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: mash
https://packages.ecosyste.ms/registries/pypi.org/packages/mash
Python lib for converting dict to objects recursive
1 version
Latest release: about 9 years ago
50 downloads last month
Papers Mentioning mash 28
10.3390/ijms22052244
The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensisCited 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 monocytogenesCited by: 10
Author(s): Stefanie Lüth, Carlus Deneke, Sylvia Kleta, Sascha Al Dahouk
Software Mentions: 9
Published: almost 4 years ago
10.1186/s13059-019-1755-7
Benchmarking of alignment-free sequence comparison methodsCited 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: over 5 years ago
10.1371/journal.pcbi.1005727
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarityCited 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 assemblyCited 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: over 3 years ago
10.1371/journal.pgen.1009213
Gene regulatory effects of a large chromosomal inversion in highland maizeCited 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 studyCited 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 BeanCited 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 genesCited 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: almost 4 years ago
10.7717/peerj.5261
<i>Staphylococcus aureus</i> viewed from the perspective of 40,000+ genomesCited by: 57
Author(s): Robert A. Petit, Timothy D. Read
Software Mentions: 4
Published: over 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 studyCited 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: almost 5 years ago
10.3389/fmicb.2020.00483
Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF PlasmidsCited 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 methodCited 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 communityCited 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: about 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 InfectionsCited by: 15
Author(s): Tobias Lienen, Arne Schnitt, Jens A. Hammerl, Sven Maurischat, Bernd‐Alois Tenhagen
Software Mentions: 3
Published: almost 4 years ago
10.1186/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 severityCited 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 forsythiaCited 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 EnterobacteriaceaeCited 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 proteinsCited 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 AQUAMISCited 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 GermanyCited 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 countryCited 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 genomesCited 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 EnvironmentCited 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 GermanyCited 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 FarmsCited 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 BacteriaCited 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