cran: RDP | Projects | Ecosyste.ms: Papers

10.1186/1756-0500-3-257

A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
Cited by: 10
Author(s): Richard W. Hyman, Hui Jiang, Marilyn Fukushima, Ronald W. Davis
Software Mentions: 2
Published: about 14 years ago

10.3390/cells8040377

Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis
Cited by: 16
Author(s): Hong Li, Tong Zhou, Qiu‐Hong Wan, Sheng‐Guo Fang
Software Mentions: 2
Published: over 5 years ago

10.1186/1753-6561-7-S7-S4

Better primer design for metagenomics applications by increasing taxonomic distinguishability
Cited by: 20
Author(s): Melita Jaric, Jonathan Segal, Eugenia Silva-Herzog, Lisa Schneper, Kalai Mathee, Giri Narasimhan
Software Mentions: 2
Published: almost 11 years ago

10.1093/ve/vev009

The global distribution ofBanana bunchy top virusreveals little evidence for frequent recent, human-mediated long distance dispersal events
Cited by: 48
Author(s): Daisy Stainton, Darren P. Martin, Brejnev Muhire, Samiuela Lolohea, Mana’ia Halafihi, P. Lepoint, Guy Blomme, Kathleen S. Crew, Murray Sharman, Simona Kraberger, Anisha Dayaram, Matthew Walters, David A. Collings, Batsirai Mabvakure, Phillipe Lemey, Gordon William Harkins, J. E. Thomas, Arvind Varsani
Software Mentions: 2
Published: almost 10 years ago

10.1038/s42003-020-01548-2

Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore
Cited by: 17
Author(s): Nicholas M. Fountain-Jones, Simona Kraberger, Roderick B. Gagne, Daryl R. Trumbo, Patricia E. Salerno, W. Chris Funk, Kevin R. Crooks, Roman Biek, Mathew W. Alldredge, Ken Logan, Guy Baele, Simon Dellicour, Holly B. Ernest, Sue VandeWoude, Scott Carver, Meggan E. Craft
Software Mentions: 2
Published: almost 4 years ago

10.1111/1462-2920.13887

Torix group Rickettsia are widespread in Culicoides biting midges (Diptera: Ceratopogonidae), reach high frequency and carry unique genomic features
Cited by: 38
Author(s): Jack Pilgrim, Mats Ander, Claire Garros, Matthew Baylis, Gregory D. D. Hurst, Stefanos Siozios
Software Mentions: 2
Published: about 7 years ago

10.1186/s12867-017-0081-4

Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants
Cited by: 8
Author(s): Jiang Qian, Yong Liu, Naixia Chao, Chunyan Ma, Qicong Chen, Jian Sun, Yaosheng Wu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12985-020-01466-z

Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya
Cited by: 2
Author(s): Edith Khamonya Avedi, Adedapo Olutola Adediji, Dora Kilalo, Florence Olubayo, Isaac Macharia, Elijah Ateka, Eunice Machuka, J. Musembi Mutuku
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0207512

Remote access protocols for Desktop-as-a-Service solutions
Cited by: 11
Author(s): Eduardo Magaña, Iris Sesma, D. Morató, Mikel Izal
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0056710

454 Pyrosequencing Analysis on Faecal Samples from a Randomized DBPC Trial of Colicky Infants Treated with Lactobacillus reuteri DSM 17938
Cited by: 90
Author(s): Stefan Roos, Johan Dicksved, Valentina Tarasco, Emanuela Locatelli, Fulvio Ricceri, Ulf Grandin, Francesco Savino
Software Mentions: 2
Published: over 11 years ago

10.1186/s12985-019-1243-4

Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4
Cited by: 7
Author(s): Jati Adiputra, Sridhar Jarugula, Rayapati A. Naidu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0227705

Regional adaptations and parallel mutations in Feline panleukopenia virus strains from China revealed by nearly-full length genome analysis
Cited by: 7
Author(s): Élcio Leal, Ruiying Liang, Qi Liu, Fabiola Villanova, Lisong Shi, Lin Liang, Jinxiang Li, Steven S. Witkin, Shangjin Cui
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0032942

Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection
Cited by: 152
Author(s): Giske Biesbroek, Elisabeth A. M. Sanders, Guus Roeselers, Xinhui Wang, Martien P. M. Caspers, Krzysztof Trzciński, Debby Bogaert, Bart J. F. Keijser
Software Mentions: 2
Published: over 12 years ago

