cran: RDP | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0099953

The Effect of Silver Nanoparticles on Seasonal Change in Arctic Tundra Bacterial and Fungal Assemblages
Cited by: 43
Author(s): Niraj Kumar, G.R. Palmer, Vishal Shah, Virginia K. Walker
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0027949

Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment
Cited by: 280
Author(s): Jessica L. Danzeisen, Hyeun Bum Kim, Richard E. Isaacson, Zheng Jin Tu, Timothy J. Johnson
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0038241

Novel Evidence of HBV Recombination in Family Cluster Infections in Western China
Cited by: 13
Author(s): Bin Zhou, Zhanhui Wang, Jie Yang, Jian Sun, Hua Li, Yasuhito Tanaka, Masashi Mizokami, Jilun Hou
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0044243

The Role of Coral-Associated Bacterial Communities in Australian Subtropical White Syndrome of Turbinaria mesenterina
Cited by: 32
Author(s): Scott Godwin, Elizabeth Bent, James Borneman, Lily Pereg
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0064293

Description of HIV-1 Group M Molecular Epidemiology and Drug Resistance Prevalence in Equatorial Guinea from Migrants in Spain
Cited by: 13
Author(s): Gonzalo Yebra, Miguel de Mulder, África Holguín
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0055390

The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes
Cited by: 79
Author(s): Stefanos Siozios, Panagiotis Ioannidis, Lisa Klasson, Siv G. E. Andersson, Henk R. Braig, Kostas Bourtzis
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0038401

Assessment of Microbial Diversity in Biofilms Recovered from Endotracheal Tubes Using Culture Dependent and Independent Approaches
Cited by: 67
Author(s): Ilse Vandecandelaere, Nele Matthijs, Filip Van Nieuwerburgh, Dieter Deforce, Peter Vosters, Liesbet De Bus, Hans Nelis, Pieter Depuydt, Tom Coenye
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0115024

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China
Cited by: 58
Author(s): Yuanyuan Li, Hongyu Wen, Longqian Chen, Tingting Yin
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0070722

The Complete Genomic Sequence of Pepper Yellow Leaf Curl Virus (PYLCV) and Its Implications for Our Understanding of Evolution Dynamics in the Genus Polerovirus
Cited by: 24
Author(s): Aviv Dombrovsky, Eyal Glanz, Oded Lachman, Noa Sela, Adi Doron‐Faigenboim, Y. Antignus
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0033971

Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination
Cited by: 22
Author(s): Weilong Hao, Vanessa Allen, Frances Jamieson, Donald E. Low, David C. Alexander
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0131410

Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China
Cited by: 4
Author(s): Yu Zhou, Jianfeng Weng, Yanping Chen, Juan Wu, Qingchang Meng, Xiaohua Han, Hao Zhang, Mingshun Li, Hongjun Yong, Degui Zhang, Shihuang Zhang, Xinhai Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0046048

Genome Sequencing and Phylogenetic Analysis of 39 Human Parainfluenza Virus Type 1 Strains Isolated from 1997–2010
Cited by: 20
Author(s): Eric T. Beck, Jun He, Martha I. Nelson, Michael E. Bose, Jun Fan, Swati Kumar, Kelly J. Henrickson
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0124261

Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013
Cited by: 38
Author(s): Jingjing Wang, Hualei Liu, Wei Liu, Dong Zheng, Yanyan Zhao, Yin Li, Yingli Wang, Shengxiang Ge, Yan Liu, Yunjuan Zuo, Yu Song, Zhiliang Wang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0188944

Molecular characterization of hepatitis B virus in Bangladesh reveals a highly recombinant population
Cited by: 22
Author(s): Saif Ullah Munshi, Tuan Tran, Truc Nhu Thanh Vo, Shahina Tabassum, Nahida Sultana, Trang Nguyen, Munira Jahan, Chau Ngoc Le, Stephen Baker, Motiur Rahman
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0091883

Independent Evolutionary Origin of fem Paralogous Genes and Complementary Sex Determination in Hymenopteran Insects
Cited by: 26
Author(s): Vasco Koch, Inga Nissen, Björn D. Schmitt, Martin Beye
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0020546

Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia
Cited by: 32
Author(s): Anna Stenkova, Marina Isaeva, Ф. Н. Шубин, В. А. Рассказов, Alexander Rakin
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0076465

Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome
Cited by: 44
Author(s): Manoeli Lupatini, Afnan Khalil Ahmad Suleiman, Rodrigo Josemar Seminoti Jacques, Zaida Inês Antoniolli, Eiko E. Kuramae, Flávio Anastácio de Oliveira Camargo, Luiz Fernando Würdig Roesch
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0026404

Dissolution of Calcite in the Twilight Zone: Bacterial Control of Dissolution of Sinking Planktonic Carbonates Is Unlikely
Cited by: 10
Author(s): Andrew Bissett, Thomas R. Neu, Dirk de Beer
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0043543

Multiple Origins of the Sodium Channel kdr Mutations in Codling Moth Populations
Cited by: 16
Author(s): Pierre Franck, Myriam Siegwart, Jérôme Olivares, Jean‐François Toubon, Claire Lavigne
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0074582

Genome Sequence Analysis of Dengue Virus 1 Isolated in Key West, Florida
Cited by: 18
Author(s): Dong Ho Shin, Stephanie L. Richards, Barry W. Alto, David Bettinardi, Chelsea T. Smartt
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0151161

Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses
Cited by: 41
Author(s): Huma Saleem, Nazia Nahid, Sara Shakir, Siddra Ijaz, Ghulam Murtaza, Asif Ali Khan, Muhammad Mubin, Muhammad Shah Nawaz-ul-Rehman
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0206406

Prevalence of HIV-1 pretreatment drug resistance among treatment naïve pregnant women in Bissau, Guinea Bissau
Cited by: 11
Author(s): Sten Wilhelmson, Fredrik Månsson, Jacob Lindman, Ansu Biai, Joakim Esbjörnsson, Hans Norrgren, Marianne Jansson, Patrik Medstrand
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0191893

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire
Cited by: 17
Author(s): Taylor K Dunivin, Justine Miller, Ashley Shade
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0075797

Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns
Cited by: 18
Author(s): Sergio Álvarez‐Pérez, Clara de Vega, Carlos M. Herrera
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0088807

Genomic Evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Isolates Revealed by Deep Sequencing
Cited by: 42
Author(s): Manreetpal Singh Brar, Mǎng Shī, Raymond Kin-Hi Hui, Frederick Chi-Ching Leung
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0224731

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF
Cited by: 14
Author(s): Craig D. Soutar, John Stavrinides
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0224569

Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus
Cited by: 5
Author(s): Hongyue Zu, Hong Zhang, Minhao Yao, Jiayue Zhang, Hong Di, Lin Zhang, Lü Dong, Zhenhua Wang, Yu Zhou
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0109840

Intragenic Recombination Has a Critical Role on the Evolution of Legionella pneumophila Virulence-Related Effector sidJ
Cited by: 14
Author(s): Joana Costa, Paulo Gonçalves Teixeira, Ana Filipa d’Avó, Célio Dias Santos Júnior, António Veríssimo
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0082854

Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle, Platysternon megacephalum
Cited by: 23
Author(s): Chenfei Zheng, Liuwang Nie, Jue Wang, Huaxing Zhou, Huazhen Hou, Hao Wang, Juanjuan Liu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0146558

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Cited by: 45
Author(s): Javier Pascual, Silvia Blanco, Marina García-López, Adela García‐Salamanca, Sergey A. Bursakov, Olga Genilloud, Gerald F. Bills, Juan L. Ramos, Pieter van Dillewijn
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0207480

Analysis and insights into recombination signals in lumpy skin disease virus recovered in the field
Cited by: 74
Author(s): Alexander Sprygin, Yu.Yu. Babin, Yana Pestova, Svetlana Kononova, David B. Wallace, Antoinette van Schalkwyk, Olga Byadovskaya, В. И. Диев, D. A. Lozovoy, А. В. Кононов
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0096197

Novel PCR Primers for the Archaeal Phylum Thaumarchaeota Designed Based on the Comparative Analysis of 16S rRNA Gene Sequences
Cited by: 8
Author(s): Jin-Kyung Hong, Hye-Jin Kim, Jae-Chang Cho
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0116499

Genetic Variation of the Major Histocompatibility Complex (MHC Class II B Gene) in the Threatened Hume’s Pheasant, Syrmaticus humiae
Cited by: 9
Author(s): Weicai Chen, Yi Bei, Hanhua Li
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0009554

