cran: RDP | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0048882

Chaos of Wolbachia Sequences Inside the Compact Fig Syconia of Ficus benjamina (Ficus: Moraceae)
Cited by: 14
Author(s): Caiqiong Yang, Jin‐Hua Xiao, Li‐Ming Niu, Guang-Chang Ma, James M. Cook, Sheng‐Nan Bian, Yanlong Fu, Dawei Huang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0026624

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Cited by: 74
Author(s): Samuel V. Angiuoli, James R. White, Malcolm Matalka, Owen White, W. Florian Fricke
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0134953

Diversity of Vibrio spp in Karstic Coastal Marshes in the Yucatan Peninsula
Cited by: 6
Author(s): Icela Ortiz-Carrillo, Neyi Estrella-Gómez, Marcela Zamudio-Maya, Rafael Rojas-Herrera
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0129272

Transmission and Demographic Dynamics of Coxsackievirus B1
Cited by: 15
Author(s): Pei‐Yu Chu, Yu‐Chang Tyan, Yao-Shen Chen, Hsiu-Lin Chen, Po‐Liang Lu, Yu-Hsien Chen, Bao-Chen Chen, Tsi-Shu Huang, Chufeng Wang, Hui-Ju Su, Yipeng Shi, Bintou Sanno-Duanda, Kuei-Hsiang Lin, Kazushi Motomura
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0160568

Impact of Environmental Microbes on the Composition of the Gut Microbiota of Adult BALB/c Mice
Cited by: 8
Author(s): Zhimao Bai, Honglin Zhang, Na Li, Zhiyu Bai, Liling Zhang, Zhencheng Xue, Haitao Jiang, Sheng Yuan, Dongrui Zhou
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0048420

Phylogeographic Characterization of Tick-Borne Encephalitis Virus from Patients, Rodents and Ticks in Slovenia
Cited by: 31
Author(s): Luka Fajs, Emina Durmiši, Nataša Knap, Franc Strle, Tatjana Avšič-Županc
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0036934

Comparison of Storage Conditions for Human Vaginal Microbiome Studies
Cited by: 58
Author(s): Guoyun Bai, Pawel Gajer, Melissa Nandy, Bing Ma, Hongqiu Yang, Joyce M. Sakamoto, May Hsieh Blanchard, Jacques Ravel, Rebecca M. Brotman
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0038571

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
Cited by: 160
Author(s): Phillip B. Pope, Alasdair Mackenzie, Ivan Gregor, Wendy Smith, Monica A. Sundset, Alice C. McHardy, Mark Morrison, Vincent G. H. Eijsink
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0034233

Increased Gut Permeability and Microbiota Change Associate with Mesenteric Fat Inflammation and Metabolic Dysfunction in Diet-Induced Obese Mice
Cited by: 474
Author(s): Yan Y. Lam, Connie Ha, Craig Campbell, Andrew J. Mitchell, Anuwat Dinudom, Jan Oscarsson, David I. Cook, Nicholas H. Hunt, Ian D. Caterson, Andrew Holmes, L. H. Storlien
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0061564

Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain
Cited by: 8
Author(s): Leonor Sánchez-Busó, Mireia Coscollá, Marta Pinto‐Carbó, Vicente Catalán, Fernando González‐Candelas
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0060670

Composition of the Vaginal Microbiota in Women of Reproductive Age – Sensitive and Specific Molecular Diagnosis of Bacterial Vaginosis Is Possible?
Cited by: 186
Author(s): Elena Shipitsyna, Anna-Karin Roos, Raluca Datcu, A Hallén, Hans Fredlund, Jørgen Skov Jensen, Lars Engstrand, Magnus Unemo
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0085641

The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus
Cited by: 45
Author(s): Ryosuke Yasaka, Hien Thi Nguyen, Simon Y. W. Ho, Sebastián Duchêne, Savaş Korkmaz, N. I. Katis, Hideki Takahashi, Adrian Gibbs, Kazusato Ohshima
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0005065

Extensive HIV-1 Intra-Host Recombination Is Common in Tissues with Abnormal Histopathology
Cited by: 45
Author(s): Susanna L. Lamers, Marco Salemi, Derek Galligan, Túlio de Oliveira, Gary B. Fogel, Sara C. Granier, Li Zhao, Joseph N. Brown, Alanna Morris, Eliezer Masliah, Michael S. McGrath
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0096582

Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
Cited by: 46
Author(s): Shahideh Nouri, Rafael Arévalo, Bryce W. Falk, Russell L. Groves
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0221099

Effects of α-pinene on the pinewood nematode (Bursaphelenchus xylophilus) and its symbiotic bacteria
Cited by: 11
Author(s): Xu Wang, Yanxue Yu, Jianjun Ge, Bingyan Xie, Shuifang Zhu, Xinyue Cheng
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0058474

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis
Cited by: 67
Author(s): Nadia Mhedbi-Hajri, Ahmed Hajri, Tristan Boureau, Armelle Darrasse, Karine Durand, Chrystelle Brin, Marion Fischer-Le Saux, Charles Manceau, Stéphane Poussier, Olivier Pruvost, Christophe Lemaire, Marie‐Agnès Jacques
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0032545

Standard Colonic Lavage Alters the Natural State of Mucosal-Associated Microbiota in the Human Colon
Cited by: 128
Author(s): Laura Harrell, Yunwei Wang, Dionysios A. Antonopoulos, Vincent B. Young, Lev Lichtenstein, Yong Huang, Stephen B Hanauer, Eugene B. Chang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0025042

Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity
Cited by: 91
Author(s): Pei‐Ying Hong, Jennifer A. Croix, E. P. Greenberg, H. Rex Gaskins, Roderick I. Mackie
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0005854

Tracing the Evolution of Competence in Haemophilus influenzae
Cited by: 23
Author(s): Heather Maughan, Rosemary J. Redfield
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0058118

Analysis of Metagenomic Data Containing High Biodiversity Levels
Cited by: 14
Author(s): José Ramón Valverde, Rafael P. Mellado
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0103712

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing
Cited by: 57
Author(s): Junko Obata, Toru Takeshita, Yukie Shibata, Wataru Yamanaka, Masako Unemori, Akifumi Akamine, Yoshihisa Yamashita
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0114185

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity
Cited by: 89
Author(s): Vanessa Nienhouse, Xiang Gao, Qunfeng Dong, David E. Nelson, David E. Nelson, Kathleen McKinley, Paul C. Schreckenberger, Noriko Shibata, Cynthia S. Fok, Elizabeth R. Mueller, Linda Brubaker, Alan J. Wolfe, Katherine A. Radek
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0070783

Intestinal Microbiota Composition of Interleukin-10 Deficient C57BL/6J Mice and Susceptibility to Helicobacter hepaticus-Induced Colitis
Cited by: 86
Author(s): Ines Yang, Daniel Eibach, Friederike Kops, Birgit Brenneke, Sabrina Woltemate, Jessika Schulze, André Bleich, Achim D. Gruber, Sureshkumar Muthupalani, James G. Fox, Christine Josenhans, Sebastian Suerbaum
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0129256

Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China
Cited by: 19
Author(s): Qingye Zhuang, Kaicheng Wang, Shuo Liu, Guangyu Hou, Wenming Jiang, Suchun Wang, Jinping Li, Jianmin Yu, Jiming Chen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0032118

Analyses of the Microbial Diversity across the Human Microbiome
Cited by: 200
Author(s): Kelvin Li, Monika Bihan, Shibu Yooseph, Barbara A. Methé
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0045962

Genetic Diversity and Selection in Three Plasmodium vivax Merozoite Surface Protein 7 (Pvmsp-7) Genes in a Colombian Population
Cited by: 19
Author(s): Diego Garzón‐Ospina, Carolina López, Johanna Forero-Rodríguez, Manuel A. Patarroyo
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0125356

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions
Cited by: 69
Author(s): Julia Birtel, Jean‐Claude Walser, Samuel Pichon, Helmut Bürgmann, Blake Matthews
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0105098

Subtype Classification of Iranian HIV-1 Sequences Registered in the HIV Databases, 2006-2013
Cited by: 19
Author(s): Kazem Baesi, Samaneh Moallemi, Molood Farrokhi, Esmaeil Mehraeen, Hong‐Ha M. Truong
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0046403

Contrasting Evolutionary Dynamics and Information Content of the Avian Mitochondrial Control Region and ND2 Gene
Cited by: 22
Author(s): F. Keith Barker, Mariah K. Benesh, Arion J. Vandergon, Scott M. Lanyon
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0020843