10.1186/s13071-014-0496-4

Leishmania donovani populations in Eastern Sudan: temporal structuring and a link between human and canine transmission
Cited by: 15
Author(s): Rania M. H. Baleela, Martin S. Llewellyn, Sinead Fitzpatrick, Katrin Kuhls, Gabriele Schönian, Michael A. Miles, Isabel Maurício
Software Mentions: 2
Published: about 10 years ago

10.1128/AEM.02015-20

Pairing of Parental Noroviruses with Unequal Competitiveness Provides a Clear Advantage for Emergence of Progeny Recombinants
Cited by: 1
Author(s): Eung Seo Koo, Yong Seok Jeong
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0063139

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome
Cited by: 169
Author(s): Kelvin Li, Monika Bihan, Barbara A. Methé
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0101384

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China
Cited by: 8
Author(s): Kaifa Wei, Yanhui Chen, Yi Lin, Yutian Pan
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0024785

Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition
Cited by: 82
Author(s): Michaël Dumas, Shawn W. Polson, Don Ritter, Jacques Ravel, Jack Gelb, Robin Morgan, K. Eric Wommack
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0028088

Comparing the Bacterial Diversity of Acute and Chronic Dental Root Canal Infections
Cited by: 116
Author(s): Adriana Lopes dos Santos, José F. Siqueira, Isabela N. Rôças, Ederson C Jesus, Alexandre Soares Rosado, James M. Tiedje
Software Mentions: 2
Published: about 13 years ago

10.1186/s12862-017-0899-x

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta
Cited by: 22
Author(s): Daniele Salvi, Catarina Pinho, D. James Harris
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0062580

Characterisation of the Bacterial and Fungal Communities Associated with Different Lesion Sizes of Dark Spot Syndrome Occurring in the Coral Stephanocoenia intersepta
Cited by: 38
Author(s): Michael Sweet, Deborah Burn, Aldo Cróquer, P. M. Leary
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0126931

Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters
Cited by: 321
Author(s): Virginie Lecomte, Nadeem O. Kaakoush, Chris Maloney, Mukesh Raipuria, Karina D. Huinao, Hazel M. Mitchell, Margaret J. Morris
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0015220

Robust Computational Analysis of rRNA Hypervariable Tag Datasets
Cited by: 16
Author(s): Maksim Sipos, Patricio Jeraldo, Nicholas Chia, Ani Qu, A. S. Dhillon, Michael E. Konkel, Karen E. Nelson, Bryan A. White, Nigel Goldenfeld
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0255425

Canine bocavirus-2 infection and its possible association with encephalopathy in domestic dogs
Cited by: 6
Author(s): Chutchai Piewbang, Sabrina Wahyu Wardhani, Wichan Dankaona, Sitthichok Lacharoje, Poowadon Chai‐in, Jakarwan Yostawonkul, Jira Chanseanroj, Suwimon Boonrungsiman, Tanit Kasantikul, Yong Poovorawan, Somporn Techangamsuwan
Software Mentions: 2
Published: over 3 years ago

10.3390/v12020143

Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses
Cited by: 24
Author(s): Joseph P. Orton, Matheo Morales, Rafaela S. Fontenele, Kara Schmidlin, Simona Kraberger, Daniel J. Leavitt, Timothy H. Webster, Melissa A. Wilson, Kenro Kusumi, Greer A. Dolby, Arvind Varsani
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-9-215

Binning sequences using very sparse labels within a metagenome
Cited by: 77
Author(s): Chon‐Kit Kenneth Chan, Arthur Hsu, Saman K. Halgamuge, Sen‐Lin Tang
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0106662

Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil?
Cited by: 179
Author(s): Loredana Canfora, Giovanni Bacci, Flavia Pinzari, Giuseppe Lo Papa, Carmelo Dazzi, Antonio Benedetti
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0220298

Prevalence, epidemiology and molecular studies of Tomato chlorosis virus (ToCV) in South Africa
Cited by: 8
Author(s): Vaneson Moodley, Augustine Gubba, Paramu Mafongoya
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.237

