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: vsearch

https://packages.ecosyste.ms/registries/pypi.org/packages/vsearch

The Head First Python Search Tools
2 versions
Latest release: over 5 years ago
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Papers Mentioning vsearch 284

10.3390/v13081647
Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-020-70249-x
Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Cited by: 5
Author(s): Tereza Matějková, Petra Hájková, Romana Stopková, Michał Stanko, Jean‐François Martin, Jakub Kreisinger, Pavel Stopka
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
10.1093/femsec/fiz128
Biogeographical patterns in soil bacterial communities across the Arctic region
Cited by: 49
Author(s): Lucie Malard, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, David A. Pearce
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2021.658927
Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?
Cited by: 14
Author(s): Carolina Calero Preciado, Joby Boxall, Víctor Soria‐Carrasco, Santiago Martínez, Isabel Douterelo
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2020.01390
Alterations in Circulating Fatty Acid Are Associated With Gut Microbiota Dysbiosis and Inflammation in Multiple Sclerosis
Cited by: 94
Author(s): Marina Saresella, Ivana Marventano, Monica Barone, Francesca La Rosa, Federica Piancone, Laura Mendozzi, Alessia d’Arma, Valentina Rossi, Luigi Pugnetti, Gabriella Roda, Eleonora Casagni, Michele Dei, Rita Paroni, Patrizia Brigidi, Silvia Turroni, Mario Clerici
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2019.01332
Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland
Cited by: 68
Author(s): Anna Maria Fiore-Donno, Tim Richter-Heitmann, Florine Degrune, Kenneth Dumack, Kathleen M. Regan, Sven Marhan, Runa S. Boeddinghaus, Matthias C. Rillig, Michael W. Friedrich, Ellen Kandeler, Michael Bonkowski
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2021.708475
Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice
Cited by: 8
Author(s): Hyun Kim, Yong-Hwan Lee
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2017.01786
Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter
Cited by: 31
Author(s): Oscar A. Sosa, Daniel J. Repeta, Sara Ferrón, Jessica A. Bryant, Daniel R. Mende, David M. Karl, Edward F. DeLong
Software Mentions: 4
Published: about 7 years ago
10.3389/fmicb.2021.675048
A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments
Cited by: 6
Author(s): Zhongdong Huang, Shiqing Mo, Lifei Yan, Xiaomei Wei, Yangze Huang, Lizhen Zhang, Shuhui Zhang, Jianzong Liu, Qing Xiao, Hong Lin, Yu Guo
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2019.00473
Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease
Cited by: 44
Author(s): William L. King, Nachshon Siboni, Nathan L. R. Williams, Tim Kahlke, Khue Viet Nguyen, Cheryl Jenkins, Michael Dove, Wayne A. O’Connor, Justin R. Seymour, Maurizio Labbate
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2019.02886
Microbial Communities in Human Milk Relate to Measures of Maternal Weight
Cited by: 26
Author(s): Sara Lundgren, Juliette C. Madan, Margaret R. Karagas, Hilary G. Morrison, Anne G. Hoen, Brock C. Christensen
Software Mentions: 4
Published: almost 5 years ago
10.3390/nu12051257
Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota—Results from the PAGODA Trial
Cited by: 35
Author(s): Simon Reider, Simon Moosmang, J Tragust, Lovro Trgovec-Greif, Simon Tragust, Lorenz Perschy, Nicole Przysiecki, Sonja Sturm, Herbert Tilg, Hermann Stuppner, Thomas Rattei, Alexander R. Moschen
Software Mentions: 4
Published: over 4 years ago
