Ecosyste.ms: Papers

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 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: over 3 years ago

10.1186/s13059-019-1755-7

Benchmarking of alignment-free sequence comparison methods
Cited by: 134
Author(s): Andrzej Zieleziński, Hani Z. Girgis, Guillaume Bernard, Chris-André Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S. Waterman, Matteo Comin, Sung‐Hou Kim, Susana Vinga, Jonas S. Almeida, Cheong Xin Chan, Benjamin James, Fengzhu Sun, Burkhard Morgenstern, Wojciech M. Karłowski
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: about 7 years ago

10.1186/s13059-021-02427-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Cited by: 56
Author(s): Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Vallès-Colomer, Willem M. de Vos, Nicola Segata
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pgen.1009213

Gene regulatory effects of a large chromosomal inversion in highland maize
Cited by: 38
Author(s): Taylor M. Crow, James Ta, Saghi Nojoomi, M. Rocío Aguilar-Rangel, Jorge Vladimir Torres Rodríguez, David M. Gates, Rubén Rellán‐Álvarez, Ruairidh J. H. Sawers, Daniel E. Runcie
Software Mentions: 5
Published: almost 4 years ago

10.12688/wellcomeopenres.14265.2

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Cited by: 37
Author(s): John A. Lees, Michaela Kendall, Julian Parkhill, Caroline Colijn, SD Bentley, Rachel Harris
Software Mentions: 5
Published: over 6 years ago

10.1534/genetics.120.303038

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-80145-z

Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes
Cited by: 10
Author(s): Michelle M. Stein, Mitchell Conery, Kevin M. Magnaye, Selene M. Clay, Christine Billstrand, Raluca Nicolae, Katherine A. Naughton, Carole Ober, Emma E. Thompson
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.5261

<i>Staphylococcus aureus</i> viewed from the perspective of 40,000+ genomes
Cited by: 57
Author(s): Robert A. Petit, Timothy D. Read
Software Mentions: 4
Published: about 6 years ago

10.1099/mgen.0.000335

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study
Cited by: 56
Author(s): Ronan Doyle, Denise M O’Sullivan, Sean Aller, Sebastian Bruchmann, Taane G. Clark, Andreu Coello Pelegrin, Martin Cormican, Ernest Diez Benavente, Matthew J. Ellington, Elaine McGrath, Yair Motro, Thi Phuong Thuy Nguyen, Jody Phelan, Liam Shaw, Richard Stabler, Alex van Belkum, Lucy van Dorp, Neil Woodford, Jacob Moran-Gilad, Jim F. Huggett, Kathryn Harris
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.00483

Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids
Cited by: 46
Author(s): Pierre-Emmanuel Douarre, Ludovic Mallet, Nicolas Radomski, Arnaud Felten, Michel‐Yves Mistou
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-020-00937-3

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
Cited by: 25
Author(s): Lei Liu, Yulin Wang, Ying Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Kewei Chen, Tong Zhang
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.37090

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
Cited by: 58
Author(s): Kevin D’hoe, Stefan Vet, Karoline Faust, Frédéric Moens, Gwen Falony, Didier Gonze, Verónica Lloréns‐Rico, Lendert Gelens, Jan Danckaert, Luc De Vuyst, Jeroen Raes
Software Mentions: 3
Published: almost 6 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: over 3 years ago

10.1186/s12864-020-6555-7

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity
Cited by: 10
Author(s): Amber C. A. Hendriks, Frans A.G. Reubsaet, A.M.D. Kooistra-Smid, John W. A. Rossen, Bas E. Dutilh, Aldert Zomer, Maaike van den Beld
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-6535-y

Comparative genome characterization of the periodontal pathogen Tannerella forsythia
Cited by: 8
Author(s): Nikolaus F. Zwickl, Nancy Stralis‐Pavese, Christina Schäffer, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 2
Published: over 4 years ago

10.1126/sciadv.abe3868

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Cited by: 32
Author(s): Liam P. Shaw, Kevin Chau, James Kavanagh, Manal AbuOun, Emma Stubberfield, Hyun S. Gweon, Leanne Barker, Gillian Rodger, Michael J. Bowes, Alasdair T. M. Hubbard, Hayleah Pickford, Jeremy Swann, Daniel Gilson, Richard P. Smith, Sarah Hoosdally, Robert Sebra, Howard Brett, Tim Peto, Mark Bailey, Derrick W. Crook, Daniel S. Read, Muna F. Anjum, A Sarah Walker, Nicole Stoesser
Software Mentions: 2
Published: over 3 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: over 3 years ago

10.3390/genes12050644

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
Cited by: 32
Author(s): Carlus Deneke, Holger Brendebach, Laura Uelze, Maria Blettner, Burkhard Malorny, Simon H. Tausch
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

10.7554/eLife.50468

Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country
Cited by: 12
Author(s): Thomas Crellen, Paul Turner, Sreymom Pol, Stephen Baker, To Nguyen Thi Nguyen, Nicole Stoesser, Nicholas P. J. Day, Claudia Turner, Ben S. Cooper
Software Mentions: 2
Published: almost 5 years ago

10.1093/bioinformatics/btz903

<tt>Phylonium</tt>: fast estimation of evolutionary distances from large samples of similar genomes
Cited by: 11
Author(s): Fabian Klötzl, Bernhard Haubold
Software Mentions: 2
Published: almost 5 years ago

10.1128/AAC.02513-18

<i>Klebsiella quasipneumoniae</i> Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment
Cited by: 39
Author(s): Amy J Mathers, Derrick W. Crook, Alison Vaughan, Barry Ke, Kasi Vegesana, Nicole Stoesser, Hardik I. Parikh, Robert Sebra, Shireen Meher Kotay, A. Sarah Walker, Anna E. Sheppard
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.626941

Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
Cited by: 14
Author(s): Laura Uelze, Natalie Becker, Maria Blettner, Ulrich Busch, Alexandra Dangel, Carlus Deneke, Jennie Fischer, Antje Flieger, Sabrina Hepner, Ingrid Huber, Ulrich Methner, Jörg Linde, Michael Pietsch, Sandra Simon, Andreas Sing, Simon H. Tausch, István Szabó, Burkhard Malorny
Software Mentions: 2
Published: over 3 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

10.1128/AAC.00823-19

Repeated Isolation of Extended-Spectrum-β-Lactamase-Positive <i>Escherichia coli</i> Sequence Types 648 and 131 from Community Wastewater Indicates that Sewage Systems Are Important Sources of Emerging Clones of Antibiotic-Resistant Bacteria
Cited by: 23
Author(s): Erik Paulshus, Kaisa Thorell, Jessica Guzman-Otazo, Enrique Joffré, Patricia Colque, Inger Kühn, R. Möllby, Henning Sørum, Åsa Sjöling
Software Mentions: 1
Published: about 5 years ago