cran: RDP | Projects | Ecosyste.ms: Papers

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: almost 5 years ago

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: almost 4 years ago

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pone.0237368

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?
Cited by: 9
Author(s): Gian Maria Niccolò Benucci, Bryan Rennick, Gregory Bonito
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: almost 4 years ago

10.1186/s40168-018-0569-2

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: about 6 years ago

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 7 years ago

10.3389/fmicb.2020.01391

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland
Cited by: 31
Author(s): Tim Richter-Heitmann, Benjamin Hofner, Franz‐Sebastian Krah, Johannes Sikorski, Pia K. Wüst, Boyke Bunk, Sixing Huang, Kathleen M. Regan, Doreen Berner, Runa S. Boeddinghaus, Sven Marhan, Daniel Prati, Ellen Kandeler, Jörg Overmann, Michael W. Friedrich
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: about 5 years ago

10.1186/1471-2148-14-9

Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli
Cited by: 36
Author(s): Robert W. Bryson, Lorenzo Prendini, Warren E. Savary, Peter B. Pearman
Software Mentions: 9
Published: almost 11 years ago

10.1264/jsme2.ME18109

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields
Cited by: 33
Author(s): Turgut Yiğit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saitô, Tatsuhiro Ezawa, Shusei Sato
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pone.0217804

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons
Cited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-021-96160-7

Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota
Cited by: 6
Author(s): Stefanie U. Wetzels, Cameron Strachan, Beate Conrady, Martin Wagner, Iwan Burgener, Zsófia Virányi, Evelyne Selberherr
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-021-92658-2

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP
Cited by: 10
Author(s): Abhijeet Singh, Bettina Müller, Anna Schnürer
Software Mentions: 8
Published: over 3 years ago

10.1155/2021/8892849

Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy
Cited by: 17
Author(s): Genxia Li, Pan Yin, Shuhui Chu, Wen Gao, Shihong Cui, Shuhua Guo, Yajuan Xu, Enwu Yuan, Texuan Zhu, Jie You, Junya Zhang, Manman Yang
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-018-19607-4

Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations
Cited by: 26
Author(s): Luke Braidwood, Diego F. Quito-Avila, Darlene Cabanas, Alberto Bressan, Anne Wangai, David C. Baulcombe
Software Mentions: 7
Published: almost 7 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: about 5 years ago

10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation
Cited by: 9,402
Author(s): Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 7
Published: almost 14 years ago

10.3389/fmicb.2019.02197

Composition of Bacterial and Archaeal Communities in an Alkali-Surfactant-Polyacrylamide-Flooded Oil Reservoir and the Responses of Microcosms to Nutrients
Cited by: 14
Author(s): Peike Gao, Li Yu, Liang Tan, Feifei Guo, Ting Ma
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2019.00659

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions
Cited by: 62
Author(s): Marion Pohlner, Leon Dlugosch, Bernd Wemheuer, Heath J. Mills, Bert Engelen, Brandi Kiel Reese
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-016-1420-z

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
Cited by: 9
Author(s): Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
Software Mentions: 6
Published: almost 8 years ago

10.1038/srep26648

Effect of short-term room temperature storage on the microbial community in infant fecal samples
Cited by: 38
Author(s): Yong Guo, Shenghui Li, Yashu Kuang, Jianxing He, Jinhua Lu, Bei-Jun Luo, Feng-Ju Jiang, Yaozhong Liu, Christopher J. Papasian, Huimin Xia, Hong‐Wen Deng, Xiu Qiu
Software Mentions: 6
Published: over 8 years ago

10.3389/fpls.2021.683681

Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
Cited by: 9
Author(s): Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D. W. Geering, Pierre‐Yves Teycheney
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.66797

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
Cited by: 6
Author(s): Kai He, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-ichiro Kawada, Mark S. Springer, Michael Berenbrink, Kevin L. Campbell
Software Mentions: 6
Published: over 3 years ago

