pypi: quast | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 3 years ago

10.1111/1755-0998.13220

High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm Lamellibrachia barhami
Cited by: 6
Author(s): Corinna Breusing, Darrin T. Schultz, Sebastian Sudek, Alexandra Z. Worden, Charles W. Young
Software Mentions: 11
Published: over 4 years ago

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

10.1111/1755-0998.12443

The de novo genome assembly and annotation of a female domestic dromedary of North African origin
Cited by: 56
Author(s): Robert R. Fitak, Elmira Mohandesan, Jukka Corander, Pamela A. Burger
Software Mentions: 9
Published: over 9 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

10.1111/mec.14860

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Cited by: 43
Author(s): Robert Hooper, Jaelle C. Brealey, Tom van der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul R. Wade, M. Thomas P. Gilbert, Phillip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski
Software Mentions: 7
Published: about 6 years ago

10.1111/1755-0998.12939

Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula
Cited by: 42
Author(s): Robert Lehmann, Damien J. Lightfoot, Celia Schunter, Craig Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Forêt, Michael L. Berumen, David J. Miller, Manuel Aranda, Takashi Gojobori, Philip L. Munday, Timothy Ravasi
Software Mentions: 5
Published: over 6 years ago

10.1186/s12862-020-01689-2

Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity
Cited by: 2
Author(s): Britta Bueker, Marco Alexandre Guerreiro, Michael E. Hood, Andreas Brachmann, Sven Rahmann, Dominik Begerow
Software Mentions: 4
Published: over 4 years ago

10.1099/ijsem.0.004795

Listeria cossartiae sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments
Cited by: 51
Author(s): Catharine R Carlin, Jingqiu Liao, Daniel Weller, Xiaodong Guo, Renato H. Orsi, Martin Wiedmann
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1009183

COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity
Cited by: 5
Author(s): В. А. Наумов, Evgeny Putin, Stefan Pushkov, E. Kozlova, Konstantin Romantsov, Alexander Kalashnikov, Fedor Galkin, Nina Tihonova, Anastasia Shneyderman, Egor Galkin, Arsenii Zinkevich, Stephanie M. Cope, Ramanathan Sethuraman, Tudor I. Oprea, Alexander T. Pearson, Savaş Tay, Nishant Agrawal, Alexey Dubovenko, Quentin Vanhaelen, Ivan V. Ozerov, Alex Aliper, Evgeny Izumchenko, Alex Zhavoronkov
Software Mentions: 4
Published: over 3 years ago

10.1093/ve/veaa012

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Cited by: 13
Author(s): Florent Lassalle, Mathew A. Beale, Tehmina Bharucha, Charlotte A. Williams, Rachel Williams, Juliana Cudini, Richard A. Goldstein, Tanzina Haque, Daniel P. Depledge, Judith Breuer
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pntd.0007850

A glance of the blood stage transcriptome of a Southeast Asian Plasmodium ovale isolate
Cited by: 5
Author(s): Awtum Brashear, Wanlapa Roobsoong, Faiza Amber Siddiqui, Wang Nguitragool, Jetsumon Sattabongkot, Margarita M. López‐Uribe, Jun Miao, Liwang Cui
Software Mentions: 3
Published: about 5 years ago

10.1111/mec.15168

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation
Cited by: 34
Author(s): Jasper R L Depotter, Xiaoqian Shi-Kunne, Hélène Missonnier, Tingli Liu, Luigi Faino, Grardy C. M. van den Berg, Thomas A. Wood, Baolong Zhang, Alban Jacques, Michael Seidl, B.P.H.J. Thomma
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000347

Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis
Cited by: 29
Author(s): Floriana Gona, Francesco Comandatore, Simone Battaglia, Aurora Piazza, Alberto Trovato, Giovanni Lorenzin, Paola Cichero, Anna Biancardi, Paola Nizzero, Matteo Moro, Daniela María Cirillo
Software Mentions: 3
Published: over 4 years ago

