pypi: Swarm | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.550420

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Cited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 3 years ago

10.3389/fgene.2020.489357

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Cited by: 13
Author(s): Alejandro Abdala Asbun, Marc Besseling, Sergio Balzano, Judith van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
Software Mentions: 11
Published: about 4 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: about 4 years ago

10.1126/sciadv.abg1921

Environmental vulnerability of the global ocean epipelagic plankton community interactome
Cited by: 47
Author(s): Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Patrick Wincker, Lee Karp‐Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard
Software Mentions: 9
Published: about 3 years ago

10.1038/s41396-019-0563-0

Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere
Cited by: 11
Author(s): Matti O. Ruuskanen, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 8
Published: almost 5 years ago

10.1186/s13059-018-1616-9

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Cited by: 61
Author(s): Matthew E.B. Hansen, Meagan A Rubel, Aubrey Bailey, Alessia Ranciaro, S. R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe George Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian C. Abnet, Stephen J. Chanock, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 8
Published: almost 6 years ago

10.1111/1365-2656.13065

Host genetics and geography influence microbiome composition in the sponge Ircinia campana
Cited by: 48
Author(s): Sarah M. Griffiths, Rachael E. Antwis, Luca Lenzi, Anita Lucaci, Donald C. Behringer, Mark J. Butler, Richard F. Preziosi
Software Mentions: 8
Published: about 5 years ago

10.3389/fmicb.2020.592189

From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies
Cited by: 6
Author(s): Robin-Tobias Jauss, Susanne Walden, Anna Maria Fiore‐Donno, Kenneth Dumack, Stefan Schaffer, Ronny Wolf, Martin Schlegel, Michael Bonkowski
Software Mentions: 7
Published: almost 4 years ago

10.1093/gigascience/giaa022

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Cited by: 28
Author(s): Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis
Software Mentions: 7
Published: over 4 years ago

10.1128/mSphereDirect.00073-17

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
Cited by: 312
Author(s): Sarah L. Westcott, Patrick D. Schloss
Software Mentions: 7
Published: over 7 years ago

10.1186/s40168-017-0314-2

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
Cited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2021.614634

Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard)
Cited by: 14
Author(s): Lisa-Marie Delpech, Tobias R. Vonnahme, Maeve McGovern, Rolf Gradinger, Kim Præbel, Amanda Poste
Software Mentions: 6
Published: over 3 years ago

10.1111/1462-2920.15260

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche‐driven microbial community assembly processes
Cited by: 11
Author(s): Alizée Le Moigne, Maciej Bartosiewicz, Gabriela Schaepman‐Strub, Samuel Abiven, Jakob Pernthaler
Software Mentions: 6
Published: about 4 years ago

10.3389/fnbeh.2020.581296

A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats
Cited by: 6
Author(s): Valérie Daugé, Catherine Philippe, Mahendra Mariadassou, Olivier Rué, Jean‐Charles Martin, Marie Rossignol, Nathalie Dourmap, Ljubica Svilar, Franck Tourniaire, Magali Monnoye, Déborah Jardet, Marie Bangratz, Sophie Holowacz, Sylvie Rabot, Laurent Naudon
Software Mentions: 6
Published: about 4 years ago

10.1038/s42003-021-02012-5

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans
Cited by: 22
Author(s): Alexandra Schoenle, Manon Hohlfeld, Karoline Hermanns, Frédéric Mahé, Colomban de Vargas, Frank Nitsche, Hartmut Arndt
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2020.574361

Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back
Cited by: 16
Author(s): Aline Sondra Adler, Christof Holliger
Software Mentions: 6
Published: almost 4 years ago

10.1038/srep33555

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Cited by: 65
Author(s): Anna Gimmler, Ralf Korn, Colomban de Vargas, Stéphane Audic, Thorsten Stoeck
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0240041

Towards an open and decentralized case law curation ecosystem
Cited by: 1
Author(s): Eleni Panagou, Manolis Vavalis
Software Mentions: 6
Published: about 4 years ago