10.3390/ijms21093262
Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 4 years ago
10.1128/mSystems.00783-19
Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale
Cited by: 61
Author(s): Kaoping Zhang, Manuel Delgado‐Baquerizo, Yong‐Guan Zhu, Haiyan Chu
Software Mentions: 4
Published: over 4 years ago
10.1186/s40168-018-0472-x
Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum
Cited by: 252
Author(s): Mie Crusell, Tue H. Hansen, Trine Nielsen, Kristine H. Allin, Malte Rühlemann, Peter Damm, Henrik Vestergaard, Christina Rørbye, Niklas Rye Jørgensen, Ole Bjarne Christiansen, Femke-Anouska Heinsen, André Franke, Jeannet Lauenborg, Oluf Pedersen
Software Mentions: 4
Published: over 6 years ago
10.1186/s40168-020-00859-0
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing
Cited by: 22
Author(s): Luyang Song, Kabin Xie
Software Mentions: 4
Published: over 4 years ago
10.3390/microorganisms9091876
The Terrestrial Plastisphere: Diversity and Polymer-Colonizing Potential of Plastic-Associated Microbial Communities in Soil
Cited by: 21
Author(s): Joana MacLean, Sathish Mayanna, Liane G. Benning, Fabian Horn, Alexander Bartholomäus, Yosri Wiesner, Dirk Wagner, Susanne Liebner
Software Mentions: 4
Published: about 3 years ago
10.3390/microorganisms9051038
Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert
Cited by: 15
Author(s): Dirk Schulze‐Makuch, Daniel Lipus, Felix L. Arens, Mickaël Baqué, Till L. V. Bornemann, Jean Pierre Paul de Vera, Markus Flury, Jan Frösler, Jacob Heinz, Yunha Hwang, Samuel P. Kounaves, Kai Mangelsdorf, Rainer U. Meckenstock, Mark Pannekens, Alexander J. Probst, Johan S. Sáenz, Janosch Schirmack, Michael Schloter, Philippe Schmitt‐Kopplin, Bernd Uwe Schneider, Jenny Uhl, Gisle Vestergaard, Bernardita Valenzuela, Pedro Zamorano, Dirk Wagner
Software Mentions: 4
Published: over 3 years ago
10.3390/ijerph18126348
Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test
Cited by: 4
Author(s): Francesco Spennati, Salvatore La China, G. Siracusa, Simona Di Gregorio, A. Bardi, Valeria Tigini, Greg Mori, David Gabriel, Giulio Munz
Software Mentions: 4
Published: over 3 years ago
10.7717/peerj.4705
DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
Cited by: 149
Author(s): Owen S. Wangensteen, Creu Palacín, Magdalena Guardiola, Xavier Turon
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-019-46106-x
Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome
Cited by: 32
Author(s): Caroline De Tender, Bart Mesuere, Felix Van der Jeugt, Annelies Haegeman, Tom Ruttink, Bart Vandecasteele, Peter Dawyndt, Jane Debode, Eiko E. Kuramae
Software Mentions: 4
Published: over 5 years ago
10.1038/s41597-020-00752-3
Soil bacterial community structures in relation to different oil palm management practices
Cited by: 11
Author(s): Dirk Hölscher, Dominik Schneider, Nina Hennings, Anja Meryandini, Rolf Daniel
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pbio.3000106
A census-based estimate of Earth's bacterial and archaeal diversity
Cited by: 124
Author(s): Stilianos Louca, Florent Mazel, Michael Doebeli, Laura Wegener Parfrey
Software Mentions: 4
Published: almost 6 years ago
10.1128/AEM.00305-19
Bacterial and Fungal Endophytic Microbiomes of <i>Salicornia europaea</i>
Cited by: 46
Author(s): Bliss Ursula Furtado, Marcin Gołębiewski, Monika Skorupa, Piotr Hulisz, Katarzyna Hrynkiewicz
Software Mentions: 4
Published: over 5 years ago
10.1073/pnas.2001337117
Natural selection maintains species despite frequent hybridization in the desert shrub <i>Encelia</i>
Cited by: 21