10.1186/s12917-014-0282-8

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives
Cited by: 115
Author(s): Brian B. Oakley, R. J. Buhr, Casey W. Ritz, Brian H. Kiepper, M. E. Berrang, Bruce S. Seal, N. A. Cox
Software Mentions: 6
Published: almost 10 years ago

10.3389/fmicb.2019.00618

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.6174

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
Cited by: 9
Author(s): Paul Greenfield, Nai Tran‐Dinh, David J. Midgley
Software Mentions: 6
Published: almost 6 years ago

10.1128/mSystems.00043-17

The Skin Microbiome of Cohabiting Couples
Cited by: 86
Author(s): Ashley A. Ross, Andrew C. Doxey, Josh D. Neufeld
Software Mentions: 6
Published: about 7 years ago

10.1186/s13059-016-0969-1

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
Cited by: 136
Author(s): Steven Flygare, Keith E. Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, Keith D. Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V. Voelkerding, Anne J. Blaschke, Carrie L. Byington, Seema Jain, Andrew T. Pavia, Kwabena Krow Ampofo, Karen Eilbeck, Gábor Marth, Mark Yandell, Robert Salais
Software Mentions: 6
Published: over 8 years ago

10.1186/s12864-019-5914-8

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
Cited by: 36
Author(s): Marco Meola, Étienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud, Christophe Chassard
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-018-0586-6

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
Cited by: 96
Author(s): Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael B. Mundy, Jingwen Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason M. Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Reséndis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan Mai Petterson, Jaeyun Sung, Ran Blekhman, Lisa A. Boardman, David W. Larson, Heidi Nelson, Nicholas Chia
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0006462

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota
Cited by: 193
Author(s): Lance B. Price, Cindy M. Liu, Johan H. Melendez, Yelena M. Frankel, David M. Engelthaler, Maliha Aziz, Jolene R. Bowers, Rogan Rattray, Jacques Ravel, Chris Kingsley, Paul Keim, Gerald S. Lazarus, Jonathan M. Zenilman
Software Mentions: 6
Published: over 15 years ago

10.1371/journal.pone.0248030

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome
Cited by: 22
Author(s): Heidi M.-L. Wipf, Devin Coleman‐Derr
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms8040559

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Cited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-020-00841-w

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
Cited by: 49
Author(s): Isabel F. Escapa, Yanmei Huang, Tsute Chen, Maoxuan Lin, Alexis Kokaras, Floyd E. Dewhirst, Katherine P. Lemon
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-021-01001-4

The bacterial communities of Alaskan mosses and their contributions to N2-fixation
Cited by: 26
Author(s): Hannah Holland‐Moritz, Julia Stuart, Lily R. Lewis, Samantha N. Miller, Michelle C. Mack, José Miguel Ponciano, Stuart F. McDaniel, Noah Fierer
Software Mentions: 5
Published: over 3 years ago

10.3897/mycokeys.39.28109

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
Cited by: 52
Author(s): Sten Anslan, R. Henrik Nilsson, Christian Wurzbacher, Petr Baldrián, Leho Tedersoo, Mohammad Bahram
Software Mentions: 5
Published: about 6 years ago

10.1186/s40168-019-0668-8

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin
Cited by: 91
Author(s): Allison M. Veach, Reese M. Morris, Daniel Z. Yip, Zamin K. Yang, Nancy L. Engle, Melissa Cregger, Timothy J. Tschaplinski, Christopher W. Schadt
Software Mentions: 5
Published: over 5 years ago

10.3389/fmolb.2019.00115

Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil
Cited by: 26
Author(s): Vadakattu V. S. R. Gupta, Bangzhou Zhang, C. Ryan Penton, Julian Yu, James M. Tiedje
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-63278-z

Phylogenetic Inference of H3N2 Canine Influenza A Outbreak in Ontario, Canada in 2018
Cited by: 6
Author(s): Wanhong Xu, J. Scott Weese, Davor Ojkić, Oliver Lung, Katherine Handel, Yohannes Berhane
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2019.01439

Genome-Wide Variation in Potyviruses
Cited by: 75
Author(s): Deepti Nigam, Katherine LaTourrette, Pedro Filho Noronha Souza, Hernán García-Ruíz
Software Mentions: 5
Published: about 5 years ago