10.1111/1462-2920.15114

Heterogeneity of the rice microbial community of the Chinese centuries‐old Honghe Hani rice terraces system
Cited by: 8
Author(s): Pascal Alonso, Laurence Blondin, Pierre Gladieux, Frédéric Mahe, Hervé Sanguin, Romain Ferdinand, Denis Filloux, Érick Desmarais, Frédérique Cerqueira, Baocheng Jin, Huichuan Huang, Xiahong He, Jean-Benoît Morel, Darren P. Martin, Philippe Roumagnac, Christian Vernière
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.01138

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada
Cited by: 43
Author(s): Matti O. Ruuskanen, Kyra A. St. Pierre, Vincent L. St. Louis, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj-cs.232

On-demand virtual research environments using microservices
Cited by: 10
Author(s): Marco Capuccini, Anders Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Toor, Ola Spjuth
Software Mentions: 5
Published: about 5 years ago

10.3389/fpls.2019.01018

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks
Cited by: 17
Author(s): Daniel Revillini, Gail W. T. Wilson, R. M. Miller, Ryan C. Lancione, Nancy Collins Johnson
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.00098

Bdellovibrio and Like Organisms in Lake Geneva: An Unseen Elephant in the Room?
Cited by: 18
Author(s): Jade Ezzedine, Louis Jacas, Yves Desdevises, Stéphan Jacquet
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2020.02023

Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode
Cited by: 12
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Lucile Durand, Johanne Aubé, Nicolas Gayet, Roberto Sandulli, Christophe Brandily, Daniela Zeppilli
Software Mentions: 5
Published: over 4 years ago

10.1002/ece3.6482

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area
Cited by: 46
Author(s): Natalia Fraija-Fernández, Marie-Catherine Bouquieaux, Anaïs Rey, Iñaki Mendibil, Unai Cotano, Xabier Irigoien, M.B. Santos, Naiara Rodríguez-Ezpeleta
Software Mentions: 5
Published: over 4 years ago

10.1186/s12866-016-0885-2

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories
Cited by: 41
Author(s): François-Joël Gatesoupe, Christine Huelvan, Nicolas Le Bayon, Hervé Le Delliou, Lauriane Madec, Olivier Mouchel, Patrick Quazuguel, David Mazurais, José‐Luis Zambonino-Infante
Software Mentions: 5
Published: about 8 years ago

10.1128/mSystems.00003-15

Open-Source Sequence Clustering Methods Improve the State Of the Art
Cited by: 139
Author(s): Evguenia Kopylova, José A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Zhou Hong, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.1487

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Cited by: 224
Author(s): Sarah L. Westcott, Patrick D. Schloss
Software Mentions: 4
Published: almost 9 years ago

10.7717/peerj.4458

Characterization of the salivary microbiome in people with obesity
Cited by: 63
Author(s): Yujia Wu, Xiaopei Chi, Qian Zhang, Feng Chen, Xuliang Deng
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9030549

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network
Cited by: 16
Author(s): Dominik Forster, Zhishuai Qu, Gianna Pitsch, Estelle P. Bruni, Barbara Kammerlander, Thomas Pröschold, Bettina Sonntag, Thomas Posch, Thorsten Stoeck
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.647921

Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs
Cited by: 11
Author(s): Gabrielle Maria Fonseca Pierangeli, Mércia Regina Domingues, Tatiane Araújo de Jesus, Lúcia Helena Gomes Coelho, Werner Siegfried Hanisch, Marcelo Luiz Martins Pompêo, Flávia Talarico Saia, Gustavo Bueno Gregoracci, Roseli Frederigi Benassi
Software Mentions: 4
Published: over 3 years ago

10.3390/s18092986

Future Spaces: Reinventing the Home Network for Better Security and Automation in the IoT Era
Cited by: 17
Author(s): Mathieu Boussard, Dinh Thai Bui, Richard Douville, Pascal Justen, Nicolas Le Sauze, Pierre Peloso, Frederik Vandeputte, Vincent Verdot
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2018.01290

