pypi: pyani | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.580691

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago

10.1186/s40168-021-01140-8

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Cited by: 18
Author(s): Olga María Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Fortin, Ben Shapiro
Software Mentions: 8
Published: almost 3 years ago

10.1128/mSystems.00264-19

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex
Cited by: 46
Author(s): Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.xcrm.2020.100077

Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study
Cited by: 108
Author(s): Cristina Alcon-Giner, Matthew J. Dalby, Shabhonam Caim, Jennifer Ketskemety, Alexander Shaw, Kathleen Sim, Melissa A. Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska, Suparna Mitra, Fahmina Fardus‐Reid, Gusztav Belteki, Katherine McColl, Jonathan R. Swann, J. Simon Kroll, Paul Clarke, Lindsay J. Hall
Software Mentions: 6
Published: about 4 years ago

10.1186/s13073-020-00825-3

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals
Cited by: 15
Author(s): Sergio Arredondo-Alonso, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2019.01.001

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Cited by: 956
Author(s): Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi, María Carmen Collado, Benjamin L. Rice, Casey DuLong, Xochitl C. Morgan, Christopher D. Golden, Christopher Quince, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pntd.0008018

Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis
Cited by: 5
Author(s): Anne Busch, Timo Homeier‐Bachmann, Mostafa Y. Abdel-Glil, Anja Hackbart, Helmut Hotzel, Herbert Tomaso
Software Mentions: 6
Published: almost 4 years ago

10.3390/nu13082833

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes
Cited by: 8
Author(s): Lauren Tso, Kevin S. Bonham, Alyssa Fishbein, Sophie Rowland, Vanja Klepac‐Ceraj
Software Mentions: 6
Published: about 3 years ago

10.1128/mBio.02146-20

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System
Cited by: 20
Author(s): Charlotte B. Francoeur, Lily Khadempour, Rolando D. Moreira-Soto, Kirsten Gotting, Adam J. Book, Adrián A. Pinto‐Tomás, Ken Keefover‐Ring, Cameron R. Currie
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2021.665858

Multi-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni
Cited by: 6
Author(s): Hai‐Yan Cao, Hanxiao Xu, Ning Cai, Xiang Li, Ren Qiu-fang, Tiantian Zhang, Yusen Zhang, Rui Gao
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2021.629449

Diversity of Weissella confusa in Pozol and Its Carbohydrate Metabolism
Cited by: 5
Author(s): Diana Hernández-Oaxaca, Rafael López-Sánchez, Luis Lozano, Carmen Wacher, Lorenzo Segovia, Agustín López Munguía
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.4694

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
Cited by: 89
Author(s): A. McCann, Feargal J. Ryan, Stephen R. Stockdale, Marion Dalmasso, Tony Blake, C. Anthony Ryan, Catherine Stanton, Susan Mills, R. Paul Ross, Colin Hill
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2019.01491

Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes
Cited by: 26
Author(s): Anisha M. Thanki, Nathan Brown, Andrew Millard, Martha R. J. Clokie
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms9091906

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota
Cited by: 9
Author(s): Romina Díaz, Alexis Torres-Miranda, Guillermo Orellana, Daniel Garrido
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2021.690251

Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs
Cited by: 16
Author(s): Marta Nierychlo, Caitlin M. Singleton, Francesca Petriglieri, Lisette Thomsen, Jette Fischer Petersen, Miriam Peces, Zivile Kondrotaite, Morten Simonsen Dueholm, Per Halkjær Nielsen
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2018.00973

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
Cited by: 15
Author(s): Xiangchen Li, Wenjun Tong, Lina Wang, Siddiq Ur Rahman, Gehong Wei, Shiheng Tao
Software Mentions: 5
Published: over 6 years ago

10.1099/mgen.0.000297

Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids
Cited by: 16
Author(s): Raymond Kiu, Shabhonam Caim, Anaïs Painset, Derek Pickard, Craig Swift, Gordon Dougan, Alison E. Mather, Corinne Amar, Lindsay J. Hall
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.8544

SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species
Cited by: 9
Author(s): Matthias Dreier, Hélène Berthoud, Noam Shani, Daniel Wechsler, Pilar Junier
Software Mentions: 4
Published: over 4 years ago

10.3390/v12101065

Genome Sequence and Characterization of Five Bacteriophages Infecting Streptomyces coelicolor and Streptomyces venezuelae: Alderaan, Coruscant, Dagobah, Endor1 and Endor2
Cited by: 14
Author(s): Aël Hardy, Vikas Sharma, Larissa Kever, Julia Frunzke
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-86148-8

Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential
Cited by: 15
Author(s): Mostafa Y. Abdel-Glil, Prasad Thomas, Jörg Linde, Anne Busch, Lothar H. Wieler, Heinrich Neubauer, Christian Seyboldt
Software Mentions: 4
Published: over 3 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

10.1128/JB.00272-19

Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota
Cited by: 10
Author(s): Kaisa Thorell, Linn Inganäs, Annette Backhans, Lars Agréus, Åke Öst, Marjorie M. Walker, Nicholas J. Talley, Lars Kjellström, Anna Andréasson, Lars Engstrand
Software Mentions: 4
Published: almost 5 years ago

10.1093/gbe/evz178

Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter
Cited by: 50
Author(s): Valeria Mateo-Estrada, Lucía Graña-Miraglia, Gamaliel López-Leal, Santiago Castillo-Ramírez
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-021-07432-5

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus
Cited by: 12
Author(s): Yisong Li, Zhuo Sun, Jin-Cheng Rong, Bin-Bin Xie
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2017.02269

Bacterial Succession on Sinking Particles in the Ocean's Interior
Cited by: 40
Author(s): Erik A. Pelve, Kristina M. Fontanez, Edward F. DeLong
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2020.01192

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera
Cited by: 7
Author(s): Pei Wang, Liang Zhi Li, Yipeng Qin, Zong Lin Liang, Xiu Tong Li, Hua Yin, Li Jun Liu, Shuang‐Jiang Liu, Cheng‐Ying Jiang
Software Mentions: 4
Published: about 4 years ago

10.1128/MRA.00832-19

Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals
Cited by: 2
Author(s): Kazuki Tanaka, Tsubasa Watabe, Koichi Kato, Tomoya Tsukimi, Mitsuhiko Sato, Toshitaka Odamaki, Masaru Tomita, Shinji Fukuda
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.chom.2018.06.005

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
Cited by: 714
Author(s): Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Valentina Gorfer, Sabina Fedi, Federica Armanini, Duy Tin Truong, Serena Manara, Moreno Zolfo, Francesco Beghini, Roberto Bertorelli, Veronica De Sanctis, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Alice Viappiani, Moran Yassour, Hera Vlamakis, Ramnik J. Xavier, María Carmen Collado, Omry Koren, Saverio Tateo, Massimo Soffiati, Anna Pedrotti, Marco Ventura, Curtis Huttenhower, Peer Bork, Nicola Segata
Software Mentions: 4
Published: about 6 years ago

10.1186/s40168-018-0539-8

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis
Cited by: 31
Author(s): Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William P. Inskeep, Natalia Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas, Tanja Woyke
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-021-01132-8

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
Cited by: 12
Author(s): Lena Granehäll, Kun Huang, Adrian Tett, Paolo Manghi, Alice Paladin, Niall O’Sullivan, Omar Rota‐Stabelli, Nicola Segata, Albert Zink, Frank Maixner
Software Mentions: 4
Published: almost 3 years ago

10.3389/fmicb.2019.00060

Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors
Cited by: 5
Author(s): Ricardo Ulloa, Ana Moya-Beltrán, Camila Rojas-Villalobos, Harold Núñez, P. Chiacchiarini, Edgardo R. Donati, Alejandra Giaveno, Raquel Quatrini
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-018-4701-2

Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes
Cited by: 22
Author(s): Daniel R. Bogema, Melinda L. Micallef, Mengmeng Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling, Cheryl Jenkins
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-5313-6

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa
Cited by: 70
Author(s): Cormac Brian Fitzgerald, Andrey N. Shkoporov, Thomas D.S. Sutton, Andrei V. Chaplin, Vimalkumar Velayudhan, R. Paul Ross, Colin Hill
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12866-020-01770-2