Threatened Corals Provide Underexplored Microbial Habitats
Cited by: 255
Author(s): Shinichi Sunagawa, Cheryl M. Woodley, Mónica Medina
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0026147

Complete Genome Characterisation of a Novel 26th Bluetongue Virus Serotype from Kuwait
Cited by: 155
Author(s): Sushila Maan, Narender S. Maan, Kyriaki Nomikou, Eva Veronesi, Katarzyna Bachanek‐Bankowska, Manjunatha N. Belaganahalli, Houssam Attoui, Peter P. C. Mertens
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0112378

Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity
Cited by: 33
Author(s): Yongming Sang, Joseph Bergkamp, Frank Blecha
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0094746

Circulating HFMD-Associated Coxsackievirus A16 Is Genetically and Phenotypically Distinct from the Prototype CV-A16
Cited by: 16
Author(s): Wei Wei, Hao Guo, Jingliang Li, Sangsang Ren, Zhenhong Wei, Wanguo Bao, Xiaoming Hu, Ke Zhao, Wenyan Zhang, Yulai Zhou, Fenyong Sun, Richard B. Markham, Xiao Fang Yu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0086950

Mucosa-Associated Bacterial Microbiome of the Gastrointestinal Tract of Weaned Pigs and Dynamics Linked to Dietary Calcium-Phosphorus
Cited by: 94
Author(s): Evelyne Mann, Stephan Schmitz‐Esser, Qendrim Zebeli, Martin Wagner, M. Ritzmann, Barbara U. Metzler‐Zebeli
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0055336

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago
Cited by: 76
Author(s): Hien Thi Nguyen, Yasuhiro Tomitaka, Simon Y. W. Ho, Sebastián Duchêne, Heinrich‐Josef Vetten, D.‐E. Lesemann, John A. Walsh, Adrian Gibbs, Kazusato Ohshima
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0032491

Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms
Cited by: 134
Author(s): Yemin Lan, Qiong Wang, James R. Cole, Gail Rosen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0139321

Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation
Cited by: 68
Author(s): Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Francesca Stomeo, Solomon Maina, Appolinaire Djikeng, Monica A. Kehoe, Laura M. Boykin
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0006149

Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)
Cited by: 107
Author(s): Hae Ji Kang, Shannon N. Bennett, Laarni Sumibcay, Satoru Arai, Andrew G. Hope, Gábor Mócz, Jin Won Song, Joseph A. Cook, Richard Yanagihara
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0184615

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production
Cited by: 79
Author(s): Valerio Mezzasalma, Anna Sandionigi, Ilaria Bruni, Antonia Bruno, G. Lovicu, Andrea Galimberti, Massimo Labra
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0110941

Genetic Diversity of the Coat Protein of Olive Mild Mosaic Virus (OMMV) and Tobacco Necrosis Virus D (TNV-D) Isolates and Its Structural Implications
Cited by: 12
Author(s): Carla Varanda, M. A. Machado, Paulo Martel, Gustavo Nolasco, María Clara, Maria R. Félix
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0063816

Microbial Diversity Analysis of Fermented Mung Beans (Lu-Doh-Huang) by Using Pyrosequencing and Culture Methods
Cited by: 9
Author(s): Shiou Huei Chao, Hui Yu Huang, Chia Hui Chang, Chih Hsien Yang, Wei Shen Cheng, Ya Huei Kang, Koichi Watanabe, Yao‐Chou Tsai
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0041175

The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion
Cited by: 15
Author(s): Matthew A. Carrigan, Oleg Uryasev, Ross P. Davis, Lan Min Zhai, Thomas D. Hurley, Steven A. Benner
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0039315