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes
Cited by: 23
Author(s): Christina Böck, Michaela M. Salcher, Manfred Jensen, Ram Vinay Pandey, Jens Boenigk
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.602404

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Cited by: 7
Author(s): Lucie Rault, Pierre-Alexandre Lévêque, Sarah Barbey, Frédéric Launay, Hélène Larroque, Yves Le Loir, Pierre Germon, Jocelyne Guinard-Flament, Sergine Even
Software Mentions: 4
Published: almost 4 years ago

10.1007/s10339-021-01012-x

Landmarks in wayfinding: a review of the existing literature
Cited by: 33
Author(s): Demet Yeşiltepe, Ruth Dalton, Ayşe Özbil Torun
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.02682

Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP
Cited by: 29
Author(s): Anne E. Dekas, Alma E. Parada, Xavier Mayali, Jed A. Fuhrman, Jessica Wollard, Peter K. Weber, Jennifer Pett‐Ridge
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40623-020-01284-1

Dipolar elementary current systems for ionospheric current reconstruction at low and middle latitudes
Cited by: 4
Author(s): Heikki Vanhamäki, Astrid Maute, Patrick Alken, Huixin Liu
Software Mentions: 4
Published: about 4 years ago

10.1002/ece3.4742

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
Cited by: 45
Author(s): Natalie A. Sawaya, Anni Djurhuus, Collin J. Closek, Megan Hepner, Emily Olesin, Lindsey A. Visser, Christopher R. Kelble, Katherine A. Hubbard, Mya Breitbart
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.7788

Method for quick DNA barcode reference library construction
Cited by: 11
Author(s): Yanlei Liu, Chao Xu, Yuzhe Sun, Xun Chen, Wenpan Dong, Xiaopan Yang, Shi–Liang Zhou
Software Mentions: 4
Published: over 3 years ago

10.1128/AEM.02343-19

Reintroducing mothur: 10 Years Later
Cited by: 132
Author(s): Patrick D. Schloss
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.6931

Metabarcoding reveals a high diversity of woody host-associatedPhytophthoraspp. in soils at public gardens and amenity woodlands in Britain
Cited by: 36
Author(s): Carolyn Riddell, Debbie Frederickson-Matika, April C. Armstrong, Matthew Elliot, Jack Forster, Pete E. Hedley, Jenny Morris, Peter Thorpe, D. E. L. Cooke, Leighton Pritchard, Paul M. Sharp, Sarah Green
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9821

Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
Cited by: 10
Author(s): Monika Reczuga, Christophe V. W. Seppey, Matthieu Mulot, Vincent E. J. Jassey, Alexandre Buttler, Sandra Słowińska, Michael Słowiński, Enrique Lara, Mariusz Lamentowicz, Edward A. D. Mitchell
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-017-1690-0

Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities
Cited by: 48
Author(s): Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman, David N. Fredricks
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.1420

Swarm v2: highly-scalable and high-resolution amplicon clustering
Cited by: 397
Author(s): Frédéric Mahé, Torbjørn Rognes, Christopher Quince, Colomban de Vargas, Micah Dunthorn
Software Mentions: 3
Published: almost 9 years ago

10.1093/femsec/fix029

Reconciliation between operational taxonomic units and species boundaries
Cited by: 54
Author(s): Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek‐Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
Software Mentions: 3
Published: over 7 years ago

10.1111/cogs.12939

Attention Does Not Affect the Speed of Subjective Time, but Whether Temporal Information Guides Performance: A Large‐Scale Study of Intrinsically Motivated Timers in a Real‐Time Strategy Game
Cited by: 2
Author(s): Robbert van der Mijn, Hedderik van Rijn
Software Mentions: 3
Published: over 3 years ago

10.3390/s18124226

Design Methodology of Microservices to Support Predictive Analytics for IoT Applications
Cited by: 25
Author(s): Sajjad Ali, Muhammad Aslam Jarwar, Ilyoung Chong
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41396-019-0551-4