Succession of the turkey gastrointestinal bacterial microbiome related to weight gain
Cited by: 74
Author(s): Jessica L. Danzeisen, A. Calvert, Sally Noll, Brian McComb, Julie S. Sherwood, Catherine M. Logue, Timothy J. Johnson
Software Mentions: 2
Published: almost 11 years ago

10.3389/fmicb.2020.571104

Recirculation of Giardia lamblia Assemblage A After Metronidazole Treatment in an Area With Assemblages A, B, and E Sympatric Circulation
Cited by: 7
Author(s): Maria Fantinatti, Luiz Antonio Pimentel Lopes-Oliveira, Tiara Cascais-Figueredo, Phelipe Austriaco-Teixeira, Erika Verissimo, Alexandre Ribeiro Bello, Alda Maria Da‐Cruz
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0054326

Sediment Bacterial Communities Reflect the History of a Sea Basin
Cited by: 20
Author(s): Christina Lyra, Hanna Sinkko, Matias Rantanen, Lars Paulín, Aarno Kotilainen
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12862-018-1127-z

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Cited by: 26
Author(s): Jonna Sofia Eriksson, Filipe de Sousa, Yann Bertrand, Alexandre Antonelli, Bengt Oxelman, Bernard E. Pfeil
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0223847

Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants
Cited by: 121
Author(s): C.Y. Dong, Lingling Wang, Qian Li, Qingmao Shang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1007368

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
Cited by: 19
Author(s): Pilar Domingo‐Calap, Benjamin Schubert, Mélanie Joly, Morgane Solis, Meiggie Untrau, Raphaël Carapito, Philippe Georgel, Sophie Caillard, Samira Fafi‐Kremer, Nicodème Paul, Oliver Kohlbacher, Fernando González‐Candelas, Seiamak Bahram
Software Mentions: 2
Published: about 6 years ago

10.1186/s12866-017-0947-0

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage
Cited by: 98
Author(s): Lysiane Dunière, Shaofa Xu, Long Jin, Chijioke O. Elekwachi, Yuxi Wang, Kelly Turkington, Robert Forster, Tim A. McAllister
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0113253

Progressive Degradation of Crude Oil n-Alkanes Coupled to Methane Production under Mesophilic and Thermophilic Conditions
Cited by: 56
Author(s): Lei Cheng, Shengbao Shi, Qiang Li, Jianfa Chen, Hui Zhang, Yahai Lu
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0085904

Microbiota of Cow’s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters
Cited by: 153
Author(s): Georgios Oikonomou, M.L.S. Bicalho, E.B.S. Meira, Rubiana Falopa Rossi, Carla Foditsch, Vinicius Machado, A.G.V. Teixeira, Carlos Santisteban, Y.H. Schukken, R.C. Bicalho
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0085301

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times
Cited by: 182
Author(s): Jun Zhao, Tian Ni, Yong Li, Wu Xiong, Ran Wei, Biao Shen, Qirong Shen, Ruifu Zhang
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2180-12-20

Defining the "core microbiome" of the microbial communities in the tonsils of healthy pigs
Cited by: 67
Author(s): Beth A. Lowe, Terence L. Marsh, Natasha Isaacs-Cosgrove, Roy N. Kirkwood, Matti Kiupel, Martha H. Mulks
Software Mentions: 2
Published: almost 13 years ago

10.1093/aob/mcw048

Molecular phylogeny and genome size evolution of the genusBetula(Betulaceae)
Cited by: 62
Author(s): Nian Wang, Hugh A. McAllister, Paul R. Bartlett, Richard J. A. Buggs
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0181427

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change
Cited by: 51
Author(s): Cheng-Yu Chen, Po‐Cheng Chen, Francis Cheng-Hsuan Weng, Grace Tzun-Wen Shaw, Daryi Wang
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0051075

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production
Cited by: 75
Author(s): Eva Lucía Margarita Figuerola, Leandro D. Guerrero, Silvina Mariana Rosa, Leandro Simonetti, Matías Ezequiel Duval, Juán Alberto Galantini, José Camilo Bedano, Luis Gabriel Wall, Leonardo Erijman
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0090115

Microbial Successions and Metabolite Changes during Fermentation of Salted Shrimp (Saeu-Jeot) with Different Salt Concentrations
Cited by: 31
Author(s): Se Hee Lee, Ji Young Jung, Che Ok Jeon
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0025617