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
Cited by: 233
Author(s): Doyle V. Ward, Dirk Gevers, Georgia Giannoukos, Ashlee M. Earl, Barbara A. Methé, Erica Sodergren, Michael Feldgarden, Dawn Ciulla, Diana Tabbaa, Cesar Arze, Elizabeth L. Appelbaum, Leigh Aird, Scott Anderson, Tulin Ayvaz, Edward A. Belter, Monika Bihan, Toby Bloom, Jonathan Crabtree, Laura Courtney, Lynn K. Carmichael, David J. Dooling, Rachel Erlich, Candace N. Farmer, Lucinda L. Fulton, Robert S. Fulton, Hongyu Gao, John A. Gill, Brian J. Haas, Lisa Hemphill, Otis Hall, Susanna Hamilton, Theresa A. Hepburn, Niall J. Lennon, Vandita Joshi, Cristyn Kells, Christie Kovar, Dipak Kalra, Kelvin Li, Lora Lewis, Shawn Leonard, Donna M. Muzny, Elaine R. Mardis, Kathie A. Mihindukulasuriya, Vincent Magrini, Michelle O’Laughlin, Craig Pohl, Xiang Qin, Keenan Ross, Matthew C. Ross, Yu Hui Rogers, Navjeet Singh, Yue Shang, Katarzyna Wilczek-Boney, Jennifer Wortman, Kim C. Worley, Bonnie P. Youmans, Shibu Yooseph, Yanjiao Zhou, Patrick D. Schloss, Richard K. Wilson, Richard A. Gibbs, Karen E. Nelson, George M. Weinstock, Todd Z. DeSantis, Joseph F. Petrosino, Sarah K. Highlander, Bruce W. Birren
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0050631

The Recent Recombinant Evolution of a Major Crop Pathogen, Potato virus Y
Cited by: 45
Author(s): Johan Christiaan Visser, Baoheng Du, Michael D. Pirie
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0022789

A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template
Cited by: 12
Author(s): Tõnu Margus, Maido Remm, Tanel Tenson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0190986

Molecular typing of Legionella pneumophila isolates from environmental water samples and clinical samples using a five-gene sequence typing and standard Sequence-Based Typing
Cited by: 3
Author(s): Xiao-Yong Zhan, Qing-Yi Zhu
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0048417

Intra-Host Diversity and Emergence of Unique GBV-C Viral Lineages in HIV Infected Subjects in Central China
Cited by: 8
Author(s): Haoming Wu, Abinash Padhi, Jin Xu, Xun Gong, Po Tien
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0120768

Platinum Anniversary: Virus and Lichen Alga Together More than 70 Years
Cited by: 9
Author(s): Karel Petrzik, Jan Vondrák, Jana Kvíderová, Jaromír Lukavský
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0134897

A Genomic Approach to Unravel Host-Pathogen Interaction in Chelonians: The Example of Testudinid Herpesvirus 3
Cited by: 16
Author(s): Francesco C. Origgi, Marco Tecilla, Paola Pilo, Aloisio Fabio, Patricia Otten, Lisandra Aguilar-Bultet, Ursula Sattler, P. Roccabianca, Carlos H. Romero, David C. Bloom, Elliott R. Jacobson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0105443

Genetic Diversity and Molecular Evolution of Plum bark necrosis stem pitting-associated virus from China
Cited by: 8
Author(s): Linning Qu, Hongguang Cui, Guanwei Wu, J. F. Zhou, Jiaming Su, Guoping Wang, Ní Hóng
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0033188

Symbionts as Major Modulators of Insect Health: Lactic Acid Bacteria and Honeybees
Cited by: 347
Author(s): Alejandra Vásquez, Eva Forsgren, Ingemar Fries, Robert J. Paxton, Emilie Flaberg, L. Szekeres, Tobias Olofsson
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0079731

Identification and Diversity of Killer Cell Ig-Like Receptors in Aotus vociferans, a New World Monkey
Cited by: 7
Author(s): Diego Garzón‐Ospina, Carolina López, Luis F. Cadavid, Manuel Elkín Patarroyo, Manuel A. Patarroyo
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0023321

Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing
Cited by: 200
Author(s): Oezguel Inceoglu, Waleed Abu Al‐Soud, Joana Falcão Salles, A. Semenov, Jan Dirk van Elsas
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080097

Phylogenetic Diversity of the Bacillus pumilus Group and the Marine Ecotype Revealed by Multilocus Sequence Analysis
Cited by: 83
Author(s): Yang Liu, Qiliang Lai, Chunming Dong, Fei Sun, Liping Wang, Guangyu Li
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0063098

Protein Clustering and RNA Phylogenetic Reconstruction of the Influenza a Virus NS1 Protein Allow an Update in Classification and Identification of Motif Conservation
Cited by: 8
Author(s): Edgar Sevilla-Reyes, David A. Chavaro-Pérez, Elvira Pitén-Isidro, Luis H. Gutiérrez‐González, Teresa Santos‐Mendoza
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0198999