Biodiversity of protists and nematodes in the wild nonhuman primate gut
Cited by: 30
Author(s): Allison E. Mann, Florent Mazel, Matthew A. Lemay, Evan Morien, Vincent Billy, Martín M. Kowalewski, Anthony Di Fiore, Andrés Link, Tony L. Goldberg, Stacey R. Tecot, Andrea L. Baden, Andrés Gómez, Michelle L. Sauther, Frank P. Cuozzo, Gillian A.O. Rice, Nathaniel J. Dominy, Rebecca M. Stumpf, Rebecca J. Lewis, Larissa Swedell, Katherine R. Amato, Laura Wegener Parfrey
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.1692

Comparison of three clustering approaches for detecting novel environmental microbial diversity
Cited by: 24
Author(s): Dominik Forster, Micah Dunthorn, Thorsten Stoeck, Frédéric Mahe
Software Mentions: 3
Published: over 8 years ago

10.1093/gigascience/giz041

Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments
Cited by: 6
Author(s): Fabiano Bezerra Menegídio, David Aciole Barbosa, Rafael Dos S Gonçalves, Marcio M Nishime, Daniela Jabés, Regina Costa de Oliveira, Luiz R. Nunes
Software Mentions: 3
Published: over 5 years ago

10.3390/jof6040335

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence
Cited by: 12
Author(s): Vladimir Gorshkov, Elena Osipova, М. Л. Пономарева, Sergey Ponomarev, Natalia Gogoleva, Olga Petrova, Olga Gogoleva, Azat Meshcherov, Alexander S. Balkin, Е. П. Ветчинкина, Kim O. Potapov, Alexander A. Kamnev, Viktor Korzun
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-16-S12-S2

Multiscale modeling of mucosal immune responses
Cited by: 28
Author(s): Yefeng Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang, Pinyi Lu, Casandra Philipson, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Josep Bassaganya‐Riera
Software Mentions: 3
Published: about 9 years ago

10.3389/fcimb.2020.00129

Pathobionts in the Vaginal Microbiota: Individual Participant Data Meta-Analysis of Three Sequencing Studies
Cited by: 26
Author(s): Janneke van de Wijgert, Marijn C. Verwijs, A. Christina Gill, Hanneke Borgdorff, Charlotte van der Veer, Philippe Mayaud
Software Mentions: 3
Published: over 4 years ago

10.3390/foods10020362

Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage
Cited by: 16
Author(s): Aurélien Maillet, Pauline Denojean, Agnès Bouju-Albert, Erwan Scaon, Sébastien Leuillet, Xavier Dousset, Emmanuel Jaffrès, Jérôme Combrisson, Hervé Prévost
Software Mentions: 3
Published: almost 4 years ago

10.1128/MRA.00257-21

Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing
Cited by: 2
Author(s): Nikola Palevich, Paul Maclean, Luis Carvalho, Ruy Jáuregui
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008977

Swarm: A federated cloud framework for large-scale variant analysis
Cited by: 2
Author(s): Amir Bahmani, Kyle Ferriter, Vandhana Krishnan, Arash Alavi, Amir Alavi, Philip S. Tsao, M Snyder, Cuiping Pan
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-43517-8

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode
Cited by: 14
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Stéphane Hourdez, Mohamed Jebbar, Aurélie Tasiemski, Lucile Durand, Nicolas Gayet, Daniela Zeppilli
Software Mentions: 3
Published: over 5 years ago

10.1186/1756-0500-3-289

Dockomatic - automated ligand creation and docking
Cited by: 21
Author(s): Casey W. Bullock, Reed B. Jacob, Owen M. McDougal, Greg Hampikian, Tim Andersen
Software Mentions: 3
Published: about 14 years ago

10.1002/lom3.10237

Evaluation of marine zooplankton community structure through environmental DNA metabarcoding
Cited by: 97
Author(s): Anni Djurhuus, Kathleen J. Pitz, Natalie A. Sawaya, Jaimie Rojas‐Márquez, Brianna Michaud, Enrique Montes, Frank E. Müller-Karger, Mya Breitbart
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2020.01093

Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis
Cited by: 24
Author(s): Emilie Lejal, Agustı́n Estrada-Peña, Maud Marsot, Jean-François Cosson, Olivier Rué, Mahendra Mariadassou, Cédric Midoux, Muriel Vayssier‐Taussat, Thomas V. Pollet
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0116955

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform
Cited by: 262
Author(s): Lucas Sinclair, Omneya Ahmed Osman, Stefan Bertilsson, Alexander Eiler
Software Mentions: 3
Published: almost 10 years ago

10.1111/jeu.12519

Clarifying the Relationships between Microsporidia and Cryptomycota
Cited by: 87
Author(s): David Bass, Lucas Czech, Bryony A. P. Williams, Cédric Berney, Micah Dunthorn, Frédéric Mahé, Guifré Torruella, Grant D. Stentiford, Tom A. Williams
Software Mentions: 3
Published: over 6 years ago

10.3390/ijerph15102319

Fear of Missing Out as a Predictor of Problematic Social Media Use and Phubbing Behavior among Flemish Adolescents
Cited by: 162
Author(s): Vittoria Franchina, Mariek Vanden Abeele, Antonius J. van Rooij, Gianluca Lo Coco, Lieven De Marez
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-56599-1

Precursory worldwide signatures of earthquake occurrences on Swarm satellite data
Cited by: 75
Author(s): Angelo De Santis, Dedalo Marchetti, F. J. Pavón‐Carrasco, Gianfranco Cianchini, Loredana Perrone, Cristoforo Abbattista, Lucilla Alfonsi, Leonardo Amoruso, Saioa A. Campuzano, Marianna Carbone, Claudio Cesaroni, Giorgiana De Franceschi, Rita Di Giovambattista, Alessandro Ippolito, Alessandro Piscini, Dario Sabbagh, Maurizio Soldani, Francesca Santoro, Luca Spogli, Roger Haagmans
Software Mentions: 2
Published: almost 5 years ago

10.1186/s42523-020-00047-3

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis
Cited by: 3
Author(s): Aline Aparecida Zanotti, Gustavo Bueno Gregoracci, K. C. C. Capel, Marcelo V. Kitahara
Software Mentions: 2
Published: over 4 years ago

10.1186/s12911-020-01275-y

Towards developing a secure medical image sharing system based on zero trust principles and blockchain technology
Cited by: 41
Author(s): Maliha Sultana, Afrida Hossain, Fabiha Laila, Kazi Abu Taher, Muhammad Nazrul Islam
Software Mentions: 2
Published: about 4 years ago

10.3390/microorganisms9061188

Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves
Cited by: 7
Author(s): Jake Burgoyne, Robin Crepeau, Jacob Reinholdt Jensen, Hayden Smith, Gretchen M. Baker, Steven D. Leavitt
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9020361

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions
Cited by: 36
Author(s): Davide Francioli, Guillaume Lentendu, Simon Lewin, Steffen Kolb
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13071-019-3402-2

The composition and abundance of bacterial communities residing in the gut of Glossina palpalis palpalis captured in two sites of southern Cameroon
Cited by: 17
Author(s): Jean Marc Tsagmo Ngoune, Julie Réveillaud, Guilhem Sempéré, Flobert Njiokou, Tresor Tito Tanekou Melachio, Luc Abate, Majoline T. Tchioffo, Anne Geiger
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.593

Swarm: robust and fast clustering method for amplicon-based studies
Cited by: 636
Author(s): Frédéric Mahe, Torbjørn Rognes, Christopher Quince, Colomban de Vargas, Micah Dunthorn
Software Mentions: 2
Published: about 10 years ago

10.7717/peerj.11717

On the use of sequence-quality information in OTU clustering
Cited by: 2
Author(s): Robert Müller, Markus E. Nebel
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.2341

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units
Cited by: 34
Author(s): Matthew A. Jackson, Jordana T. Bell, Tim D. Spector, Claire J. Steves
Software Mentions: 2
Published: about 8 years ago

10.14814/phy2.13639

Acute intraperitoneal lipopolysaccharide influences the immune system in the absence of gut dysbiosis
Cited by: 9
Author(s): Kristyn E. Sylvia, Gregory E. Demas
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0151064

