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: demux
https://packages.ecosyste.ms/registries/pypi.org/packages/demux
Application for demultiplexing sequence data
4 versions
Latest release: over 3 years ago
22 downloads last month
Papers Mentioning demux 37
10.3389/fmicb.2020.550420
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing PipelineCited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: almost 4 years ago
10.1186/s13059-020-02020-4
Lifestyle and the presence of helminths is associated with gut microbiome composition in CamerooniansCited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 4 years ago
10.3389/fmicb.2019.01775
Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect SeasonalityCited by: 23
Author(s): Hannah E. Epstein, Hillary A. Smith, Neal E. Cantin, Véronique J. L. Mocellin, Gergely Torda, Madeleine J. H. van Oppen
Software Mentions: 14
Published: about 5 years ago
10.1186/s12866-021-02211-4
Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphanaCited by: 10
Author(s): Justin Maire, Linda L. Blackall, Madeleine J. H. van Oppen
Software Mentions: 9
Published: over 3 years ago
10.1038/s41396-021-00902-4
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefsCited by: 51
Author(s): Justin Maire, Sam K. Girvan, Sophie E. Barkla, Alexis Perez‐Gonzalez, David J. Suggett, Linda L. Blackall, Madeleine J. H. van Oppen
Software Mentions: 8
Published: over 3 years ago
10.3389/fmicb.2019.02118
Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)Cited by: 20
Author(s): Elizabeth M. Reinhart, Benjamin J. Korry, Aislinn D. Rowan-Nash, Peter Belenky
Software Mentions: 5
Published: about 5 years ago
10.1038/s41598-020-67362-2
Integrated metabolomics and gut microbiome to the effects and mechanisms of naoxintong capsule on type 2 diabetes in ratsCited by: 22
Author(s): Zenghao Yan, Hao Wu, Haokui Zhou, Shuo Chen, Yan He, Weijian Zhang, Taobin Chen, Hongliang Yao, Weiwei Su
Software Mentions: 5
Published: about 4 years ago
10.3389/fmicb.2021.667257
Microbiome Structure of the Aphid Myzus persicae (Sulzer) Is Shaped by Different Solanaceae Plant DietsCited by: 12
Author(s): Bin He, Xiaoyulong Chen, Hong Yang, Tomislav Cernava
Software Mentions: 4
Published: about 3 years ago
10.1186/s42523-021-00120-5
Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)Cited by: 7
Author(s): Klara Filek, Adriana Trotta, Romana Gračan, Antonio Di Bello, Marialaura Corrente, Sunčica Bosak
Software Mentions: 4
Published: about 3 years ago
10.1002/cam4.1965
Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma developmentCited by: 62
Author(s): Talima Pearson, J. Gregory Caporaso, Monica Yellowhair, Nicholas A. Bokulich, Megha Padi, Denise J. Roe, Betsy C. Wertheim, Mark Linhart, Jessica A. Martinez, Cherae Bilagody, Heidie Hornstra, David S. Alberts, Peter Lance, Patricia A. Thompson
Software Mentions: 4
Published: over 5 years ago
10.1186/s40168-018-0470-z
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier pluginCited by: 2,605
Author(s): Nicholas A. Bokulich, Benjamin Kaehler, Jai Ram Rideout, Matthew R. Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso
Software Mentions: 4
Published: over 6 years ago
10.3390/microorganisms9091818
Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in KazakhstanCited by: 10
Author(s): Д. Ш. Соколова, Е. М. Семенова, Denis S. Grouzdev, Salimat K. Bidzhieva, Т. Л. Бабич, Н. Г. Лойко, A. P. Ershov, Vitaly V. Kadnikov, Alexey V. Beletsky, Andrey V. Mardanov, Nurlan S. Zhaparov, Т. Н. Назина
Software Mentions: 4
Published: about 3 years ago
10.7717/peerj.8492
Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed<i> Pheidole</i> antsCited by: 9
Author(s): Carla Braga Martins, Corrie S. Moreau
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2020.01363
Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping SystemCited by: 47
Author(s): Ali Srour, Hala A. Ammar, Arjun Subedi, Mirian F. Pimentel, Rachel L. Cook, Jason P. Bond, Ahmad M. Fakhoury
Software Mentions: 4
Published: about 4 years ago
10.1186/s40104-021-00545-7
Evaluation of curcumin and copper acetate against Salmonella Typhimurium infection, intestinal permeability, and cecal microbiota composition in broiler chickensCited by: 20
Author(s): Anaisa A. Leyva-Diaz, Daniel Hernández-Patlán, Bruno Solís-Cruz, Bishnu Adhikari, Young Min Kwon, Juan D. Latorre, Xóchitl Hernández-Velasco, Benjamín Fuente-Martínez, Billy M. Hargis, Raquel López‐Arellano, Guillermo Téllez–Isaías
Software Mentions: 4
Published: over 3 years ago
10.1128/mSystems.01114-20
Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar CheeseCited by: 7
Author(s): Zhengyao Xue, Jason T. Brooks, Zachary Quart, Eric Stevens, Mary E. Kable, J. Heidenreich, J. W. McLeod, Maria L. Marco
Software Mentions: 4
Published: over 3 years ago
10.1128/mSystems.00633-21
Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global LandscapeCited by: 13
Author(s): Zhanshan Sam
Software Mentions: 4
Published: about 3 years ago
10.1186/s13020-021-00436-z
Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patientsCited by: 6
Author(s): Yinping Guo, Li Shao, Li Wang, Man‐Yun Chen, Wei Zhang, Weihua Huang
Software Mentions: 3
Published: over 3 years ago
10.3390/microorganisms8030438
The Interplay between Mucosal Microbiota Composition and Host Gene-Expression is Linked with Infliximab Response in Inflammatory Bowel DiseasesCited by: 41
Author(s): Nikolas Dovrolis, George Michalopoulos, George Theodoropoulos, Konstantinos Arvanitidis, George Kolios, Leonardo Antonio Sechi, Aristidis G. Eliopoulos, Maria Gazouli
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2018.01664
Microbial Community Changes in a Chlorinated Solvents Polluted Aquifer Over the Field Scale Treatment With Poly-3-Hydroxybutyrate as AmendmentCited by: 26
Author(s): Bruna Matturro, Lucia Pierro, Emanuela Frascadore, Marco Petrangeli Papini, Simona Rossetti
Software Mentions: 3
Published: about 6 years ago
10.3389/fmicb.2020.592248
Gut Microbial Dysbiosis and Plasma Metabolic Profile in Individuals With VitiligoCited by: 19
Author(s): Qingrong Ni, Zhubiao Ye, Yinghan Wang, Jianru Chen, Weigang Zhang, Cuiling Ma, Kai Li, Yu Liu, Ling Liu, Zheyi Han, Tianwen Gao, Zhe Jian, Shuli Li, Chunying Li
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpsyt.2020.00353
Association of the Salivary Microbiome With Animal Contact During Early Life and Stress-Induced Immune Activation in Healthy ParticipantsCited by: 3
Author(s): Dominik Langgartner, Cristian A. Zambrano, Jared D. Heinze, Christopher E. Stamper, Till S. Böbel, Sascha B. Hackl, Marc N. Jarczok, Nicolas Rohleder, G. A. W. Rook, Harald Gündel, Christiane Waller, Christopher A. Lowry, Stefan O. Reber
Software Mentions: 3
Published: over 4 years ago
10.3389/fvets.2020.00331
Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production PhaseCited by: 9
Author(s): Bishnu Adhikari, Se‐Ran Jun, Young Min Kwon, Aaron S. Kiess, Pratima Adhikari
Software Mentions: 3
Published: about 4 years ago
10.3389/fvets.2020.596933
Comprehensive Survey of the Litter Bacterial Communities in Commercial Turkey FarmsCited by: 7
Author(s): Bishnu Adhikari, Guillermo Téllez–Isaías, Tieshan Jiang, Brian Wooming, Young Min Kwon
Software Mentions: 3