HIV-1 diversity among young women in rural South Africa: HPTN 068
Cited by: 10
Author(s): Mariya V. Sivay, Sarah E. Hudelson, Jing Wang, Yaw Agyei, Erica L. Hamilton, Amanda Selin, Ann M. Dennis, Kathleen Kahn, Francesc Xavier Gómez‐Olivé, Catherine MacPhail, James P. Hughes, Audrey Pettifor, Susan H. Eshleman, Mary Kathryn Grabowski
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0041997

Recombination in Hepatitis C Virus: Identification of Four Novel Naturally Occurring Inter-Subtype Recombinants
Cited by: 32
Author(s): Weifeng Shi, Ines Freitas, Chao‐Dong Zhu, Wei Zheng, William W. Hall, Desmond G. Higgins
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0126819

Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus
Cited by: 31
Author(s): Hans J. Maree, Michael D. Pirie, Kristin Oosthuizen, Rachelle Bester, D. J. G. Rees, Johan T. Burger
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0031981

First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses
Cited by: 25
Author(s): Yann Bertrand, Mats Töpel, Annelie Elväng, Wessam Melik, Magnus Johansson
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0055929

Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation
Cited by: 148
Author(s): Stéphane Uroz, Panagiotis Ioannidis, Juliette Lengellé, Aurélie Cébron, Emmanuelle Morin, Marc Buée, Francis Martin
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0105770

Split Personality of a Potyvirus: To Specialize or Not to Specialize?
Cited by: 28
Author(s): Monica A. Kehoe, B. A. Coutts, Bevan Buirchell, R. A. C. Jones
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0210510

Tandem gene duplication and recombination at the AT3 locus in the Solanaceae, a gene essential for capsaicinoid biosynthesis in Capsicum
Cited by: 10
Author(s): Ashley N. Egan, Sally Falk Moore, Giulia M. Stellari, Byoung-Cheorl Kang, Molly M. Jahn
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0164435

Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach
Cited by: 18
Author(s): Yann Bertrand, Magnus Johansson, Peter Norberg
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0206010

Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data
Cited by: 16
Author(s): Shaheen Nourinejhad Zarghani, Jean-Michel Hily, Miroslav Glasa, Armelle Marais, Thierry Wetzel, Chantal Faure, Emmanuelle Vigne, Amandine Velt, Olivier Lemaire, Jean Michel Boursiquot, Arnela Okić, Ana Belén Ruiz-García, Antonio Olmos, Thierry Lacombe, Thierry Candresse
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0202243

Genetic diversity of the enteroviruses detected from cerebrospinal fluid (CSF) samples of patients with suspected aseptic meningitis in northern West Bank, Palestine in 2017
Cited by: 7
Author(s): Kamal Dumaidi, Amer Al-Jawabreh, Fekri Samarah, Areej Zraiqi, Dirgham Yaseen
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0049992

Isolation and Identification of a Novel Rabies Virus Lineage in China with Natural Recombinant Nucleoprotein Gene
Cited by: 17
Author(s): Cheng-Qiang He, Meng Shao, Hongyan Yan, Nai-Zheng Ding, Hongbin He, Jiaxin Yan, Guiyun Xu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0081040

Characterization of Persistent Virus-Like Particles in Two Acetate-Fed Methanogenic Reactors
Cited by: 15
Author(s): I-Chieh Chien, John Scott Meschke, Heidi L. Gough, John F. Ferguson
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0145674

Enterovirus Migration Patterns between France and Tunisia
Cited by: 7
Author(s): Ines Othman, Audrey Mirand, Ichrak Slama, Maha Mastouri, H. Peigue-Lafeuille, Mahjoub Aouni, Jean‐Luc Bailly
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0176716

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
Cited by: 88
Author(s): Chongqing Wen, Liyou Wu, Yujia Qin, Joy D. Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0009073

Generation of Diversity in Streptococcus mutans Genes Demonstrated by MLST
Cited by: 40
Author(s): Thuy Do, Steven C. Gilbert, Douglas Clark, Farida Ali, Clarissa Cavalcanti Fatturi Parolo, Marisa Maltz, R. R. B. Russell, Peter R. Holbrook, William Wade, David Beighton
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0020447

Towards the Human Colorectal Cancer Microbiome
Cited by: 465
Author(s): Julian R. Marchesi, Bas E. Dutilh, Neil Hall, Wilbert H.M. Peters, Rian Roelofs, Annemarie Boleij, Harold Tjalsma
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0192081