Author(s): Christopher Todd DiVittorio, Sonal Singhal, Adam B. Roddy, Felipe Zapata, David D. Ackerly, Bruce G. Baldwin, Craig R. Brodersen, Alberto Búrquez, Paul V. A. Fine, Mayra Padilla Flores, Elizabeth Solis, Jaime Morales-Villavicencio, David Morales-Arce, Donald W. Kyhos
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pntd.0008615
The Aedes albopictus (Diptera: Culicidae) microbiome varies spatially and with Ascogregarine infection
Cited by: 14
Author(s): Priscilla Seabourn, Helen Spafford, Nicole M. Yoneishi, Matthew C. I. Medeiros
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pntd.0009597
Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections
Cited by: 8
Author(s): Katharina Stracke, Poom Adisakwattana, Suparat Phuanukoonnon, Tippayarat Yoonuan, Akkarin Poodeepiyasawat, Paron Dekumyoy, Kittipong Chaisiri, Alexandra Roth Schulze, Stephen Wilcox, Harin Karunajeewa, Rebecca J. Traub, Aaron R. Jex
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0220843
Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs
Cited by: 89
Author(s): Donghyun Shin, Sung-Ho Chang, Paul Bogere, KyeongHye Won, Jae-Ho Choi, Yun‐Sang Choi, Hak Kyo Lee, Jin Hur, Byung-Yong Park, Young-Hoon Kim, Jae-Young Heo
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0242158
Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro
Cited by: 7
Author(s): Yoshibumi Sato, Keiko Tominaga, Hirotatsu Aoki, Masayuki Murayama, Kazato Oishi, Hiroyuki Hirooka, Takashi Yoshida, Hajime Kumagai
Software Mentions: 4
Published: about 4 years ago
10.1111/gcb.14657
Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants
Cited by: 39
Author(s): Rutger A. Wilschut, Stefan Geisen, Henk Martens, Olga Kostenko, Mattias de Hollander, Freddy C. ten Hooven, Carolin Weser, L. Basten Snoek, J. Bloem, Danka Caković, Tatjana Čelik, Kadri Koorem, Nikos Krigas, Marta Manrubia, Kelly S. Ramirez, Maria A. Tsiafouli, Branko Vreš, Wim H. van der Putten
Software Mentions: 4
Published: over 5 years ago
10.1111/1751-7915.13496
Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state‐associated and mobile multidrug resistance‐carrying bacteria
Cited by: 15
Author(s): Dorota A. Dobrzanska, Matthew T F Lamaudière, Jess Rollason, Lauren Acton, Michael Duncan, Sharon Compton, John Simms, Gareth D. Weedall, Igor Y. Morozov
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0237108
Comparison of microbiota in the cloaca, colon, and magnum of layer chicken
Cited by: 10
Author(s): Seo-Jin Lee, Seongwoo Cho, Tae-Min La, Hong-Jae Lee, Joong‐Bok Lee, Seung‐Yong Park, Chang‐Seon Song, In‐Soo Choi
Software Mentions: 4
Published: over 4 years ago
10.1038/s42003-020-01562-4
Shifts in honeybee foraging reveal historical changes in floral resources
Cited by: 27
Author(s): Laura Jones, Georgina Brennan, Abigail Lowe, Simon Creer, Col R. Ford, Natasha de Vere
Software Mentions: 4
Published: almost 4 years ago
10.1111/1365-2435.13453
Soil functional responses to drought under range‐expanding and native plant communities
Cited by: 14
Author(s): Marta Manrubia, Wim H. van der Putten, Carolin Weser, Freddy C. ten Hooven, Henk Martens, E.P. Brinkman, Stefan Geisen, Kelly S. Ramirez, G. F. Veen
Software Mentions: 4
Published: about 5 years ago
10.1002/ece3.4360
RAD sequencing resolved phylogenetic relationships in European shrub willows (<i>Salix</i>L. subg.<i>Chamaetia</i>and subg.<i>Vetrix</i>) and revealed multiple evolution of dwarf shrubs
Cited by: 31
Author(s): Natascha D. Wagner, S.M. Gramlich, Elvira Hörandl
Software Mentions: 4
Published: over 6 years ago
10.3389/fvets.2020.00126
Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest
Cited by: 12