New Insights into the Evolution of Wolbachia Infections in Filarial Nematodes Inferred from a Large Range of Screened Species
Cited by: 148
Author(s): Emanuele Ferri, O. Bain, Michela Barbuto, Coralie Martin, Nathan Lo, Shigehiko Uni, Frédéric Landmann, Sara G. Baccei, Ricardo Guerrero, Sueli de Souza Lima, Claudio Bandi, Samuel Wanji, Mamadou Diagne, Maurizio Casiraghi
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0016553

Microbial Diversity of a Brazilian Coastal Region Influenced by an Upwelling System and Anthropogenic Activity
Cited by: 46
Author(s): José Cury, Fábio Vieira de Araújo, Sérgio A. Coelho-Souza, Raquel S. Peixoto, Joana Oliveira, Henrique F. Santos, Alberto M. R. Dávila, Alexandre Soares Rosado
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0068410

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting
Cited by: 37
Author(s): Chandrika Ramadugu, Bernard E. Pfeil, Manjunath L. Keremane, Richard F. Lee, Iván J. Maureira-Butler, Mikeal L. Roose
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0009964

Comparative Analysis of Fecal Microbiota in Infants with and without Eczema
Cited by: 90
Author(s): Pei‐Ying Hong, Bee Wah Lee, Marion Aw, Lynette Pei‐Chi Shek, Gaik Chin Yap, Kaw Yan Chua, Wen Tso Liu
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0020338

The Intestinal Microbiota Plays a Role in Salmonella-Induced Colitis Independent of Pathogen Colonization
Cited by: 145
Author(s): Rosana B. R. Ferreira, Navkiran Gill, Benjamin P. Willing, L. Caetano M. Antunes, Sarah Russell, Matthew A. Croxen, B. Brett Finlay
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0030423

Considerable MHC Diversity Suggests That the Functional Extinction of Baiji Is Not Related to Population Genetic Collapse
Cited by: 7
Author(s): Shixia Xu, Jianfeng Ju, Xuming Zhou, Lian Wang, Kaiya Zhou, Guang Yang
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0083125

Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera)
Cited by: 217
Author(s): Kirk E. Anderson, Timothy H. Sheehan, Brendon M. Mott, Patrick Maes, Lucy Snyder, Melissa R. Schwan, Alexander Walton, Beryl M. Jones, Vanessa Corby‐Harris
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0088376

Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium
Cited by: 42
Author(s): Sandra Appelt, Fabrice Armougom, Matthieu Le Bailly, Caroline Robert, Michel Drancourt
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0050070

Comparative Genomic and Phylogenetic Approaches to Characterize the Role of Genetic Recombination in Mycobacterial Evolution
Cited by: 21
Author(s): Silvia E. Smith, Patrice Showers-Corneli, Caitlin Nora Dardenne, Henry H. Harpending, Darren P. Martin, Robert G. Beiko
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0025200

Barcoded Pyrosequencing Reveals That Consumption of Galactooligosaccharides Results in a Highly Specific Bifidogenic Response in Humans
Cited by: 260
Author(s): Lauren M. G. Davis, Inés Martínez, Jens Walter, Caitlin Goin, Robert W. Hutkins
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0143605

Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses
Cited by: 6
Author(s): Casper-Emil Tingskov Pedersen, Peter Frandsen, Sabenzia Nabalayo Wekesa, Rasmus Heller, Abraham Sangula, Jemma Wadsworth, Nick J. Knowles, Vincent B. Muwanika, Hans R. Siegismund
Software Mentions: 1
Published: almost 9 years ago

10.1002/ctm2.112

Modulation of gut microbiota mediates berberine‐induced expansion of immuno‐suppressive cells to against alcoholic liver disease
Cited by: 35
Author(s): Sha Li, Ning Wang, Hor‐Yue Tan, Fan Chueng, Zhang‐Jin Zhang, Man–Fung Yuen, Yibin Feng
Software Mentions: 1
Published: over 4 years ago

10.1155/2009/510270

Evidence of Extensive Homologous Recombination in the Core Genome ofRickettsia
Cited by: 4
Author(s): Jinyu Wu, Tonghai Yu, Qiyu Bao, Fangqing Zhao
Software Mentions: 1
Published: almost 16 years ago

10.1155/2018/4276291

A Classifier Graph Based Recurring Concept Detection and Prediction Approach
Cited by: 6
Author(s): Yuan Sun, Zhihai Wang, Yang Bai, Honghua Dai, Saeid Nahavandi
Software Mentions: 1
Published: over 6 years ago

Projects: cran: RDP

Papers Mentioning RDP 1,243