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project
Cited by: 17
Author(s): Gonzalo Yebra, Dan Frampton, Tiziano Gallo Cassarino, Jade Raffle, Jonathan Hubb, R. Bridget Ferns, Laura Waters, C. Y. William Tong, Zisis Kozlakidis, Andrew Hayward, Paul Kellam, Deenan Pillay, Duncan A. Clark, Eleni Nastouli, Andrew Brown
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0059666

Detailed Molecular Epidemiologic Characterization of HIV-1 Infection in Bulgaria Reveals Broad Diversity and Evolving Phylodynamics
Cited by: 17
Author(s): Ivailo Alexiev, Danail Beshkov, Anupama Shankar, Debra L. Hanson, Dimitrios Paraskevis, V. Georgieva, Lyudmila Karamacheva, Hristo Taskov, Tonka Varleva, Ivaylo Elenkov, M Stoicheva, Daniela Nikolova, William M. Switzer
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0200820

Exploring temporal patterns of bacterial and fungal DNA accumulation on a ventilation system filter for a Singapore university library
Cited by: 7
Author(s): Irvan Luhung, Yan Wu, Siyu Xu, Naomichi Yamamoto, Victor Wei-Chung Chang, William W. Nazaroff
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0129004

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities
Cited by: 20
Author(s): Renee J. Smith, James S. Paterson, Cally A. Sibley, J. L. Hutson, James G. Mitchell
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0015191

Diversity of Bacteria Associated with Bursaphelenchus xylophilus and Other Nematodes Isolated from Pinus pinaster Trees with Pine Wilt Disease
Cited by: 78
Author(s): Diogo Neves Proença, Romeu Francisco, Clara Vieira Santos, Antônio Sergio de Santis Andrade Lopes, Luís Fonseca, Isabel Abrantes, Paula V. Morais
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0069662

Comprehensive Phylogenetic Reconstructions of African Swine Fever Virus: Proposal for a New Classification and Molecular Dating of the Virus
Cited by: 42
Author(s): Vincent Michaud, Tantely Randriamparany, Emmanuel Albina
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0038991

Microbial Diversity of Genital Ulcer Disease in Men Enrolled in a Randomized Trial of Male Circumcision in Kisumu, Kenya
Cited by: 19
Author(s): Supriya D. Mehta, Stefan J. Green, Ian Maclean, Haidong Hu, Robert C. Bailey, Patrick M. Gillevet, Greg T. Spear
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0160856

Microbiota in Breast Milk of Chinese Lactating Mothers
Cited by: 80
Author(s): Olga Sakwińska, D Moine, Michèle Delley, Séverine Combremont, Enea Rezzonico, Patrick Descombes, Gerard Vinyes-Parès, Yumei Zhang, Peiyu Wang, Sagar K. Thakkar
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0047720

ExpI and PhzI Are Descendants of the Long Lost Cognate Signal Synthase for SdiA
Cited by: 22
Author(s): Anice Sabag-Daigle, Brian M. M. Ahmer
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0068081

Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections
Cited by: 17
Author(s): Hak Kim, Kisoon Kim, Dae Won Kim, Hee Dong Jung, Hyang Min Cheong, Ki Hwan Kim, Dong Soo Kim, You Jin Kim
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0100400

Patterns of Recombination in HIV-1M Are Influenced by Selection Disfavouring the Survival of Recombinants with Disrupted Genomic RNA and Protein Structures
Cited by: 10
Author(s): Michael Golden, Brejnev Muhire, Yves Semegni, Darren P. Martin
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0035481

Effect of Cry1Ab Protein on Rhizobacterial Communities of Bt-Maize over a Four-Year Cultivation Period
Cited by: 39
Author(s): Jorge Barriuso, José Ramón Valverde, Rafael P. Mellado
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0060802

Bacterial Population in Intestines of the Black Tiger Shrimp (Penaeus monodon) under Different Growth Stages
Cited by: 121
Author(s): Wanilada Rungrassamee, Amornpan Klanchui, Sage Chaiyapechara, Sawarot Maibunkaew, Sithichoke Tangphatsornruang, Pikul Jiravanichpaisal, Nitsara Karoonuthaisiri
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0145072

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems
Cited by: 75
Author(s): Е. В. Першина, Jari P. T. Valkonen, Päivi Kurki, Е. А. Иванова, Е. Л. Чирак, Ilia Korvigo, Н. А. Проворов, E. E. Andronov
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0091853