Author(s): Augusta Zannoni, Marco Pietra, Alba Gaspardo, Pier Attilio Accorsi, Monica Barone, Silvia Turroni, Luca Laghi, Chenglin Zhu, Patrizia Brigidi, Monica Forni
Software Mentions: 4
Published: over 4 years ago
10.1002/ece3.6042
Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol
Cited by: 22
Author(s): Maurício M. Zenker, Alexandre Specht, Vera G. Fonseca
Software Mentions: 4
Published: over 4 years ago
10.1002/ece3.6093
Using genomic information for management planning of an endangered perennial,<i>Viola uliginosa</i>
Cited by: 9
Author(s): Kyung Min Lee, Pertti Ranta, Jarmo Saarikivi, Lado Kutnar, Branko Vreš, М. А. Джус, Marko Mutanen, Laura Kvist
Software Mentions: 4
Published: almost 5 years ago
10.12688/f1000research.24751.2
Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity
Cited by: 9
Author(s): Evan Bolyen, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, Jason W. Sahl, Andrew Sanchez, Chris Holdgraf, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew R. McKay, Anthony Simard, David M. Engelthaler, Michael Worobey, Paul Keim, J. Gregory Caporaso
Software Mentions: 4
Published: about 4 years ago
10.1093/gigascience/giab020
A chromosome-level genome assembly for the Pacific oyster <i>Crassostrea gigas</i>
Cited by: 70
Author(s): Carolina Peñaloza, Alejandro P. Gutiérrez, Lél Eöry, Shan Wang, Ximing Guo, Alan Archibald, Tim P. Bean, Ross D. Houston
Software Mentions: 3
Published: over 3 years ago
10.1186/s42523-021-00073-9
Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats
Cited by: 25
Author(s): Juan Manuel Palma-Hidalgo, Elisabeth Jiménez, Milka Popova, Diego P. Morgavi, A. I. Martin-García, D. R. Yáñez-Ruíz, Alejandro Belanche
Software Mentions: 3
Published: almost 4 years ago
10.1128/AEM.01394-18
Persistent Bacterial and Fungal Community Shifts Exhibited in Selenium-Contaminated Reclaimed Mine Soils
Cited by: 36
Author(s): Carla E. Rosenfeld, Bruce R. James, Cara M. Santelli
Software Mentions: 3
Published: over 6 years ago
10.1007/s00253-019-10242-1
Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples
Cited by: 11
Author(s): Felizitas Bajerski, Antje Bürger, Birgit Glasmacher, E. R. Keller, Karin Müller, Kristin Mühldorfer, Manuela Nagel, Heinz Rüdel, Tobias Müller, Johannes Schenkel, Jörg Overmann
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12866-020-01724-8
The influence of blood on the human gut microbiome
Cited by: 23
Author(s): Thierry Chénard, Mandy Malick, Jean Dubé, Éric Massé
Software Mentions: 3
Published: over 4 years ago
10.3390/biology10080792
Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool
Cited by: 2
Author(s): Weronika Goraj, Anna Szafranek-Nakonieczna, Jarosław Grządziel, Cezary Polakowski, Mirosław Słowakiewicz, Yongnian Zheng, Anna Gałązka, Zofia Stępniewska, Anna Pytlak
Software Mentions: 3
Published: over 3 years ago
10.3390/life11060558
The Effect of a Total Fishmeal Replacement by Arthrospira platensis on the Microbiome of African Catfish (Clarias gariepinus)
Cited by: 6
Author(s): Simon Rosenau, Elisa Oertel, Alexander C. Mott, Jens Tetens
Software Mentions: 3
Published: over 3 years ago
10.1186/s12934-020-01341-0
Impact of lignans in oilseed mix on gut microbiome composition and enterolignan production in younger healthy and premenopausal women: an in vitro pilot study
Cited by: 23
Author(s): Giulia Corona, Anna Kreimes, Monica Barone, Silvia Turroni, Patrizia Brigidi, Enver Keleszade, Adele Costabile
Software Mentions: 3
Published: over 4 years ago
10.1007/s00248-020-01556-z
Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes
Cited by: 20
Author(s): Sergio Vargas, Laura Leiva, Gert Wörheide