10.1186/s12863-020-00945-0

Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis
Cited by: 5
Author(s): Zhaohui Cai, Qiongyu Guo, Zhichao Yao, Wenping Zheng, Junfei Xie, Shuai Bai, Hongyu Zhang
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2020.575321

Genomic Distinctions of LA-MRSA ST398 on Dairy Farms From Different German Federal States With a Low Risk of Severe Human Infections
Cited by: 15
Author(s): Tobias Lienen, Arne Schnitt, Jens A. Hammerl, Sven Maurischat, Bernd‐Alois Tenhagen
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41396-019-0446-4

Linking the resistome and plasmidome to the microbiome
Cited by: 157
Author(s): Thibault Stalder, Maximilian O. Press, Shawn Sullivan, Ivan Liachko, Eva M. Top
Software Mentions: 3
Published: over 5 years ago

10.1099/ijsem.0.002303

Lactococcus petauri sp. nov., isolated from an abscess of a sugar glider
Cited by: 30
Author(s): Laura B. Goodman, Marie R. Lawton, Rebecca J. Franklin‐Guild, Renee Anderson, Lynn Schaan, Anil J. Thachil, Martin Wiedmann, Claire B. Miller, Samuel D. Alcaine, Jasna Kovač
Software Mentions: 3
Published: about 7 years ago

10.1099/ijsem.0.004167

Pseudoalteromonas rhizosphaerae sp. nov., a novel plant growth-promoting bacterium with potential use in phytoremediation
Cited by: 14
Author(s): Salvadora Navarro‐Torre, Lorena Carro, Ignacio D. Rodríguez‐Llorente, Eloísa Pajuelo, Miguel A. Caviedes, José M. Igual, Hans Peter Klenk, María del Carmen Montero-Calasanz
Software Mentions: 2
Published: over 4 years ago

10.1099/mgen.0.000270

Use of whole genome sequencing in surveillance for antimicrobial-resistant Shigella sonnei infections acquired from domestic and international sources
Cited by: 7
Author(s): Rebecca L. Abelman, Nkuchia M. M’ikanatha, Hillary M. Figler, Edward G. Dudley
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000241

Genome analysis provides insights into the epidemiology of infection with Flavobacterium psychrophilum among farmed salmonid fish in Sweden
Cited by: 7
Author(s): Robert Söderlund, Mikhayil Hakhverdyan, Anna Aspán, Eva Jansson
Software Mentions: 2
Published: about 6 years ago

10.3390/microorganisms9061119

Phylogenetic Tracking of LA-MRSA ST398 Intra-Farm Transmission among Animals, Humans and the Environment on German Dairy Farms
Cited by: 9
Author(s): Tobias Lienen, Arne Schnitt, Christiane Cuny, Sven Maurischat, Bernd‐Alois Tenhagen
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9040698

Clinically Relevant Escherichia coli Isolates from Process Waters and Wastewater of Poultry and Pig Slaughterhouses in Germany
Cited by: 15
Author(s): Mykhailo Savin, Gabriele Bierbaum, Judith Kreyenschmidt, Ricarda Maria Schmithausen, Esther Sib, Silvia Schmoger, Annemarie Käsbohrer, Jens A. Hammerl
Software Mentions: 2
Published: over 3 years ago

10.1111/ppa.12834

Characterization of the pathogenicity of strains of Pseudomonas syringae towards cherry and plum
Cited by: 35
Author(s): Michelle T. Hulin, John W. Mansfıeld, P. Brain, Xiuhong Xu, Robert W. Jackson, Richard J. Harrison
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0222004

Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids
Cited by: 14
Author(s): Michael V. Westbury, Bent Petersen, Eline D. Lorenzen
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-50076-5

Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence
Cited by: 14
Author(s): Pamela Gan, Ayako Tsushima, Ryoko Hiroyama, Mari Narusaka, Yoshitaka Takano, Yoshihiro Narusaka, Mitsuo Kawaradani, Ulrike Damm, Ken Shirasu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-85461-6