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment
Cited by: 10
Author(s): Jeongsu Oh, Chi-Hoon Choi, Minkyu Park, Byung Kwon Kim, Ki-Hwan Hwang, Sang‐Heon Lee, Soon Gyu Hong, Arshan Nasir, Wan-Sup Cho, Kyung Mo Kim
Software Mentions: 2
Published: over 8 years ago

10.1002/ece3.6071

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments
Cited by: 28
Author(s): Anaïs Rey, Oihane C. Basurko, Naiara Rodríguez-Ezpeleta
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41426-018-0049-6

Detection of Coccidioides posadasii from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections
Cited by: 20
Author(s): Primavera Alvarado, Marcus de Melo Teixeira, Lela V. Andrews, A. Hedrera Fernandez, Gerardo Santander, Adina Doyle, M.R. Pérez Pérez, Francisco Yegres, Bridget M. Barker
Software Mentions: 2
Published: over 6 years ago

10.3390/e23070914

Leadership Hijacking in Docker Swarm and Its Consequences
Cited by: 4
Author(s): Adi Farshteindiker, Rami Puzis
Software Mentions: 2
Published: over 3 years ago

10.1093/femsec/fiaa140

Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change
Cited by: 9
Author(s): Edda Marie Rainer, Christophe V. W. Seppey, Alexander Tøsdal Tveit, Mette M. Svenning
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2021.644012

Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences
Cited by: 14
Author(s): Ze-Gang Wei, Xiaodan Zhang, Ming Cao, Fei Liu, Yu Qian, Shao-Wu Zhang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.03103

Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition
Cited by: 32
Author(s): Norman Wiernasz, Françoise Leroi, Frédérique Chevalier, Josiane Cornet, Mireille Cardinal, Jens Rohloff, Delphine Passerini, Sigurlaug Skírnisdóttir, Marie-France Pilet
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2018.02246

A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship
Cited by: 16
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Lucile Durand, Nicolas Gayet, Daniela Zeppilli
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2016.01946

Detection of Invertebrate Suppressive Soils, and Identification of a Possible Biological Control Agent for Meloidogyne Nematodes Using High Resolution Rhizosphere Microbial Community Analysis
Cited by: 26
Author(s): N.L. Bell, Katharine H. Adam, Rhys J. Jones, Richard D. Johnson, Yeukai F. Mtandavari, G. Burch, Vanessa M. Cave, C. A. Cameron, Paul Maclean, Alison J. Popay, Damien J. Fleetwood
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-018-1450-0

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
Cited by: 28
Author(s): Qi Zheng, Casey Bartow‐McKenney, Jacquelyn S. Meisel, Elizabeth A. Grice
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-18179-z

Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval
Cited by: 32
Author(s): Ildikó Szelecz, Sandra Lösch, Christophe V. W. Seppey, Enrique Lara, David Singer, Franziska Sorge, Joëlle Tschui, M. Alejandra Perotti, Edward A. D. Mitchell
Software Mentions: 2
Published: almost 7 years ago

10.1186/s42523-020-00067-z

The intestinal microbial composition in Greylag geese differs with steatosis induction mode: spontaneous or induced by overfeeding
Cited by: 1
Author(s): Christelle Knudsen, Julien Arroyo, Maxime Even, Laurent Cauquil, Géraldine Pascal, Xavier Fernández, Franck Lavigne, Stéphane Davail, Sylvie Combes, Karine Ricaud
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-76293-x

Implications of increasing Atlantic influence for Arctic microbial community structure
Cited by: 9
Author(s): Michael Carter-Gates, Cecilia Balestreri, Sally Thorpe, Finlo Cottier, Alison J. Baylay, Thomas S. Bibby, C. Mark Moore, Declan C. Schroeder
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-80752-w

Reconstructing GRACE-type time-variable gravity from the Swarm satellites
Cited by: 26
Author(s): Hartmut Richter, Christina Lück, Anna Kłos, Michael G. Sideris, Elena Rangelova, Jürgen Kusche
Software Mentions: 2
Published: almost 4 years ago

