s): Natsuki Tomariguchi, Kentaro Miyazaki
Software Mentions: 1
Published: about 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 InfectionCited 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 JapanCited 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 JapanCited 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 CultureCited by: 2
Author(s): Masahiro Toyokawa, Makoto Taniguchi, Kazuma Uesaka, Keiko Nishimura
Software Mentions: 1
Published: almost 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 ChildrenCited 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 OutbreaksCited 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 <sup>T</sup>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, JapanCited by: 1
Author(s): Yasunori Suzuki, Hiroaki Kubota, Tsutomu Kakuda, Shinji Takaı̈, Kenji Sadamasu
Software Mentions: 1
Published: over 3 years ago
10.1128/MRA.00383-21
Closed Genome Sequence of Clostridium botulinum Strain IBCA10-7060 Type BhCited by: 2
Author(s): Nir Dover, Jason R. Barash, John Bell, Matthew Sylvester, Stephen S. Arnon
Software Mentions: 1
Published: about 3 years ago
10.1128/MRA.00873-19
Complete Genome Sequencing of Thermus thermophilus Strain HC11, Isolated from Mine Geyser in JapanCited by: 7
Author(s): Kentaro Miyazaki
Software Mentions: 1
Published: about 5 years ago
10.1128/MRA.01591-19
Complete Genome Sequence of Vibrio rotiferianus Strain AM7Cited by: 1
Author(s): Kentaro Miyazaki, Apirak Wiseschart, Kusol Pootanakit, Kei Kitahara
Software Mentions: 1
Published: over 4 years ago