Published: almost 4 years ago
10.1128/AEM.02885-19
Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide EffectivenessCited by: 48
Author(s): Silvia J. Salgar-Chaparro, Kateřina Lepková, Thunyaluk Pojtanabuntoeng, Adam Darwin, Laura L. Machuca
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0235422
Non-specific protection from respiratory tract infections in cattle generated by intranasal administration of an innate immune stimulantCited by: 8
Author(s): William H. Wheat, Lyndah Chow, Vanessa Rozo, Julia A. Herman, Kelly Still Brooks, Aimée C. Colbath, R.L. Hunter, Steven Dow
Software Mentions: 3
Published: about 4 years ago
10.3390/microorganisms8121967
Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus SoehngeniaCited by: 12
Author(s): Т. Н. Назина, Salimat K. Bidzhieva, Denis S. Grouzdev, Д. Ш. Соколова, T. P. Tourova, Sofiya N. Parshina, Alexander N. Avtukh, А. Б. Полтараус, Azhdar K Talybly
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13568-020-01040-4
Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomassCited by: 7
Author(s): Alessandra Fontana, M. Soldano, Paolo Bellassi, C. Fabbri, Francesco Gallucci, L. Morelli, Fabrizio Cappa
Software Mentions: 2
Published: over 4 years ago
10.18632/aging.203460
Activation of the gut microbiota-kynurenine-liver axis contributes to the development of nonalcoholic hepatic steatosis in nondiabetic adultsCited by: 8
Author(s): Guoyuan Sui, Jia Lu, Dongmei Quan, Ning Zhao, Guanlin Yang
Software Mentions: 2
Published: about 3 years ago
10.3390/microorganisms9091813
Screening of Rhizosphere Bacteria and Nematode Populations Associated with Soybean Roots in the Mpumalanga Highveld of South AfricaCited by: 4
Author(s): Gerhard Engelbrecht, Sarina Claassens, Charlotte Mienie, Hendrika Fourie
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0253133
Effects of cat ownership on the gut microbiota of ownersCited by: 7
Author(s): Guankui Du, Hairong Huang, Qiwei Zhu, Ying Li
Software Mentions: 2
Published: over 3 years ago
10.3390/s20113055
Gloxinia—An Open-Source Sensing Platform to Monitor the Dynamic Responses of PlantsCited by: 5
Author(s): Olivier Pieters, Tom De Swaef, Peter Lootens, Michiel Stock, Isabel Roldán‐Ruiz, Francis wyffels
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2020.551444
Rhizosphere Bacterial Community Response to Continuous Cropping of Tibetan BarleyCited by: 9
Author(s): Youhua Yao, Xiaohua Yao, Likun An, Yang Bai, Dexin Xie, Kaiyi Wu
Software Mentions: 2
Published: almost 4 years ago
10.1128/MRA.00248-20
16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in ThailandCited by: 6
Author(s): Sangam Kandel, Supaphen Sripiboon, Piroon Jenjaroenpun, David W. Ussery, Intawat Nookaew, Michael S. Robeson, Thidathip Wongsurawat
Software Mentions: 1
Published: over 4 years ago
10.1186/s13568-020-0950-y
Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River EstuaryCited by: 17
Author(s): Wenxiu Wang, Jianchang Tao, Haodong Liu, Penghui Li, Songze Chen, Peng Wang, Chuanlun Zhang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0245180
Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouseCited by: 5
Author(s): Senlin Liu, Muzammil Hassan Khan, Zhongyuan Yuan, Sarfraz Hussain, Hui Cao, Yabo Liu
Software Mentions: 1
Published: almost 3 years ago
10.1128/mSystems.00229-18
Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight InfantsCited by: 47
Author(s): Alyson L. Yee, Elizabeth M. Miller, Larry J. Dishaw, Jessica Gordon, Ming Ji, Samia Valéria Ozório Dutra, Thao Ho, Jack A. Gilbert, Maureen Groër
Software Mentions: 1
Published: over 5 years ago