10.3390/s17030635

Precise Orbit Solution for Swarm Using Space-Borne GPS Data and Optimized Pseudo-Stochastic Pulses
Cited by: 6
Author(s): Bingbing Zhang, Zhengtao Wang, Lv Zhou, Jiagui Feng, Qiu Yaodong, Fupeng Li
Software Mentions: 2
Published: over 7 years ago

10.3390/s17102177

A Methodology for the Design of Application-Specific Cyber-Physical Social Sensing Co-Simulators
Cited by: 13
Author(s): Borja Bordel, Álvaro Sánchez-Picot
Software Mentions: 2
Published: about 7 years ago

10.3390/s18092938

A Capillary Computing Architecture for Dynamic Internet of Things: Orchestration of Microservices from Edge Devices to Fog and Cloud Providers
Cited by: 75
Author(s): Salman Taherizadeh, Vlado Stankovski, Marko Grobelnik
Software Mentions: 2
Published: about 6 years ago

10.3390/s19102408

Research on Attitude Models and Antenna Phase Center Correction for Jason-3 Satellite Orbit Determination
Cited by: 8
Author(s): Mingming Liu, Yunbin Yuan, Junfei Ou, Chai Yan-ju
Software Mentions: 2
Published: over 5 years ago

10.3390/s20030918

A Location Privacy Attack Based on the Location Sharing Mechanism with Erroneous Distance in Geosocial Networks
Cited by: 4
Author(s): Tu-Liang Lin, Hong-Yi Chang, Shenglin Li
Software Mentions: 2
Published: almost 5 years ago

10.1128/mBio.01814-19

Anaerobic Degradation of Non-Methane Alkanes by “ Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico
Cited by: 58
Author(s): Rafael Laso-Pérez, Cedric Jasper Hahn, Daan M. van Vliet, Halina E. Tegetmeyer, Florence Schubotz, Nadine T. Smit, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Antje Boetius, Katrin Knittel, Gunter Wegener
Software Mentions: 2
Published: about 5 years ago

10.1029/2021JA029292

Multi‐Instrument Characterization of Magnetospheric Cold Plasma Dynamics in the June 22, 2015 Geomagnetic Storm
Cited by: 4
Author(s): M. Vellante, Kazue Takahashi, Alfredo Del Corpo, Irina Zhelavskaya, J. Goldstein, I. R. Mann, E. Pietropaolo, Jan Reda, B. Heilig
Software Mentions: 2
Published: over 3 years ago

10.2196/10163

Blockchain Technology for Detecting Falsified and Substandard Drugs in Distribution: Pharmaceutical Supply Chain Intervention
Cited by: 164
Author(s): Patrick G. Sylim, Fang Liu, Alvin Marcelo, Paul Fontelo
Software Mentions: 2
Published: about 6 years ago

10.2174/1874285801812010071

Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks
Cited by: 7
Author(s): Maxime Even, Stéphane Davail, Mikael Rey, Annabelle Tavernier, Marianne Houssier, Marie Bernadet, Karine Gontier, Géraldine Pascal, Karine Ricaud
Software Mentions: 2
Published: over 6 years ago

10.3390/nu12113451

Maternal Linoleic Acid Overconsumption Alters Offspring Gut and Adipose Tissue Homeostasis in Young but Not Older Adult Rats
Cited by: 3
Author(s): Justine Marchix, Charlène Alain, Sandrine Le Gall‐David, Luis A. Amador, Céline Druart, Nathalie M. Delzenne, Frédérique Barloy-Hubler, Philippe Legrand, Gaëlle Boudry
Software Mentions: 2
Published: about 4 years ago

10.1186/s40623-018-0967-5

On the modelling of M2 tidal magnetic signatures: effects of physical approximations and numerical resolution
Cited by: 12
Author(s): Jakub Velı́mský, Alexander Grayver, Alexey Kuvshinov, Libor Šachl
Software Mentions: 1
Published: almost 6 years ago

Projects: pypi: Swarm

Papers Mentioning Swarm 151