Bacteriophage genotyping using BOXA repetitive-PCR
Cited by: 1
Author(s): Dragica Damnjanović, Xabier Vázquez-Campos, Daniel L. Winter, M. Harvey, Wallace Bridge
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8010007

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum
Cited by: 20
Author(s): Korin Albert, Asha Rani, David A. Sela
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9040757

Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters
Cited by: 11
Author(s): Qingmei Li, Yingli Zhou, Zhanfei Wei, Yong Wang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0194368

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts
Cited by: 22
Author(s): Anoop Alex, Agostinho Antunes
Software Mentions: 3
Published: over 6 years ago

10.1002/2211-5463.13201

Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis
Cited by: 1
Author(s): Marcos André Schörner, Hemanoel Passarelli‐Araujo, Mara Cristina Scheffer, Fernando Hartmann Barazzetti, Jéssica Motta Martins, Hanalydia de Melo Machado, Jussara Kasuko Palmeiro, Maria Luiza Bazzo
Software Mentions: 3
Published: over 3 years ago

10.1093/femsle/fny069

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies
Cited by: 15
Author(s): Ainsley Beaton, Cédric Lood, Edward Cunningham-Oakes, Alison Macfadyen, Alex J. Mullins, Walid E.l. Bestawy, João Botelho, Sylvie Chevalier, Shannon R. Coleman, Chloe Dalzell, Stephen K. Dolan, Alberto Faccenda, Maarten G. K. Ghequire, Steven A. Higgins, Alexander Kutschera, Jordan Murray, Martha L. Redway, Talal Sabhan Salih, Ana C. da Silva, Brian A. Smith, Nathan Smits, R. P.M. Thomson, Stuart Daniel Woodcock, Martin Welch, Pierre Cornélis, Rob Lavigne, Vera van Noort, Nicholas P. Tucker
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.714920

Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems
Cited by: 2
Author(s): Michael Hoffert, Rika E. Anderson, Julie Réveillaud, Leslie G. Murphy, Ramunas Stepanauskas, J. A. Huber
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2017.02434

Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex
Cited by: 16
Author(s): Jeff Gauthier, Antony T. Vincent, Steve J. Charette, Nicolas Derôme
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2018.02611

Genetic Signatures of Dairy Lactobacillus casei Group
Cited by: 15
Author(s): Alessandra Fontana, C. Zacconi, L. Morelli
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2020.585374

Phylogenomic Analysis of Campylobacter fetus Reveals a Clonal Structure of Insertion Element ISCfe1 Positive Genomes
Cited by: 4
Author(s): Mostafa Y. Abdel-Glil, Helmut Hotzel, Herbert Tomaso, Jörg Linde
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.01100

Characterization of a Novel Functional Trimeric Catechol 1,2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico
Cited by: 16
Author(s): Julieta Rodríguez-Salazar, Arisbeth G Almeida-Juarez, Katya Ornelas-Ocampo, Sofía Millán-López, Enrique Raga-Carbajal, José Luis Rodríguez-Mejía, Luis Felipe Muriel-Millán, Elizabeth Ernestina Godoy-Lozano, Nancy Rivera-Gómez, E. Rudiño-Piñera, Liliana Pardo-López
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.00053

Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa
Cited by: 29
Author(s): Utkarsh Sood, Princy Hira, Roshan Kumar, Abhay Bajaj, D. L. N. Rao, Rup Lal, Mallikarjun Shakarad
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.03070

Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica
Cited by: 12
Author(s): Stephanie Maria Anna Redl, Anja Poehlein, Carola Esser, Frank R. Bengelsdorf, Troy Jensen, Christian Bille Jendresen, Brian J. Tindall, Rolf Daniel, Peter Dürre, Alex Toftgaard Nielsen
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.00472

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning
Cited by: 47
Author(s): John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne‐Kristin Kaster
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2018.00364

Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers
Cited by: 27
Author(s): Camila Carlos, Huan Fan, Cameron R. Currie
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12020187

Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source
Cited by: 3
Author(s): Carla Gallardo-Benavente, Jessica L. Campo-Giraldo, Juan Castro‐Severyn, Andrés Quiróz, José M. Pérez-Donoso
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-74033-9

Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales
Cited by: 1
Author(s): Lucía Graña-Miraglia, Silvie Šikutová, Marie Vancová, Tomáš Bílý, Volker Fingerle, Andreas Sing, Santiago Castillo-Ramírez, Gabriele Margos, Ivo Rudolf
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-020-75637-x

Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails
Cited by: 25
Author(s): Maria Kornienko, Nikita Kuptsov, Roman Gorodnichev, Dmitry Bespiatykh, Andrei Guliaev, Maria A. Letarova, Eugene E. Kulikov, Vladimir A. Veselovsky, М В Малахова, Andrey V. Letarov, Elena N. Ilina, Egor Shitikov
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-020-78439-3

Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov.
Cited by: 14
Author(s): Sara Skøtt Paulsen, Thomas Isbrandt, Markus Kirkegaard, Yannick Buijs, Mikael Lenz Strube, Eva C. Sonnenschein, Thomas Ostenfeld Larsen, Lone Gram
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41396-021-00907-z

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication
Cited by: 18
Author(s): Jannick Van Cauwenberghe, Rosa I. Santamaría, Patricia Bustos, Soledad Juárez, Maria Antonella Ducci, Trinidad Figueroa Fleming, Ángela Virginia Etcheverry, Víctor González
Software Mentions: 3
Published: over 3 years ago

10.7150/jgen.38516

Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals
Cited by: 0
Author(s): Tomoya Tsukimi, Tsubasa Watabe, Kazuki Tanaka, Mitsuhiko Sato, Haruo Suzuki, Masaru Tomita, Shinji Fukuda
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.01377

Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics
Cited by: 19
Author(s): Hang T. Dam, John Vollmers, Morgan S. Sobol, Angela Cabezas, Anne‐Kristin Kaster
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2020.01928

Exploring the Diversity Within the Genus Francisella – An Integrated Pan-Genome and Genome-Mining Approach
Cited by: 14
Author(s): Rajender Kumar, Jeanette E. Bröms, Anders Sjöstedt
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-020-06905-3

Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe
Cited by: 10
Author(s): Tanvi Taparia, M.C. Krijger, Edward Haynes, J. G. Elphinstone, R. Noble, Jan van der Wolf
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-94820-2

Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome
Cited by: 5
Author(s): Tongda Li, Ross Mann, Jatinder Kaur, Germán Spangenberg, Tim Sawbridge
Software Mentions: 2
Published: about 3 years ago

10.1128/MRA.01233-20

Complete Genome Sequence of Francisella sp. Strain LA11-2445 (FDC406), a Novel Francisella Species Isolated from a Human Skin Lesion
Cited by: 0
Author(s): Caroline Öhrman, Ingrid Uneklint, Linda Karlsson, Laurel B. Respicio-Kingry, Mats Forsman, Jeannine M. Petersen, Andreas Sjödin
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-019-5600-x

Genomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli
Cited by: 14
Author(s): R. Roach, Rachel Mann, Cherie Gambley, Toni A. Chapman, R. G. Shivas, Brendan Rodoni
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12010111

Defining the Rhizobium leguminosarum Species Complex
Cited by: 43
Author(s): J. Peter W. Young, Sara Moeskjær, Alexey М. Afonin, Praveen Rahi, Marta Maluk, Euan K. James, Maria Izabel A. Cavassim, M. Harun-or Rashid, Aregu Amsalu Aserse, Benjamin J. Perry, En Tao Wang, Encarna Velázquez, E. E. Andronov, Anastasia P. Tampakaki, José David Flores Félix, Raúl Rivas, Sameh H. Youseif, Marc Lepetit, Stéphane Boivin, Beatriz Jorrín, Gregory Kenicer, Álvaro Peix, Michael F. Hynes, Martha Helena Ramírez-Bahena, Arvind Gulati, Chang Fu Tian
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.00782-20

Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity
Cited by: 21
Author(s): Pernille Kjersgaard Bech, Klaus Lars Lysdal, Lone Gram, Mikkel Bentzon-Tilia, Mikael Lenz Strube
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.608832

Genomic Insights of “Candidatus Nitrosocaldaceae” Based on Nine New Metagenome-Assembled Genomes, Including “Candidatus Nitrosothermus” Gen Nov. and Two New Species of “Candidatus Nitrosocaldus”
Cited by: 11
Author(s): Zhen-Hao Luo, Manik Prabhu Narsing Rao, Hao Chen, Zheng-Shuang Hua, Qi Li, Brian P. Hedlund, Zhou-Yan Dong, Bingbing Liu, Shuxian Guo, Wen‐Sheng Shu, Wenjun Li
Software Mentions: 2
Published: over 3 years ago

10.1128/genomeA.00009-18

Draft Genome Sequences of Novel Pseudomonas , Flavobacterium , and Sediminibacterium Species Strains from a Freshwater Ecosystem
Cited by: 3
Author(s): Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Bruno Adriano, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Software Mentions: 2
Published: over 6 years ago

10.3390/biom11040560

Identification and Characterization of a Novel Genomic Island Harboring Cadmium and Arsenic Resistance Genes in Listeria welshimeri
Cited by: 6
Author(s): Sangmi Lee, Cameron Parsons, Yi Chen, Zahra Hanafy, Eric W. Brown, Sophia Kathariou
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.00058

Exploring K2G30 Genome: A High Bacterial Cellulose Producing Strain in Glucose and Mannitol Based Media
Cited by: 43
Author(s): Maria Gullo, Salvatore La China, Giulio Petroni, Simona Di Gregorio, Paolo Giudici
Software Mentions: 2
Published: over 5 years ago

10.1128/JB.00125-17

Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex
Cited by: 25
Author(s): E. Joel Loveridge, Jones Ca, Matthew Bull, Suzy C. Moody, M. W. Kahl, Zulfiqar Ali Khan, Louis Neilson, Marina Tomeva, Steven Adams, Andrew C. Wood, Daniel Rodríguez-Martín, Ingrid Pinel, Julian Parkhill, Eshwar Mahenthiralingam, John Crosby
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2017.01590

Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study
Cited by: 70
Author(s): Alfonso Esposito, Arianna Pompilio, Clotilde Bettua, Valentina Crocetta, Elisabetta Giacobazzi, Ersilia Fiscarelli, Olivier Jousson, Giovanni Di Bonaventura
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2021.683481

Bacteriomic Analyses of Asian Citrus Psyllid and Citrus Samples Infected With “Candidatus Liberibacter asiaticus” in Southern California and Huanglongbing Management Implications
Cited by: 4
Author(s): Jiaquan Huang, Zhigang Dai, Zheng Zhang, Priscila A da Silvia, Lucita Kumagai, Qijun Xiang, Jianchi Chen, Xiaoling Deng
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2020.01549

Genomic Analysis and Antimicrobial Resistance of Aliarcobacter cryaerophilus Strains From German Water Poultry
Cited by: 8
Author(s): Eva Müller, Helmut Hotzel, Christine Ahlers, Ingrid Hänel, Herbert Tomaso, Mostafa Y. Abdel-Glil
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2019.01861

Whole-Genome Sequencing Redefines Shewanella Taxonomy
Cited by: 40
Author(s): Kaisa Thorell, Jan P. Meier‐Kolthoff, Åsa Sjöling, Alberto J. Martín‐Rodríguez
Software Mentions: 2
Published: about 5 years ago

10.3390/v13030495

Genome Sequence of the Bacteriophage CL31 and Interaction with the Host Strain Corynebacterium glutamicum ATCC 13032
Cited by: 2
Author(s): Max Hünnefeld, Ulrike Viets, Vikas Sharma, Astrid Wirtz, Aël Hardy, Julia Frunzke
Software Mentions: 2
Published: over 3 years ago

10.1099/mgen.0.000178

From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions
Cited by: 18
Author(s): Francisco X. Nascimento, Cláudia S. L. Vicente, Peter J. A. Cock, M. A. Tavares, Márcio José Rossi, Koichi Hasegawa, Manuel Mota
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2016.01668

Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum
Cited by: 62
Author(s): Frederike S. Haack, Anja Poehlein, Cathrin Kröger, Christian A. Voigt, Meike Piepenbring, Helge B. Bode, Rolf Daniel, Wilhelm Schäfer, Wolfgang R. Streit
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.10906

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes
Cited by: 2
Author(s): Long Tian, Reza Mazloom, Lenwood S. Heath, Boris A. Vinatzer
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9061123

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli
Cited by: 9
Author(s): Hyun‐Hee Lee, Jung–Wook Park, Hyejung Jung, Young-Su Seo
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.6233

Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments
Cited by: 12
Author(s): Hugo R. Barajas, Miguel Romero, Shamayim Martínez-Sánchez, Luis David Alcaraz
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-020-00889-8

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community
Cited by: 30
Author(s): Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, David Páez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke, Emiley A. Eloe‐Fadrosh, Ricardo Cavicchioli
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pntd.0007270

Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
Cited by: 366
Author(s): Antony T. Vincent, Olivier Schiettekatte, Cyrille Goarant, Vasantha Kumari Neela, Ève Bernet, Roman Thibeaux, Nabilah İsmail, Mohd Khairul Nizam Mohd Khalid, Fairuz Amran, Toshiyuki Masuzawa, Ryo Nakao, Anissa Amara Korba, Pascale Bourhy, Frédéric J. Veyrier, Mathieu Picardeau
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0233363

Whole genome sequence and comparative genome analyses of multi-resistant Staphylococcus warneri GD01 isolated from a diseased pig in China
Cited by: 2
Author(s): Canying Liu, Xianjie Zhao, Honglin Xie, Xi Zhang, Kangjian Li, Ma C, Qiang Fu
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-32973-3

Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species
Cited by: 13
Author(s): Karen L. Osman, Johanna M.C. Jefferies, Christopher H. Woelk, Nathalie Devos, Thierry Pascal, Marie-Cécile Mortier, Jeanne-Marie Devaster, Tom Wilkinson, David W. Cleary, Stuart C. Clarke
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-019-0625-6

Genomic and metagenomic insights into the microbial community of a thermal spring
Cited by: 38
Author(s): Renato Pedron, Alfonso Esposito, Irene Bianconi, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Mario Cristofolini, Nicola Segata, Olivier Jousson
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00060-19

Marine Chitinolytic Pseudoalteromonas Represents an Untapped Reservoir of Bioactive Potential
Cited by: 38
Author(s): Sara Skøtt Paulsen, Mikael Lenz Strube, Pernille Kjersgaard Bech, Lone Gram, Eva C. Sonnenschein
Software Mentions: 2
Published: about 5 years ago

10.1016/j.chom.2019.08.018

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
Cited by: 248
Author(s): Adrian Tett, Kun Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin S. Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl J. Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, María Carmen Collado, Dan R. Littman, Daniel Eibach, Omar Rota‐Stabelli, Curtis Huttenhower, Frank Maixner, Nicola Segata
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-020-00826-9

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics
Cited by: 54
Author(s): Sanjie Cao, Weipeng Zhang, Wei Ding, Meng Wang, Shen Fan, Bo Yang, Andrew McMinn, Min Wang, Bin-Bin Xie, Qi‐Long Qin, Xiu-Lan Chen, Jianfeng He, Yuzhong Zhang
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-43780-9

Novel Genes and Metabolite Trends in Bifidobacterium longum subsp. infantis Bi-26 Metabolism of Human Milk Oligosaccharide 2′-fucosyllactose
Cited by: 32
Author(s): Bryan Zabel, Christian C. Yde, Paige Roos, Jørn Marcussen, Henrik Max Jensen, Krista Salli, Johanna Hirvonen, Arthur C. Ouwehand, Wesley Morovic
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.00270

Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash
Cited by: 14
Author(s): E. A. Newberry, Mohamed Ebrahim, Sujan Timilsina, Nevena Zlatković, Aleksa Obradović, Carolee T. Bull, Erica M. Goss, José C. Huguet‐Tapia, Mathews L. Paret, Jeffrey B. Jones, Neha Potnis
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-36254-x

Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution
Cited by: 23
Author(s): Marc J. A. Stevens, Taurai Tasara, Jochen Klumpp, Roger Stephan, Monika Ehling‐Schulz, Sophia Johler
Software Mentions: 1
Published: over 5 years ago

10.3389/fbioe.2020.00828

Complete Genomic Analysis of Enterococcus faecium Heat-Resistant Strain Developed by Two-Step Adaptation Laboratory Evolution Method
Cited by: 7
Author(s): Bonggyu Min, DongAhn Yoo, Young-Ho Lee, Minseok Seo, Heebal Kim
Software Mentions: 1
Published: about 4 years ago

10.3389/fcimb.2018.00089

Population Genomics of Francisella tularensis subsp. holarctica and its Implication on the Eco-Epidemiology of Tularemia in Switzerland
Cited by: 22
Author(s): Matthias Wittwer, Ekkehard Altpeter, Paola Pilo, Sebastian M. Gygli, Christian Beuret, Frédéric Foucault, Rahel Ackermann-Gäumann, Urs Karrer, Daniela Jacob, Roland Grunow, Nadia Schürch
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2019.02026

Characterization of a Linezolid- and Vancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanG Operons
Cited by: 34
Author(s): Fanshu Du, Xi Lv, Duan Duan, Liping Wang, Jinhu Huang
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00146-20

Draft Genome Sequences of Novel Campylobacter Species Isolated from Nonhuman Primates
Cited by: 0
Author(s): Anthony Mannion, Zeli Shen, Alex Sheh, James G. Fox
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.694361

Whole Genome Analysis of Three Multi-Drug Resistant Listeria innocua and Genomic Insights Into Their Relatedness With Resistant Listeria monocytogenes
Cited by: 1
Author(s): Menghan Li, Shuling Yan, Séamus Fanning, Fengqin Li, Jin Xu
Software Mentions: 1
Published: about 3 years ago

10.7554/eLife.64325

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy
Cited by: 44
Author(s): Daniel R. Knight, Korakrit Imwattana, Brian Kullin, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Xavier Didelot, Kate E. Dingle, David W Eyre, César Rodríguez, Thomas V. Riley
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00234-20

Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina
Cited by: 6
Author(s): Lindsay Rutt, Shilpa Narina, Sarah Arbaugh, Elias McComb, Mike Humphrys, Bing Ma, Matthew R. Hayward, Elizabeth K. Costello, David A. Relman, Douglas S. Kwon, Jacques Ravel
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2020.617685

Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry
Cited by: 5
Author(s): Eva Müller, Helmut Hotzel, Jörg Linde, Ingrid Hänel, Herbert Tomaso
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00249-21

Draft Genome Assemblies of Two Campylobacter novaezeelandiae and Four Unclassified Thermophilic Campylobacter Isolates from Canadian Agricultural Surface Water
Cited by: 0
Author(s): Mirena Ivanova, Bonnie Oh, Izhar U. H. Khan, Kendra K. Nightingale, Marie Bugarel, Amanda M. V. Brown, Guy H. Loneragan
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00695-21

Complete Genome Sequence of a Clinical Isolate of Acinetobacter baumannii Harboring 11 Plasmids
Cited by: 1
Author(s): Arata Sakiyama, Yuki Matsumoto, Taishi Tsubouchi, Masato Suzuki, Makoto Niki, Mamiko Niki, Ken-Ich Oinuma, Hiroshi Kakeya, Yukihiro Kaneko
Software Mentions: 1
Published: almost 3 years ago

10.1007/s10482-021-01592-w

Whole-Genome sequencing and comparative genomics of Mycobacterium spp. from farmed Atlantic and coho salmon in Chile
Cited by: 1
Author(s): Rudy Suárez, Karina Kusch, Claudio D. Miranda, Tianlu Li, Javier Campanini, Phani Rama Krishna Behra, Luis Aro, Alexis Martínez, Marcos Godoy, Daniel A. Medina
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: pyani

Papers Mentioning pyani 120