Software Mentions: 3
Published: over 4 years ago
10.1186/s40168-020-00976-w
High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice
Cited by: 32
Author(s): Joan Serrano, Kathleen R. Smith, Audra L. Crouch, Vandana Sharma, Fanchao Yi, Veronika Vargova, Traci E. LaMoia, Lydia M. Dupont, Vanida A. Serna, Fang Tang, Laisa Gomes-Dias, Joshua J. Blakeslee, Emmanuel Hatzakis, Scott N. Peterson, Matthew Anderson, Richard E. Pratley, George A. Kyriazis
Software Mentions: 3
Published: almost 4 years ago
10.1186/s40168-018-0420-9
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
Cited by: 428
Author(s): Stilianos Louca, Michael Doebeli, Laura Wegener Parfrey
Software Mentions: 3
Published: over 6 years ago
10.3390/microorganisms8040497
Investigating Algal Communities in Lacustrine and Hydro-Terrestrial Environments of East Antarctica Using Deep Amplicon Sequencing
Cited by: 6
Author(s): Yuu Hirose, Takuhei Shiozaki, Midori Õtani, Sakae Kudoh, Satoru Imura, Toshihiko Eki, Naomi Harada
Software Mentions: 3
Published: over 4 years ago
10.3390/microorganisms8040609
Incidental Prophylactic Appendectomy Is Associated with a Profound Microbial Dysbiosis in the Long-Term
Cited by: 13
Author(s): Lidia Sánchez-Alcoholado, José Carlos Fernández‐García, Carolina Gutiérrez-Repiso, María Rosa Bernal-López, Luis Ocaña-Wilhelmi, Eduardo Garcı́a-Fuentes, Isabel Moreno-Indias, Francisco J. Tinahones
Software Mentions: 3
Published: over 4 years ago
10.1111/mec.15592
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
Cited by: 75
Author(s): Luna M. van der Loos, Reindert Nijland
Software Mentions: 3
Published: about 4 years ago
10.1111/1755-0998.13002
Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology
Cited by: 46
Author(s): Robert Ferguson, Sonia García-Alcega, Frédéric Coulon, Alex J. Dumbrell, Corinne Whitby, I. Colbeck
Software Mentions: 3
Published: over 5 years ago
10.3390/molecules25235638
Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles
Cited by: 15
Author(s): Sylwia Siebielec, Grzegorz Siebielec, Piotr Sugier, Małgorzata Woźniak, Jarosław Grządziel, Anna Gałązka, Tomasz Stuczyński
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.9424
An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications
Cited by: 5
Author(s): Deborah D. Iwanowicz, Judy Wu‐Smart, Tuğçe Olgun, Matthew Smart, Clint R. V. Otto, Dawn Lopez, Jay D. Evans, Robert S. Cornman
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1005086
Likelihood-Based Inference of B Cell Clonal Families
Cited by: 86
Author(s): D. Ralph, F. A. Matsen
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pgen.1009805
A broad analysis of splicing regulation in yeast using a large library of synthetic introns
Cited by: 11
Author(s): Dvir Schirman, Zohar Yakhini, Yitzhak Pilpel, Orna Dahan
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pone.0202844
Predicting provenance of forensic soil samples: Linking soil to ecological habitats by metabarcoding and supervised classification
Cited by: 35
Author(s): Camilla Fløjgaard, Tobias Guldberg Frøslev, Ane Kirstine Brunbjerg, Hans Henrik Bruun, Jesper Erenskjold Moeslund, Anders J. Hansen, Rasmus Ejrnæs
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0237256
The abundance of arbuscular mycorrhiza in soils is linked to the total length of roots colonized at ecosystem level
Cited by: 18
Author(s): Milagros Barceló, Peter M. van Bodegom, Leho Tedersoo, Nadja den Haan, G.F. Veen, Ivika Ostonen, Krijn B. Trimbos, Nadejda A. Soudzilovskaia
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0250452
eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
Cited by: 12