Characterization of Intestinal Bacteria in Wild and Domesticated Adult Black Tiger Shrimp (Penaeus monodon)
Cited by: 190
Author(s): Wanilada Rungrassamee, Amornpan Klanchui, Sawarot Maibunkaew, Sage Chaiyapechara, Pikul Jiravanichpaisal, Nitsara Karoonuthaisiri
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0013607

Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon
Cited by: 110
Author(s): Yunwei Wang, Suzanne Devkota, Mark W. Musch, Bana Jabrì, Cathryn R. Nagler, Dionysios A. Antonopoulos, Alexander V. Chervonsky, Eugene B. Chang
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0214354

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment
Cited by: 5
Author(s): David A. Coil, Guillaume Jospin, Aaron E. Darling, Corrin Wallis, Ian J. Davis, Stephen Harris, Jonathan A. Eisen, Lucy J. Holcombe, Ciaran O’Flynn
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0013987

Newcastle Disease Virus in Madagascar: Identification of an Original Genotype Possibly Deriving from a Died Out Ancestor of Genotype IV
Cited by: 57
Author(s): Olivier Fridolin Maminiaina, Patricia Gil, François-Xavier Briand, Emmanuel Albina, Djénéba Keita, Harentsoaniaina Rasamoelina Andriamanivo, Véronique Chevalier, Renaud Lancelot, Dominique Martinez, René Rizzoli, Jean-Joseph Rajaonarison, Mahmoud Koko, Abel Andriantsimahavandy, Véronique Jestin, Renata Servan de Almeida
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0169067

African Non-Human Primates Host Diverse Enteroviruses
Cited by: 25
Author(s): Illich Manfred Mombo, Alexander N. Lukashev, Tobias Bleicker, Sebastian Brünink, Nicolás Berthet, Gaël Darren Maganga, Patrick Durand, Céline Arnathau, Larson Boundenga, Barthélémy Ngoubangoye, Vanina Boué, Florian Liégeois, Benjamin Ollomo, Franck Prugnolle, Jan Felix Drexler, Christian Drosten, François Renaud, Virginie Rougeron, Eric M. Leroy
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0196765

Polymorphism in merozoite surface protein-7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure
Cited by: 5
Author(s): Chew Weng Cheng, Chaturong Putaporntip, Somchai Jongwutiwes
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0041266

Hepatitis C Virus in Vietnam: High Prevalence of Infection in Dialysis and Multi-Transfused Patients Involving Diverse and Novel Virus Variants
Cited by: 52
Author(s): Linda Dunford, Michael J. Carr, Jonathan Dean, Allison Waters, Linh T. Nguyen, Thu Hong Ta Thi, Lan Anh Bui Thi, Huy Duong, Thu Thuy Duong Thi, Ha Thu Nguyen, Trinh Thi Diem, Quynh Phuong Luu, Jeff Connell, Suzie Coughlan, Hien Tran Nguyen, William W. Hall, Lan Anh Nguyen Thi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0151677

Molecular Evolution and Spatial Transmission of Severe Fever with Thrombocytopenia Syndrome Virus Based on Complete Genome Sequences
Cited by: 29
Author(s): Jian Wei Liu, Li Zhao, Li Luo, Miaomiao Liu, Yue Sun, Xiaomeng Su, Xue Jie Yu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0128043

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing
Cited by: 17
Author(s): Wuttichai Mhuantong, Sarunyou Wongwilaiwalin, Thanaporn Laothanachareon, Lily Eurwilaichitr, Sithichoke Tangphatsornruang, Benjaporn Boonchayaanant, Tawan Limpiyakorn, Kobchai Pattaragulwanit, Thantip Punmatharith, John McEvoy, Eakalak Khan, Manaskorn Rachakornkij, Verawat Champreda
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0097219

Tollip or Not Tollip: What Are the Evolving Questions behind It?
Cited by: 7
Author(s): Denis Prudêncio Luiz, Célio Dias Santos Júnior, Ana Maria Bonetti, Malcom Antônio Manfredi Brandeburgo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0213807

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments
Cited by: 6
Author(s): Andrew M. Leitholf, Chrystal E. Fretz, Raymond Mahanke, Zachary Santangelo, John M. Senko
Software Mentions: 1
Published: over 5 years ago

Projects: cran: RDP

Papers Mentioning RDP 1,243