Population Structure of Pseudomonas aeruginosa from Five Mediterranean Countries: Evidence for Frequent Recombination and Epidemic Occurrence of CC235
Cited by: 120
Author(s): Makaoui Maâtallah, Jihane Cheriaa, Amina Backhrouf, Aina Iversen, Hajo Grundmann, Thuy Do, Philippe Lanotte, Maha Mastouri, Mohamed Salem Elghmati, Fernando Rojo, Mejdi Snoussi, Christian G. Giske
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0039242

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease
Cited by: 237
Author(s): Eliseo Papa, Michael Docktor, Christopher Smillie, Sarah Weber, Sarah P. Preheim, Dirk Gevers, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Jay Ingram, David B. Schauer, Doyle V. Ward, Joshua R. Korzenik, Ramnik J. Xavier, Athos Bousvaros, Eric J. Alm
Software Mentions: 2
Published: over 12 years ago

10.1186/s12866-019-1546-z

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing
Cited by: 61
Author(s): Jean-Claude Ogier, Sylvie Pagès, Maxime Galan, Matthieu Barret, Sophie Gaudriault
Software Mentions: 2
Published: over 5 years ago

10.1186/1743-422X-9-43

Biology and interactions of two distinct monopartite begomoviruses and betasatellites associated with radish leaf curl disease in India
Cited by: 51
Author(s): AK Singh, B. Chattopadhyay, Supriya Chakraborty
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0038108

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem
Cited by: 72
Author(s): Wesley D. Swingley, D. R. Meyer-Dombard, Everett L. Shock, Eric Alsop, Heinz Dieter Falenski, J. R. Havig, Jason Raymond
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0076440

Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere
Cited by: 54
Author(s): Blaž Stres, Woo Jun Sul, Boštjan Murovec, James M. Tiedje
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0081977

Both Positive and Negative Selection Pressures Contribute to the Polymorphism Pattern of the Duplicated Human CYP21A2 Gene
Cited by: 9
Author(s): J. Szabó, Ágnes Szilágyi, Zoltán Doleschall, Attila Patócs, Henriette Farkas, Zoltán Prohászka, Kristóf Rácz, George Füst, Márton Doleschall
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0123365

Distinctive Patterns of Evolution of the δ-Globin Gene (HBD) in Primates
Cited by: 5
Author(s): Ana Moleirinho, Alexandra M. Lopes, Susana Seixas, Ramiro Morales‐Hojas, Maria João Prata, António Amorim
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0186273

Further insight into genetic variation and haplotype diversity of Cherry virus A from China
Cited by: 9
Author(s): Rui Gao, Yunxiao Xu, Thierry Candresse, Zhen He, Shifang Li, Yuxin Ma, Meiguang Lu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0063157

Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth
Cited by: 205
Author(s): Georgios Oikonomou, A.G.V. Teixeira, Carla Foditsch, M.L.S. Bicalho, Vinicius Machado, R.C. Bicalho
Software Mentions: 2
Published: over 11 years ago

10.3390/plants8050127

Non-cultivated Cotton Species (Gossypium spp.) Act as a Reservoir for Cotton Leaf Curl Begomoviruses and Associated Satellites
Cited by: 5
Author(s): Sara Shakir, Syed Shan-e-Ali Zaidi, Atiq-ur-Rehman, Muhammad Farooq, Imran Amin, Jodi A. Scheffler, Brian E. Scheffler, Muhammad Shah Nawaz-ul-Rehman, Shahid Mansoor
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2148-8-256

Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera
Cited by: 51
Author(s): Ave Tooming‐Klunderud, David P. Fewer, Thomas Rohrlack, Jouni Jokela, Leo Rouhiainen, Kaarina Sivonen, Tom Kristensen, Kjetill S. Jakobsen
Software Mentions: 2
Published: about 16 years ago

10.1038/s41598-017-18196-y

Deciphering the emergence, genetic diversity and evolution of classical swine fever virus
Cited by: 31
Author(s): Liliam Ríos, Liani Coronado, Dany Naranjo-Feliciano, Orlando Martínez-Pérez, Carmen Laura Perera, Lilian Hernández-Álvarez, Heidy Dı́az de Arce, José I. Núñez, Llilianne Ganges, Lester J. Pérez
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0039089