Author(s): Martin Schwentner, Reza Zahiri, Satoshi Yamamoto, Martin Husemann, Björn Kullmann, Ralf Thiel
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0177488
Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)
Cited by: 38
Author(s): J. Morrison, Kristina Baker, Richard M. Zamor, Steve Nikolai, Mostafa S. Elshahed
Software Mentions: 3
Published: over 7 years ago
10.3390/cancers12123702
Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank
Cited by: 15
Author(s): Ulrike Wirth, Debora Garzetti, Lara Jochum, Stefanie Spriewald, Florian Kühn, Matthias Ilmer, Serene M. L. Lee, Hanno Nieß, Alexandr V. Bazhin, Joachim Andrassy, Jens Werner, Bärbel Stecher, Tobias S. Schiergens
Software Mentions: 3
Published: almost 4 years ago
10.1093/database/baz155
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
Cited by: 58
Author(s): Elisa Banchi, Claudio Gennaro Ametrano, Samuele Greco, D Stanković, Alberto Pallavicini
Software Mentions: 3
Published: almost 5 years ago
10.1002/ece3.4213
<scp>eDNA</scp> metabarcoding as a new surveillance approach for coastal Arctic biodiversity
Cited by: 128
Author(s): Anaïs Lacoursière‐Roussel, Kimberly L. Howland, Éric Normandeau, Erin K. Grey, Philippe Archambault, Kristy Deiner, David M. Lodge, Cécilia Hernandez, Noémie Leduc, Louis Bernatchez
Software Mentions: 3
Published: over 6 years ago
10.1002/ece3.5871
Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
Cited by: 34
Author(s): Judith Bakker, Owen S. Wangensteen, Charles Baillie, Dayne Buddo, Demian D. Chapman, Austin J. Gallagher, Tristan L. Guttridge, Heidi Hertler, Stefano Mariani
Software Mentions: 3
Published: almost 5 years ago
10.3389/fcimb.2020.536282
Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes
Cited by: 19
Author(s): Mie Crusell, Torben Hansen, Trine Nielsen, Kristine H. Allin, Malte Rühlemann, Peter Damm, Henrik Vestergaard, Christina Rørbye, Niklas Rye Jørgensen, Ole Bjarne Christiansen, Femke Anouska Heinsen, André Franke, Jeannet Lauenborg, Oluf Pedersen
Software Mentions: 3
Published: about 4 years ago
10.3389/fmicb.2021.715991
Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World
Cited by: 6
Author(s): Tallita Cruz Lopes Tavares, Walderly Melgaço Bezerra, Leonardo Ribeiro Oliveira Normando, Alexandre Soares Rosado, Vânia Maria Maciel Melo
Software Mentions: 3
Published: about 3 years ago
10.3389/fmicb.2020.581227
Effects of Chemical and Mechanical Lysis on Microbial DNA Yield, Integrity, and Downstream Amplicon Sequencing of Rumen Bacteria and Protozoa
Cited by: 13
Author(s): Zhi Ma, Xiu Min Zhang, Rong Wang, Min Wang, Ting Liu, Zhi Liang Tan
Software Mentions: 3
Published: about 4 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
10.3389/fmicb.2019.02907
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event
Cited by: 22
Author(s): William L. King, Nachshon Siboni, Tim Kahlke, Timothy Green, Maurizio Labbate, Justin R. Seymour
Software Mentions: 3
Published: almost 5 years ago
10.3389/fmicb.2020.586387
Microbiome Profiling Reveals a Microbial Dysbiosis During a Natural Outbreak of Tenacibaculosis (Yellow Mouth) in Atlantic Salmon
Cited by: 25
Author(s): James W. Wynne, Krishna K. Thakur, Joel Slinger, Francisca Samsing, Barry Milligan, James F. F. Powell, Allison McKinnon, Omid Nekouei, Danielle New, Zina Richmond, Ian A. Gardner, Ahmed Siah
Software Mentions: 3
Published: about 4 years ago
10.3389/fmicb.2017.00821
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
Cited by: 115
Author(s): Ignacio Belda, Iratxe Zarraonaindia, Matthew Perisin, Azucena Palacios, Alberto Acedo
Software Mentions: 3
Published: over 7 years ago