10.1186/s12862-021-01856-z

Positive selection on the MHC class II DLA-DQA1 gene in golden jackals (Canis aureus) from their recent expansion range in Europe and its effect on their body mass index
Cited by: 6
Author(s): Milomir Stefanović, Duško Ćirović, Neda Bogdanović, Felix Knauer, Miklós Heltai, László Szabó, József Lanszki, Chavdar Zhelev, Helmut Schaschl, Franz Suchentrunk
Software Mentions: 5
Published: over 3 years ago

10.1126/sciadv.aau4578

Fungal diversity regulates plant-soil feedbacks in temperate grassland
Cited by: 134
Author(s): Marina Semchenko, Jonathan W. Leff, Yudi M. Lozano, Sirgi Saar, John Davison, Anna Wilkinson, Benjamin G. Jackson, William J. Pritchard, Jonathan R. De Long, Simon Oakley, Kelly E. Mason, Nicholas J. Ostle, Elizabeth M. Baggs, David Johnson, Noah Fierer, Richard D. Bardgett
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.6448

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Cited by: 10
Author(s): Stefanos Siozios, Jack Pilgrim, Alistair C. Darby, Matthew Baylis, Gregory D. D. Hurst
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.02944

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi
Cited by: 12
Author(s): Gian Maria Niccolò Benucci, Delaney Burnard, Lara D. Shepherd, Gregory Bonito, Andrew B. Munkacsi
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2013.00291

FunGene: the functional gene pipeline and repository
Cited by: 451
Author(s): Jordan A. Fish, Benli Chai, Qiong Wang, Yanni Sun, C. Titus Brown, James M. Tiedje, James R. Cole
Software Mentions: 5
Published: almost 12 years ago

10.1002/mbo3.1231

Marine biofilms on different fouling control coating types reveal differences in microbial community composition and abundance
Cited by: 16
Author(s): Maria Papadatou, Samuel Robson, Sergey Dobretsov, Joy E. M. Watts, Jennifer Longyear, Maria Salta
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pntd.0005693

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas
Cited by: 53
Author(s): Naomi L. Forrester, Joel O. Wertheim, Vivian G. Dugan, Albert J. Auguste, David L. Lin, Alexandra Adams, Rubing Chen, Rodion Gorchakov, Grace Leal, José G. Estrada-Franco, Jyotsna Pandya, Rebecca Halpin, Kumar Hari, Ravi Jain, Timothy B. Stockwell, Suman Das, David E. Wentworth, Martin D. Smith, Sergei L. Kosakovsky Pond, Scott C. Weaver
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2016.00398

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow
Cited by: 48
Author(s): Anna Lopatina, Sofia Medvedeva, Sergey Shmakov, Maria D. Logacheva, В. А. Крыленков, Konstantin Severinov
Software Mentions: 5
Published: over 8 years ago

10.1128/mSystems.00130-17

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Cited by: 284
Author(s): Marius Vital, André Karch, Dietmar H. Pieper
Software Mentions: 5
Published: almost 7 years ago

10.1099/jgv.0.000464

Evolution of infectious bronchitis virus in China over the past two decades
Cited by: 52
Author(s): Ye Zhao, Hui Zhang, Jing Zhao, Qi Zhong, Ji Hui Jin, Guo Zhong Zhang
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-74602-y

A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach
Cited by: 21
Author(s): Eneko Bachiller, Marta Albo-Puigserver, Joan Giménez, María Grazia Pennino, Neus Marí‐Mena, Antonio Esteban, Elena Lloret-Lloret, Angélique Jadaud, Belén Carro, José María Bellido, Marta Coll
Software Mentions: 5
Published: about 4 years ago

10.3389/fphys.2017.00535

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology
Cited by: 52
Author(s): Núria Mach, Aline Foury, Sandra Kittelmann, Fabrice Reigner, Marco Moroldo, María Ballester, Diane Esquerré, Julie Rivière, Guillaume Sallé, Philippe Gérard, Marie‐Pierre Moisan, Léa Lansade
Software Mentions: 5
Published: over 7 years ago