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria
Cited by: 98
Author(s): José Luis Blanco‐Pastor, Pablo Vargas, Bernard E. Pfeil
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pbio.1001265

Patterns of Gene Flow Define Species of Thermophilic Archaea
Cited by: 193
Author(s): Hinsby Cadillo‐Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera, Aaron E. Darling, Michael L. Reno, David J. Krause, Rachel J. Whitaker
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0055817

Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea
Cited by: 105
Author(s): Gregor Gorkiewicz, Gerhard G. Thallinger, Slave Trajanoski, Sonja Lackner, Gernot Stocker, Thomas Hinterleitner, Christian Gülly, Christoph Högenauer
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0102945

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context
Cited by: 83
Author(s): Thierry Candresse, Denis Filloux, Brejnev Muhire, Charlotte Julian, Serge Galzi, Guillaume Fort, Pauline Bernardo, Jean-Heinrich Daugrois, Emmanuel Fernandez, Darren P. Martin, Arvind Varsani, Denis Filloux
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0237975

A multi-omics approach to solving problems in plant disease ecology
Cited by: 43
Author(s): Sharifa G. Crandall, Kaitlin M. Gold, María del Mar Jiménez-Gasco, Camila C. Filgueiras, Denis S. Willett
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0093893

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing
Cited by: 110
Author(s): C. Ryan Penton, V. V. S. R. Gupta, James M. Tiedje, Stephen M. Neate, K. Ophel-Keller, Michael R. Gillings, Paul R. Harvey, Amanda Pham, David Roget
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0176309

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens
Cited by: 79
Author(s): Alessandra De Cesare, Federico Sirri, Gerardo Manfreda, Paola Moniaci, A. Giardini, Marco Zampiga, Adele Meluzzi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0252523

Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA
Cited by: 8
Author(s): Afsha Tabassum, Sudeep Bag, N. D. Suassuna, Kassie Conner, Peng W. Chee, Robert C. Kemerait, Phillip M. Roberts
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0051175

Pollution Impacts on Bacterioplankton Diversity in a Tropical Urban Coastal Lagoon System
Cited by: 17
Author(s): Gigliola Rhayd Boechat Sallôto, Alexander Machado Cardoso, Felipe H. Coutinho, Leonardo Henriques Pinto, Ricardo P. Vieira, Catia Chaia, J. L. F. Lima, Rodolpho Mattos Albano, Orlando B. Martins, Maysa M. Clementino
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0140282

Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows?
Cited by: 70
Author(s): Jolien B. Veneman, S. Muetzel, K. J. Hart, Catherine L. Faulkner, J. M. Moorby, H.B. Perdok, C. J. Newbold
Software Mentions: 2
Published: about 9 years ago

10.1186/1755-8794-3-41

Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing
Cited by: 108
Author(s): Drake M Smith, David E. Snow, Eric Rees, Ann M Zischkau, John D. Hanson, Randall D. Wolcott, Yan Sun, Jennifer S. White, Shiva Kumar, Scot E. Dowd
Software Mentions: 2
Published: about 14 years ago

10.14202/vetworld.2018.480-487

Molecular characterization of canine parvovirus variants (CPV-2a, CPV-2b, and CPV-2c) based on the VP2 gene in affected domestic dogs in Ecuador
Cited by: 25
Author(s): David De la Torre, Eulalia Mafla, Byron Puga, Linda Erazo, Claudete S. Astolfi-Ferreira, A. A. Ferreira
Software Mentions: 2
Published: over 6 years ago

10.3390/ani10081372

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach
Cited by: 9
Author(s): Himansu Kumar, Yu Na Jang, Kwangmin Kim, Jun Hyung Park, Min-Woong Jung, Woncheoul Park
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0035294

Novel Bacterial Taxa in the Human Microbiome
Cited by: 85
Author(s): Kristine M. Wylie, Rebecca Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George M. Weinstock, Katherine S. Pollard
Software Mentions: 2
Published: over 12 years ago

10.3390/vetsci8050081

Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea
Cited by: 3
Author(s): Taemook Park, Jungho Yoon, Ah-Ram Kim, Tatsuya Unno, Young‐Min Yun
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0195345

Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing
Cited by: 65
Author(s): Loreen Sommermann, Joerg Geistlinger, Daniel Wibberg, Annette Deubel, Jessica Zwanzig, Doreen Babin, Andreas Schlüter, Ingo Schellenberg
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0183646