10.3389/fmicb.2020.01626
Novel Antimicrobial Cellulose Fleece Inhibits Growth of Human-Derived Biofilm-Forming Staphylococci During the SIRIUS19 Simulated Space Mission
Cited by: 3
Author(s): Daniela Wischer, Dominik Schneider, Anja Poehlein, Friederike Herrmann, Harun Oruc, Junias Meinhardt, Olaf Wagner, Rameez Ahmed, С. А. Харин, Natalia Novikova, Rainer Haag, Rolf Daniel, Elisabeth Grohmann
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2021.723649
Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues
Cited by: 5
Author(s): William L. King, Mirjam Kaestli, Nachshon Siboni, Anna Padovan, Keith A. Christian, David K. Mills, Justin R. Seymour, Karen S. Gibb
Software Mentions: 3
Published: over 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: almost 6 years ago
10.1093/gbe/evz113
Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths
Cited by: 35
Author(s): Anna K. Hundsdoerfer, Kyung Min Lee, Ian J. Kitching, Marko Mutanen
Software Mentions: 3
Published: over 5 years ago
10.1186/s13568-021-01240-6
Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure
Cited by: 2
Author(s): Yanrong Gu, Dong Yan, Minna Wu, Min Li, Puze Li, Jingjing Wang, Yahan Chang, Fan Yang, Shaojun Di, Shijun Ni, Mengjie Yang, Jieyu Liu
Software Mentions: 3
Published: over 3 years ago
10.1186/s13099-021-00447-z
Microbiome diversity declines while distinct expansions of Th17, iNKT, and dendritic cell subpopulations emerge after anastomosis surgery
Cited by: 3
Author(s): Emilie E. Vomhof-DeKrey, Allie D. Stover, Marc D. Basson
Software Mentions: 3
Published: over 3 years ago
10.1128/JCM.00920-20
Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing
Cited by: 28
Author(s): Alexander Shaw, Manasi Majumdar, Catherine Troman, Áine O’Toole, Blossom Benny, Dilip Abraham, Ira Praharaj, Gagandeep Kang, Salman Sharif, Muhammad Masroor Alam, Shahzad Shaukat, Mehar Angez, Adnan Khurshid, Nayab Mahmood, Yasir Arshad, Lubna Rehman, Ghulam Mujtaba, Ribqa Akthar, Muhammad Salman, Dimitra Klapsa, Yara Hajarha, Humayun Asghar, Ananda S Bandyopadhyay, Andrew Rambaut, Javier Martı́n, Nicholas C Grassly
Software Mentions: 3
Published: about 4 years ago
10.1038/s41597-019-0232-1
16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India
Cited by: 6
Author(s): Nitin Bayal, Sunil Nagpal, Mohammed Monzoorul Haque, Milind S. Patole, V. Vijayalakshmi, Rohini Suryavanshi, Sharmila S. Mande, Shekhar C. Mande
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-017-05454-2
Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease
Cited by: 13
Author(s): Miranda E. Vidgen, Jon Hanger, Peter Timms
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-019-43280-w
Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota
Cited by: 78
Author(s): Sang‐Won Lee, Tae-Min La, Hong-Jae Lee, In‐Soo Choi, Chang‐Seon Song, Seung‐Yong Park
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-021-93571-4
Early modifications of the gut microbiome in children with hepatic sinusoidal obstruction syndrome after hematopoietic stem cell transplantation
Cited by: 15
Author(s): Riccardo Masetti, Elena Biagi, Daniele Zama, Edoardo Muratore, Federica D’Amico, Davide Leardini, Silvia Turroni, Arcangelo Prete, Patrizia Brigidi, Andrea Pession
Software Mentions: 3
Published: over 3 years ago
10.1038/s41396-020-00875-w
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance
Cited by: 27
Author(s): Andrea J. Jani, Jessie Bushell, Cédric Arisdakessian, Mahdi Belcaid, Daniel M. Boiano, Cathy Brown, Roland A. Knapp
Software Mentions: 3
Published: almost 4 years ago
10.3390/jof7070550
Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza?