Multidrug-resistant Staphylococcus cohnii and Staphylococcus urealyticus isolates from German dairy farms exhibit resistance to beta-lactam antibiotics and divergent penicillin-binding proteins
Cited by: 7
Author(s): Tobias Lienen, Arne Schnitt, Jens A. Hammerl, Stephen F. Marino, Sven Maurischat, Bernd‐Alois Tenhagen
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-017-1724-7

An improved filtering algorithm for big read datasets and its application to single-cell assembly
Cited by: 13
Author(s): Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. H. Reusch, Philip Rosenstiel
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00456

Selection of Multidrug-Resistant Bacteria in Medicated Animal Feeds
Cited by: 12
Author(s): Emily E.F. Brown, Ashley Cooper, Catherine D. Carrillo, Burton W. Blais
Software Mentions: 1
Published: almost 6 years ago

10.3390/genes10030245

Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes
Cited by: 2
Author(s): Ingrid Sassenhagen, Karin Rengefors
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-017-15539-7

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction
Cited by: 191
Author(s): Sébastien Matamoros, Jarne M. van Hattem, Maris S Arcilla, Niels Willemse, Damian C. Melles∗, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Martin Bootsma, Perry J.J. van Genderen, Abraham Goorhuis, Martin P. Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh, Henri A. Verbrugh, Menno D. de Jong, Constance Schultsz
Software Mentions: 1
Published: about 7 years ago

10.1111/1751-7915.12344

Genome Update. Let the consumer beware:Streptomycesgenome sequence quality
Cited by: 17
Author(s): David J. Studholme
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13104-020-05254-4

Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea
Cited by: 5
Author(s): Stefanie Hartmann, Michaela Preick, Silke Abelt, André Scheffel, Michael Hofreiter
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00158-18

Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
Cited by: 26
Author(s): Irina M. Velsko, Brinta Chakraborty, Marcelle M. Nascimento, Robert A. Burne, Vincent P. Richards
Software Mentions: 1
Published: about 6 years ago

10.1099/mgen.0.000487

Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm
Cited by: 21
Author(s): Emilie Lefoulon, Travis A. Clark, Ricardo Guerrero, Israel Cañizales, Jorge Manuel Cardenas-Callirgos, Kerstin Junker, Nathaly Vallarino-Lhermitte, Benjamin L. Makepeace, Alistair C. Darby, Jeremy M. Foster, Coralie Martin, Barton E. Slatko
Software Mentions: 1
Published: about 4 years ago

10.3390/microorganisms9030651

Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms
Cited by: 18
Author(s): Alice Roedel, Szilvia Vincze, Michaela Projahn, Uwe Roesler, Caroline Robé, Jens A. Hammerl, Matthias Noll, Sascha Al Dahouk, Ralf Dieckmann
Software Mentions: 1
Published: almost 4 years ago

10.1099/ijsem.0.004615

Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine
Cited by: 6
Author(s): Giovanni Ghielmetti, G. Rosato, Alberto Trovato, Ute Friedel, Constanze Kirchgaessner, Carmen Perroulaz, Wolfgang Pendl, Bettina Schulthess, Guido V. Bloemberg, Peter M. Keller, Roger Stephan, Enrico Tortoli
Software Mentions: 1
Published: about 4 years ago

10.1007/s10096-020-03993-7

MYCO WELL D-ONE detection of Ureaplasma spp. and Mycoplasma hominis in sexual health patients in Wales
Cited by: 14
Author(s): D. Morris, Lucy C. Jones, R. L. Davies, Kirsty Sands, Edward Portal, O. Brad Spiller
Software Mentions: 1
Published: over 4 years ago

10.1099/mgen.0.000185

GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015
Cited by: 29
Author(s): Ruth Timme, Hugh Rand, Maria Sanchez Leon, Maria Hoffmann, Errol Strain, Marc W. Allard, Dwayne Roberson, Joseph D. Baugher
Software Mentions: 1
Published: over 6 years ago

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Papers Mentioning quast 39