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus
Cited by: 8
Author(s): Ye Chen, Xinxin Li, Xiaojuan Chi, Song Wang, Yanmei Ma, Ji‐Long Chen
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0153554

Comparison of Methods to Identify Pathogens and Associated Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada
Cited by: 15
Author(s): Étienne Yergeau, Luke Masson, Miria Elias, Shurong Xiang, Ewa Madey, Hongsheng Huang, Brian W. Brooks, Lee A. Beaudette
Software Mentions: 2
Published: over 8 years ago

10.1016/j.vetmic.2011.01.027

Phylogenetic characterisation of naturally occurring feline immunodeficiency virus in the United Kingdom
Cited by: 14
Author(s): Ayman Samman, Elizabeth L. McMonagle, Nicola Logan, Brian J. Willett, Roman Biek, Margaret J. Hosie
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0230871

The trisaccharide melezitose impacts honey bees and their intestinal microbiota
Cited by: 16
Author(s): Victoria Seeburger, Paul D’Alvise, Basel Shaaban, Karsten Schweikert, Gertrud Lohaus, Annette Schroeder, Martin Hasselmann
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0190511

The genetic diversity of narcissus viruses related to turnip mosaic virus blur arbitrary boundaries used to discriminate potyvirus species
Cited by: 12
Author(s): Kazusato Ohshima, Shinichiro Mitoma, Adrian Gibbs
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0060811

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences
Cited by: 88
Author(s): Swee Hoe Ong, Vinutha Uppoor Kukkillaya, Andreas Wilm, Christophe Lay, Eliza Xin Pei Ho, Louie Low, Martin L. Hibberd, Niranjan Nagarajan
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0205446

HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013
Cited by: 19
Author(s): Dawit Assefa Arimide, Almaz Abebe, Yenew Kebede, Fekadu Adugna, Tesfaye Tilahun, Desta Kassa, Yibeltal Assefa, Taye Tolera Balcha, Per Björkman, Patri K. Medstrand
Software Mentions: 2
Published: about 6 years ago

10.3390/v11121116

Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile (Crocodylus porosus)
Cited by: 23
Author(s): Subir Sarker, Sally R. Isberg, Jasmin Moran, Rachel De Araujo, N Elliott, Lorna Melville, Travis Beddoe, Karla J. Helbig
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0071360

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies
Cited by: 119
Author(s): Jonas Ghyselinck, Stefan Pfeiffer, Kim Heylen, Angela Sessitsch, Paul De Vos
Software Mentions: 2
Published: over 11 years ago

10.1099/mic.0.027284-0

Population structure of Streptococcus oralis
Cited by: 56
Author(s): Thuy Do, Keith A. Jolley, Martin C. J. Maiden, Steven C. Gilbert, Douglas Clark, William Wade, David Beighton
Software Mentions: 2
Published: over 15 years ago

10.1186/s12864-016-2380-4

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami
Cited by: 17
Author(s): Satoshi Hiraoka, Asako Machiyama, Minoru Ijichi, Kentaro Inoue, Koichiro Oshima, Masahira Hattori, Susumu Yoshizawa, Kazuhiro Kogure, Wataru Iwasaki
Software Mentions: 2
Published: almost 9 years ago

10.1093/molbev/msz243

Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures
Cited by: 6
Author(s): Michael Golden, Ben Murrell, Darren P. Martin, Oliver G. Pybus, Jotun Hein
Software Mentions: 2
Published: about 5 years ago

10.1093/molbev/msu227

Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae
Cited by: 33
Author(s): Daryl Domman, Astrid Collingro, Ilias Lagkouvardos, Lena Gehre, Thomas Weinmaier, Thomas Rattei, Agathe Subtil, Matthias Horn
Software Mentions: 2
Published: over 10 years ago

10.1186/s12915-020-00839-8

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals
Cited by: 26
Author(s): Judith Neukamm, Saskia Pfrengle, Martyna Molak, Alexander Seitz, Michael Francken, Partick Eppenberger, Charlotte Avanzi, Ella Reiter, Christian Urban, Beatrix Welte, Philipp W. Stockhammer, Barbara Teßmann, Alexander Herbig, Katerina Harvati, Kay Nieselt, Johannes Krause, Verena J. Schuenemann
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0053649

Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets
Cited by: 144
Author(s): Chunye Lin, Lin Ye, Amy Tong, Si Lok, Tong Zhang
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0035749

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error
Cited by: 58
Author(s): Teresita M. Porter, G. Brian Golding
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-019-5640-2

Diversity and recombination analysis of Cotton leaf curl Multan virus: a highly emerging begomovirus in northern India
Cited by: 25
Author(s): Razia Qadir, Zainul A. Khan, D. Monga, J. A. Khan
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9081687

Altered Fecal Microbiotas and Organic Acid Concentrations Indicate Possible Gut Dysbiosis in University Rugby Players: An Observational Study
Cited by: 3
Author(s): So Morishima, Nobuyuki Oda, Hiromi Ito, Tomohiro Segawa, Machi Oda, Takamitsu Tsukahara, Yasuharu Kawase, Tomohisa Takagi, Yuji Naito, Mami Fujibayashi, Ryo Inoüe
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-536

Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus
Cited by: 27
Author(s): Mateus Ferreira Santana, José Cleydson Ferreira da Silva, Eduardo S. G. Mizubuti, Elza Fernandes de Araújo, Bradford Condon, B. Gillian Turgeon, Marisa Vieira de Queiroz
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0102934

Regime Shift in Sandy Beach Microbial Communities following Deepwater Horizon Oil Spill Remediation Efforts
Cited by: 23
Author(s): Annette Summers Engel, Axita Ajaykumar Gupta
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0232446

Dynamic changes in bacterial communities in the recirculating nutrient solution of cucumber plug seedlings cultivated in an ebb-and-flow subirrigation system
Cited by: 4
Author(s): C.Y. Dong, Qian Li, Lingling Wang, Qingmao Shang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0049138

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Cited by: 350
Author(s): Alison R. Erickson, Brandi L. Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel F. Mongodin, Chongle Pan, Manesh Shah, Jonas Halfvarson, Curt Tysk, Bernard Henrissat, Jeroen Raes, Nathan C. VerBerkmoes, Claire M. Fraser, Robert L. Hettich, Janet Jansson
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0070036

Gene Duplication and Fragment Recombination Drive Functional Diversification of a Superfamily of Cytoplasmic Effectors in Phytophthora sojae
Cited by: 40
Author(s): Danyu Shen, Tingli Liu, Wenwu Ye, Li Liu, Peihan Liu, Yuanyi Wu, Yuanchao Wang, Daolong Dou
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0065999

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region
Cited by: 25
Author(s): Abdulahi Alfonso-Morales, Orlando Martínez-Pérez, Roser Dolz, Rosa Valle, Carmen Laura Perera, Kateri Bertran, Maria Teresa Frı́as, Natàlia Majó, Llilianne Ganges, Lester J. Pérez
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0011741

Population Genetics of Streptococcus dysgalactiae Subspecies equisimilis Reveals Widely Dispersed Clones and Extensive Recombination
Cited by: 50
Author(s): David McMillan, Debra E. Bessen, Marcos D. Pinho, Candace N. Ford, Gerod S. Hall, José Melo‐Cristino, Mário Ramirez
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0006074

More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body
Cited by: 127
Author(s): Xing Yang, Lu Xie, Yixue Li, Chaochun Wei
Software Mentions: 2
Published: over 15 years ago

10.1186/s40168-017-0249-7

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms
Cited by: 64
Author(s): Tobias Weil, Carlotta De Filippo, Davide Albanese, Claudio Donati, Massimo Pindo, Lorenzo Pavarini, Federico Carotenuto, Massimiliano Pasqui, Luisa Poto, Jacopo Gabrieli, Carlo Barbante, Birgit Sattler, Duccio Cavalieri, Franco Miglietta
Software Mentions: 2
Published: over 7 years ago

10.1186/2049-2618-1-8

A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity
Cited by: 116
Author(s): Marius Vital, C. Ryan Penton, Qiong Wang, Vincent B. Young, Dion Antonopoulos, Mitchell L. Sogin, Hilary G. Morrison, Laura H. Raffals, Eugene B. Chang, Gary B. Huffnagle, Thomas M. Schmidt, James R. Cole, James M. Tiedje
Software Mentions: 2
Published: over 11 years ago

Projects: cran: RDP

Papers Mentioning RDP 1,243