10.1186/1743-422X-8-318

Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein
Cited by: 5
Author(s): Beata Hasiów‐Jaroszewska, Anna Czerwoniec, H. Pospieszny, Santiago F. Elena
Software Mentions: 5
Published: over 13 years ago

10.3389/fmicb.2016.01703

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status
Cited by: 53
Author(s): Monica Di Paola, Duccio Cavalieri, Davide Albanese, M. Sordo, Massimo Pindo, Claudio Donati, Ilaria Pagnini, Teresa Giani, Gabriele Simonini, Alessia Paladini, Paolo Lionetti, Carlotta De Filippo, Rolando Cimaz
Software Mentions: 5
Published: about 8 years ago

10.3390/nu8100660

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study
Cited by: 92
Author(s): Andrea Quagliariello, Irene Aloisio, Nicole Bozzi Cionci, Donata Luiselli, Giuseppe D’Auria, Llúcia Martínez-Priego, David Pérez-Villarroya, Tomaž Langerholc, Maša Primec, Dušanka Mičetić-Turk, Diana Di Gioia
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-017-03478-2

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis
Cited by: 5
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zongzhuan Shen
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0089323

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
Cited by: 60
Author(s): Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0037818

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
Cited by: 511
Author(s): Sujatha Srinivasan, Noah G. Hoffman, Martin Morgan, F. A. Matsen, Tina L. Fiedler, Richard Hall, Frederick J. Ross, Connor O. McCoy, Roger E. Bumgarner, Jeanne M. Marrazzo, David N. Fredricks
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0080822

Bacterial Endosymbiosis in a Chordate Host: Long-Term Co-Evolution and Conservation of Secondary Metabolism
Cited by: 50
Author(s): Jason C. Kwan, Eric W. Schmidt
Software Mentions: 5
Published: almost 11 years ago

10.1038/s41598-019-53623-2

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome
Cited by: 41
Author(s): Shijie Deng, Heidi M.-L. Wipf, Grady Pierroz, Theodore K. Raab, Rajnish Khanna, Devin Coleman‐Derr
Software Mentions: 5
Published: almost 5 years ago

10.1186/s40793-019-0342-6

The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers
Cited by: 46
Author(s): Axel Aigle, James I. Prosser, Cécile Gubry‐Rangin
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9020411

Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable
Cited by: 12
Author(s): Mark McCauley, Marlène Chiarello, Carla L. Atkinson, Colin R. Jackson
Software Mentions: 4
Published: almost 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

10.1186/s40168-018-0603-4

A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist?
Cited by: 238
Author(s): Jessica D. Forbes, Chih-Yu Chen, Natalie Knox, Ruth Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle J. Alfa, Çharles N. Bernstein, Gary Van Domselaar
Software Mentions: 4
Published: almost 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

10.1186/s40168-017-0344-9

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters
Cited by: 23
Author(s): Céline Lesaulnier, Craig W. Herbold, Claus Pelikan, David Berry, Cédric Gérard, Xavier Le Coz, Sophie Gagnot, Jutta Niggemann, Thorsten Dittmar, Gabriel Singer, Alexander Loy
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-016-1022-0

Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA
Cited by: 34
Author(s): Melissa J. Ward, Mariya I. Goncheva, Emily J. Richardson, Paul R. McAdam, Emma J. Raftis, Angela Kearns, Robert S. Daum, Michael Z. David, Tsai Ling Lauderdale, Giles Edwards, Graeme R. Nimmo, Geoffrey W. Coombs, Xander W. Huijsdens, Mark Woolhouse, J. Ross Fitzgerald
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-018-0470-z

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Cited 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

10.1371/journal.pntd.0002636

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
Cited by: 642
Author(s): Oumar Faye, Caio Castro Freire, Atila Iamarino, Juliana Velasco Castro de Oliveira, Mawlouth Diallo, Paolo Marinho de Andrade Zanotto, Amadou Alpha Sall
Software Mentions: 4
Published: almost 11 years ago