Cited by: 8
Author(s): Sarah Dellière, Éric Dannaoui, M. Fieux, P. Bonfils, Guillaume Gricourt, Vanessa Démontant, Isabelle Podglajen, Paul‐Louis Woerther, Cécile Angebault, Françoise Botterel
Software Mentions: 3
Published: over 3 years ago
10.1089/omi.2018.0146
Comparison of Microbiota Variation in Korean Healthy Adolescents with Adults Suggests Notable Maturity Differences
Cited by: 3
Author(s): Joo-Wook Kim, Jin Sook Lee, Jung Ho Kim, Joowon Jeong, Dong Hoon Lee, Seungyoon Nam
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0233878
Different wheat cultivars exhibit variable responses to inoculation with arbuscular mycorrhizal fungi from organic and conventional farms
Cited by: 27
Author(s): David García de León, Tanel Vahter, Martin Zobel, Mati Koppel, Liina Edesi, John Davison, Saleh Al‐Quraishy, Wael N. Hozzein, Mari Moora, Jane Oja, Martti Vasar, Maarja Öpik
Software Mentions: 2
Published: over 4 years ago
10.1016/j.dib.2020.105553
Dataset of foraminiferal sedimentary DNA (sedDNA) sequences from Svalbard
Cited by: 0
Author(s): Joanna Pawłowska, Jan Pawłowski, Marek Zajączkowski
Software Mentions: 2
Published: over 4 years ago
10.1186/s13742-016-0140-7
INC-Seq: accurate single molecule reads using nanopore sequencing
Cited by: 127
Author(s): Chenhao Li, Kern Rei Chng, Esther J. H. Boey, Amanda Hui Qi Ng, Andreas Wilm, Niranjan Nagarajan
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0237748
An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting
Cited by: 6
Author(s): Laura Espina
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0227967
Microbiome signatures in neonatal central line associated bloodstream infections
Cited by: 13
Author(s): Mohan Pammi, Santosh Thapa, Miriam Balderas, Jessica K. Runge, Alamelu Venkatachalam, Ruth Ann Luna
Software Mentions: 2
Published: almost 5 years ago
10.3389/fimmu.2021.639291
Long-Term Suppressive cART Is Not Sufficient to Restore Intestinal Permeability and Gut Microbiota Compositional Changes
Cited by: 16
Author(s): Giuseppe Ancona, Esther Merlini, Camilla Tincati, Alessandra Barassi, Andrea Calcagno, Matteo Augello, Valeria Bono, Francesca Bai, Elvira S. Cannizzo, Antonella d’Arminio Monforte, Giulia Marchetti
Software Mentions: 2
Published: over 3 years ago
10.7554/eLife.58461
Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest
Cited by: 17
Author(s): Noa Aharon-Hefetz, Idan Frumkin, Yoav Mayshar, Orna Dahan, Yitzhak Pilpel, Roni Rak
Software Mentions: 2
Published: almost 4 years ago
10.1080/19490976.2020.1847628
Neonatal gut colonization by <i>Bifidobacterium</i> is associated with higher childhood cytokine responses
Cited by: 18
Author(s): Hardis Rabe, Anna‐Carin Lundell, Fei Sjöberg, Annika Ljung, Anna Strömbeck, Monica Gio-Batta, Cristina Maglio, Inger Nordström, Kerstin Andersson, Intawat Nookaew, Agnes E. Wold, Ingegerd Adlerberth, Anna Rudin
Software Mentions: 2
Published: about 4 years ago
10.1186/s12864-020-07252-z
Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4
Cited by: 10
Author(s): Christine Drengenes, Tomas Mikal Eagan, Ingvild Haaland, Harald G. Wiker, Rune Nielsen
Software Mentions: 2
Published: almost 4 years ago
10.3390/insects12020129
Temporal and Spatial Blood Feeding Patterns of Urban Mosquitoes in the San Juan Metropolitan Area, Puerto Rico
Cited by: 2
Author(s): Matthew W. Hopken, Limarie J. Reyes-Torres, Nicole A. Scavo, Antoinette J. Piaggio, Zaid Abdo, Daniel R. Taylor, James C. Pierce, Donald Yee
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0196589
Molecular gut content analysis of different spider body parts
Cited by: 48
Author(s): Nuria Macías–Hernández, Kacie J. Athey, Vanina Tonzo, Owen S. Wangensteen, Miquel A. Arnedo, James D. Harwood
Software Mentions: 2
Published: over 6 years ago
10.3390/jcm9030687
Changes in the Intestinal Microbiota Are Seen Following Treatment with Infliximab in Children with Crohn’s Disease
Cited by: 16
Author(s): Kinga Kowalska-Duplaga, Przemysław Kapusta, Tomasz Gosiewski, Agnieszka Sroka-Oleksiak, Agnieszka H. Ludwig-Słomczyńska, Paweł Wołkow, Krzysztof Fyderek
Software Mentions: 2
Published: over 4 years ago