10.1186/s40168-017-0362-7

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks
Cited by: 54
Author(s): Bruno Tilocca, Katharina Burbach, Charlotte M E Heyer, Ludwig E. Hoelzle, R. Mosenthin, Volker Stefanski, Amélia Camarinha‐Silva, Jana Seifert
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0117667

Genetic and Genomic Diversity Studies of Acacia Symbionts in Senegal Reveal New Species of Mesorhizobium with a Putative Geographical Pattern
Cited by: 20
Author(s): Fatou Diouf, Diégane Diouf, Agnieszka Klonowska, Antoine Le Quéré, Niokhor Bakhoum, Dioumacor Fall, Marc Neyra, Hugues Parrinello, M. Diouf, Ibrahima Ndoye, Lionel Moulin
Software Mentions: 4
Published: almost 10 years ago

10.3389/fmicb.2015.01087

Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog
Cited by: 81
Author(s): Stuart E. Denman, Gonzalo Martínez Fernández, Takumi Shinkai, Makoto Mitsumori, Christopher S. McSweeney
Software Mentions: 4
Published: about 9 years ago

10.1002/mbo3.727

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis
Cited by: 25
Author(s): Chenhe Wang, Yanfeng Zhou, Dawei Lv, You Ge, Huan Li, You Yang
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2019.03111

Characterization of Ebinur Lake Virus and Its Human Seroprevalence at the China–Kazakhstan Border
Cited by: 11
Author(s): Han Xia, Ran Liu, Lu Zhao, Xiang Dong Sun, Zhong Zheng, Evans Atoni, Xiaomin Hu, Bo Zhang, Guilin Zhang, Zhiming Yuan
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2013.00279

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter
Cited by: 59
Author(s): C. Ryan Penton, Timothy A. Johnson, John F. Quensen, Shoko Iwai, James R. Cole, James M. Tiedje
Software Mentions: 4
Published: almost 12 years ago

10.1111/1751-7915.12308

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co‐fermentation with sugar beet silage
Cited by: 29
Author(s): Susanne Langer, Sharif Ahmed, Daniel Einfalt, Frank R. Bengelsdorf, Marian Kazda
Software Mentions: 4
Published: over 9 years ago

10.1002/lno.11361

The global Microcystis interactome
Cited by: 51
Author(s): Katherine V. Cook, Chuang Li, Haiyuan Cai, Lee R. Krumholz, K. David Hambright, Hans W. Paerl, Morgan M. Steffen, Alan E. Wilson, Michele A. Burford, Hans‐Peter Grossart, David P. Hamilton, Helong Jiang, Assaf Sukenik, Delphine Latour, Elisabeth I. Meyer, Judit Padisák, Boqiang Qin, Richard M. Zamor, Guangwei Zhu
Software Mentions: 4
Published: about 5 years ago

10.1007/s00253-018-8932-6

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site
Cited by: 63
Author(s): J.A. Siles, Rosa Margesin
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.01540

Deciphering the Composition and Functional Profile of the Microbial Communities in Chinese Moutai Liquor Starters
Cited by: 76
Author(s): Shu Heng Gan, Fan Yang, Sunil Kumar Sahu, Ru Ye Luo, Shui Lin Liao, He Yu Wang, Tao Jin, Li Wang, Peng Fan Zhang, Xin Liu, Jin Xu, Jianlong Xu, Ya Yu Wang, Huan Liu
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/bty767

Methods for automatic reference trees and multilevel phylogenetic placement
Cited by: 35
Author(s): Lucas Czech, Pierre Barbera, Alexandros Stamatakis
Software Mentions: 4
Published: about 6 years ago

10.1371/currents.RRN1237

Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)
Cited by: 26
Author(s): Mats Töpel, Magnus Lundberg, Torsten Eriksson, Bente Eriksen
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2017.01979

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy
Cited by: 177
Author(s): Carlotta De Filippo, Monica Di Paola, Matteo Ramazzotti, Davide Albanese, Giuseppe Pieraccini, Elena Banci, Franco Miglietta, Duccio Cavalieri, Paolo Lionetti
Software Mentions: 4
Published: about 7 years ago

10.1186/s12918-018-0566-x

KF-finder: identification of key factors from host-microbial networks in cervical cancer
Cited by: 15
Author(s): Jialu Hu, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.01359

Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles
Cited by: 26
Author(s): Maozhang He, Jun Gao, Jinyuan Wu, Yunyan Zhou, Hao Fu, Shanlin Ke, Hui Yang, Congying Chen, Lusheng Huang
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.4017

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro.
Cited by: 7
Author(s): Eline Vanlancker, Barbara Vanhoecke, Andrea M. Stringer, Tom Van de Wiele
Software Mentions: 4
Published: almost 8 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

10.1093/biomethods/bpab005

Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease
Cited by: 7
Author(s): Nasim Ahmed, Imran Amin, Syed Shan-e-Ali Zaidi, Saleem Ur Rahman, Muhammad Farooq, Claude Fauquet, Shahid Mansoor
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.01006

Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
Cited by: 7
Author(s): Beatriz Beamud, María Alma Bracho, Fernando González‐Candelas
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.7501

Improvement of subsoil physicochemical and microbial properties by short-term fallow practices
Cited by: 4
Author(s): Guangyu Li, Walter Timo de Vries, Cifang Wu, Hongyu Zheng
Software Mentions: 4
Published: over 5 years ago

10.1186/s40851-015-0013-4

Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston’s fish owl
Cited by: 18
Author(s): Tetsuo I. Kohyama, Keita Omote, Chizuko Nishida, Takeshi Takenaka, Keisuke Saito, Satoshi Fujimoto, Ryuichi Masuda
Software Mentions: 4
Published: over 9 years ago

10.3390/v13061044

Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China
Cited by: 3
Author(s): Weixin Wu, Xinna Ge, Yongning Zhang, Jun Han, Xin Guo, Lei Zhou, Hanchun Yang
Software Mentions: 4
Published: over 3 years ago

10.1111/1751-7915.13353

Microbial communities in swine lungs and their association with lung lesions
Cited by: 24
Author(s): Tao Huang, Mingpeng Zhang, Xinkai Tong, Jiaqi Chen, Guorong Yan, Shouguo Fang, Yuanmei Guo, Bin Yang, Shijun Xiao, Congying Chen, Lusheng Huang, Huashui Ai
Software Mentions: 4
Published: almost 6 years ago

10.1111/ppa.13001

Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species
Cited by: 8
Author(s): J. J. G. Amisse, Joseph Ndunguru, Fred Tairo, Elijah Ateka, Laura M. Boykin, Monica A. Kehoe, Nurbibi Cossa, Chrissie Rey, Peter Sseruwagi
Software Mentions: 4
Published: over 5 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.2012.00293

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat
Cited by: 30
Author(s): David Armitage, Kimberley L. Gallagher, Nicholas D. Youngblut, Daniel H. Buckley, Stephen H. Zinder
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12866-021-02182-6

Potential of fecal microbiota for detection and postoperative surveillance of colorectal cancer
Cited by: 9
Author(s): Qizheng Yao, Meifang Tang, Liuhong Zeng, Zhonghua Chu, Hui Sheng, Yuyu Zhang, Yuan Zhou, Hongyun Zhang, Huayan Jiang, Mingzhi Ye
Software Mentions: 4
Published: over 3 years ago

10.3389/fcimb.2020.00460

Reassortment Between Divergent Strains of Camp Ripley Virus (Hantaviridae) in the Northern Short-Tailed Shrew (Blarina brevicauda)
Cited by: 5
Author(s): Schuyler Liphardt, Hae Ji Kang, Satoru Arai, Se Hun Gu, Joseph A. Cook, Richard Yanagihara
Software Mentions: 4
Published: about 4 years ago

10.1002/ece3.6983

Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden
Cited by: 9
Author(s): Briana K. Whitaker, Natalie Christian, Qiang Chai, Keith Clay
Software Mentions: 4
Published: almost 4 years ago

Projects: cran: RDP

Papers Mentioning RDP 1,243