Ecosyste.ms: Papers

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: about 13 years ago

10.7554/eLife.36666

Neolithic and medieval virus genomes reveal complex evolution of hepatitis B
Cited by: 94
Author(s): Ben Krause‐Kyora, Julian Susat, Felix M. Key, Denise Kühnert, Esther Bosse, Alexander Immel, Christoph Rinne, Sabin-Christin Kornell, Diego Yepes, Sören Franzenburg, Henrike O. Heyne, Thomas Meier, Sandra Lösch, Harald Meller, Susanne Friederich, Nicole Nicklisch, Kurt W. Alt, Stefan Schreiber, Andreas Tholey, Alexander Herbig, Almut Nebel, Johannes Krause
Software Mentions: 4
Published: about 6 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: almost 3 years ago

10.1128/mSphereDirect.00283-18

Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture
Cited by: 46
Author(s): Alexander L. Greninger, Pavitra Roychoudhury, Hong Xie, Amanda M. Casto, Anne Cent, Gregory Pepper, David M. Koelle, Meei‐Li Huang, Anna Wald, Christine Johnston, Keith R. Jerome
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00731-19

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Cited by: 113
Author(s): Matthew R. Olm, Alexander Crits-Christoph, Spencer Diamond, Adi Lavy, Paula B. Matheus Carnevali, Jillian F. Banfield
Software Mentions: 4
Published: over 4 years ago

10.1128/JVI.01127-19

Evolutionary Dynamics of Oropouche Virus in South America
Cited by: 14
Author(s): Bernardo Gutierrez, Emma L. Wise, Steven T. Pullan, Christopher Logue, Thomas A. Bowden, Marina Escalera-Zamudio, Gabriel Trueba, Márcio Roberto Teixeira Nunes, Nuno Rodrigues Faria, Oliver G. Pybus
Software Mentions: 4
Published: over 4 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: over 5 years ago

10.1371/journal.pone.0174930

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
Cited by: 24
Author(s): William B. Ludington, Thaddeus D. Seher, Olin Applegate, Xunde Li, J.I. Kliegman, Charles Langelier, Edward R. Atwill, Thomas Harter, Joseph L. DeRisi
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-75225-z

Sequential laxative-probiotic usage for treatment of irritable bowel syndrome: a novel method inspired by mathematical modelling of the microbiome
Cited by: 3
Author(s): Ming Li, Ri Xu, Yanqing Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-56227-y

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing
Cited by: 13
Author(s): Luke Braidwood, Sebastian Müller, David C. Baulcombe
Software Mentions: 4
Published: over 4 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: over 3 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: almost 4 years ago

10.1371/journal.pone.0014065

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves
Cited by: 121
Author(s): Newton C. M. Gomes, Daniel F. R. Cleary, Fernando Neves Pinto, Conceição Egas, Adelaide Almeida, Ângela Cunha, Lêda C. Mendonça-Hagler, Kornelia Smalla
Software Mentions: 4
Published: over 13 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: about 6 years ago

10.1186/s12915-016-0337-3

Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread
Cited by: 32
Author(s): Irina Maljkovic Berry, Melanie C. Melendrez, Tao Li, Anthony W. Hawksworth, Gary T. Brice, Patrick J. Blair, Eric S. Halsey, M. C. Williams, Stefan Fernandez, In-Kyu Yoon, Leslie Edwards, Robert A. Kuschner, Xiangui Lin, Stephen J. Thomas, Richard G. Jarman
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-35578-y

Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage
Cited by: 1
Author(s): Puleng Letuma, Yasir Arafat, Muhammad Mohsin Waqas, Feifan Lin, Wenxiong Lin, Yiyang Zhang, Mamello Masita, Kai Fan, Zhaowei Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-20414-0

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
Cited by: 53
Author(s): Stefano Campanaro, Laura Treu, Panagiotis Kougias, Xinyu Zhu, Irini Angelidaki
Software Mentions: 4
Published: over 6 years ago

10.1038/srep35272

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz
Cited by: 21
Author(s): Francisco J. R. C. Coelho, António Louvado, Patrícia M. Domingues, Daniel F. R. Cleary, Marina Ferreira, Adelaide Almeida, Ascensão Ravara, Ângela Cunha, Newton C. M. Gomes
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-27476-0

Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)
Cited by: 20
Author(s): Erin D. Scully, Scott M. Geib, Charles J. Mason, John E. Carlson, Ming Tien, Han Yi Chen, Chung‐Jui Tsai, Chung‐Jui Tsai, Kelli Hoover
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-49134-9

Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach
Cited by: 13
Author(s): Sohini Claverie, Alassane Ouattara, Murielle Hoareau, Denis Filloux, Arvind Varsani, Philippe Roumagnac, Darren P. Martin, Jean‐Michel Lett, Pierre Lefeuvre
Software Mentions: 4
Published: over 4 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: over 5 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: almost 9 years ago

10.1038/srep11353

Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments
Cited by: 17
Author(s): Caio Castro Freire, Atila Iamarino, Peinda O. Ly Soumaré, Ousmane Faye, Amadou Alpha Sall, Paolo M. A. Zanotto
Software Mentions: 4
Published: almost 9 years ago

10.1002/lno.11361

The global <i>Microcystis</i> 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: over 4 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: almost 8 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: about 5 years ago

10.1371/journal.pone.0224676

Molecular epidemiological characteristics of dengue virus carried by 34 patients in Guangzhou in 2018
Cited by: 2
Author(s): Feng Liao, Huini Chen, Jieliang Xie, Shaofeng Zhan, Pan Pan, Zizhao Lao, Yaohua Fan, L. C.-C. Lin, Yunfeng Lai, Shuangfeng Lin, Jianguo Wu, Xiaohong Liu, Geng Li
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0184401

Think globally, act locally: Phylodynamic reconstruction of infectious bronchitis virus (IBV) QX genotype (GI-19 lineage) reveals different population dynamics and spreading patterns when evaluated on different epidemiological scales
Cited by: 46
Author(s): Giovanni Franzo, Paola Massi, Claudia Maria Tucciarone, Ilaria Barbieri, Giovanni Tosi, L. Fiorentini, Massimo Ciccozzi, Antonio Llombart‐Bosch, Mattia Cecchinato, Ana Moreno
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.01272

Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis
Cited by: 8
Author(s): Jednipit Borthong, Ryosuke Omori, Chihiro Sugimoto, Orasa Suthienkul, Ryo Nakao, Kimihito Ito
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.01499

Genome Variation in the Model Halophilic Bacterium Salinibacter ruber
Cited by: 11
Author(s): Pedro González-Torres, Toni Gabaldón
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-13-345

Microbial transformation from normal oral microbiota to acute endodontic infections
Cited by: 115
Author(s): William W. L. Hsiao, Kevin L. Li, Zhenqiu Liu, Cheron Jones, Claire M. Fraser, Ashraf F. Fouad
Software Mentions: 3
Published: almost 12 years ago

10.3389/fmicb.2018.03336

iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities
Cited by: 45
Author(s): Sunil Nagpal, Mohammed Monzoorul Haque, Rashmi Singh, Sharmila S. Mande
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-018-4701-2

Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes
Cited by: 22
Author(s): Daniel R. Bogema, Melinda L. Micallef, Mengmeng Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling, Cheryl Jenkins
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.00056

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman
Cited by: 97
Author(s): K. R. Rempfert, Hannah M. Miller, Nicolas Bompard, Daniel Nothaft, Juerg M. Matter, P. B. Kelemen, Noah Fierer, Alexis S. Templeton
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-779

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments
Cited by: 59
Author(s): Imran Khan, Emanuel Maldonado, Vı́tor Vasconcelos, Stephen J. O’Brien, Warren E. Johnson, Agostinho Antunes
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2015.00146

A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens
Cited by: 60
Author(s): Enrique Zozaya‐Valdés, Suhelen Egan, Torsten Thomas
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0167383

Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients
Cited by: 3
Author(s): Israel Pagán, Patricia Rojas, José Tomás Ramos, África Holguín
Software Mentions: 3
Published: over 7 years ago

10.1186/s13568-016-0306-9

Microbial communities in pyrene amended soil–compost mixture and fertilized soil
Cited by: 12
Author(s): Iris K. U. Adam, M. M. L. Duarte, Jananan S. Pathmanathan, Anja Miltner, Thomas Brüls, Matthias Kästner
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0182235

Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats
Cited by: 33
Author(s): Leticia Abecia, Elisabeth Jiménez, Gonzalo Martínez Fernández, A. I. Martín-García, E. Ramos-Morales, Eric Pinloche, Stuart E. Denman, C. J. Newbold, D. R. Yáñez-Ruíz
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-16-S6-S2

Probabilistic topic modeling for the analysis and classification of genomic sequences
Cited by: 41
Author(s): Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-230X-9-95

Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers
Cited by: 252
Author(s): Lotta Krogius-Kurikka, Anna Lyra, Erja Malinen, Johannes Aarnikunnas, Jarno Tuimala, Lars Paulín, Harri Mäkivuokko, Kajsa Kajander, Airi Palva
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0105707

Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy
Cited by: 50
Author(s): Christine Bäuerl, María Carmen Collado, Manuel Zúñiga, E. Blas, Gaspar Pérez‐Martínez
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2016.00161

Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community
Cited by: 16
Author(s): Enrique Zozaya‐Valdés, Alexandra J. Roth‐Schulze, Torsten Thomas
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0091092

Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges
Cited by: 55
Author(s): Jonathan Kennedy, Burkhardt Flemer, Stephen A. Jackson, John P. Morrissey, Fergal O’Gara, Alan D. W. Dobson
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0228338

Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome
Cited by: 24
Author(s): Alessandra De Cesare, Claudia Sala, Gastone Castellani, Annalisa Astolfi, Valentina Indio, A. Giardini, Gerardo Manfreda
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0080589

Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, Botswana
Cited by: 31
Author(s): Vladimir Novitsky, Hermann Bussmann, Andrew Logan, Sikhulile Moyo, Erik van Widenfelt, Lillian Okui, Mompati Mmalane, Jeannie Baca, Linda B. Buck, Eleanor Phillips, David Todem, Mary Fran McLane, Quanhong Lei, Rui Wang, Joseph Makhema, Shahin Lockman, Victor DeGruttola, Max Essex
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2021.601253

Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae
Cited by: 18
Author(s): Feng-Chun Yang, Jeffery K. Tomberlin, Heather R. Jordan
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2148-7-67

Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen
Cited by: 20
Author(s): Sergios‐Orestis Kolokotronis, R. D. E. MacPhee, Alex D. Greenwood
Software Mentions: 3
Published: about 17 years ago

10.1186/s12862-016-0609-0

Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes
Cited by: 11
Author(s): Qian-Qian Zeng, Ke He, Dandan Sun, Mei-Ying Ma, Yaming Ge, Sheng‐Guo Fang, Qiu-Hong Wan
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-021-04316-z

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Cited by: 2
Author(s): Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch‐Mizrachi, Eric P. Nawrocki
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pntd.0005048

Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil
Cited by: 181
Author(s): Claire L. Donald, Benjamin Brennan, Stephanie L. Cumberworth, Veronica V. Rezelj, Jordan J. Clark, Marli Tenório Cordeiro, Rafael Freitas de Oliveira França, Lindomar Pena, Gavin S. Wilkie, Ana da Silva Filipe, Chris Davis, Joseph Hughes, Margus Varjak, Martin Selinger, Luíza Zuvanov, Ania M. Owsianka, Arvind H. Patel, John McLauchlan, Brett D. Lindenbach, Gamou Fall, Amadou Alpha Sall, Roman Biek, Jan Rehwinkel, Esther Schnettler, Alain Kohl
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0001910

Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa
Cited by: 24
Author(s): Andrew S. Beck, Hilda Guzmán, Li Li, Brett R. Ellis, Robert B. Tesh, Alan D.T. Barrett
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2148-11-72

Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract
Cited by: 19
Author(s): Emiliano Mancini, F. Tammaro, Francesco Baldini, Allegra Via, Domenico Raimondo, Phillip George, Paolo Audisio, Igor V. Sharakhov, Anna Tramontano, Flaminia Catteruccia, Alessandra della Torre
Software Mentions: 3
Published: about 13 years ago

10.3389/fmicb.2018.02045

Design of Primers for Evaluation of Lactic Acid Bacteria Populations in Complex Biological Samples
Cited by: 37
Author(s): Qiangchuan Hou, Xiaoye Bai, Weicheng Li, Xu Gao, Faming Zhang, Zhihong Sun, Heping Zhang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3001115

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen
Cited by: 165
Author(s): Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B. Singer, Maciej F. Boni, Philippe Lemey, Sergei L. Kosakovsky Pond, David L. Robertson
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2019.02258

Composition and Drivers of Gut Microbial Communities in Arctic-Breeding Shorebirds
Cited by: 44
Author(s): Kirsten Grond, Jorge W. Santo Domingo, Richard B. Lanctot, Ari Jumpponen, Rebecca L. Bentzen, Megan L. Boldenow, Stephen C. Brown, Bruce Casler, Jenny A. Cunningham, Andrew C. Doll, Scott Freeman, Brooke L. Hill, Steven J. Kendall, Eunbi Kwon, Joseph R. Liebezeit, Lisa Pirie‐Dominix, Jennie Rausch, Brett K. Sandercock
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0003336

The Plasmodium vivax Merozoite Surface Protein 3β Sequence Reveals Contrasting Parasite Populations in Southern and Northwestern Thailand
Cited by: 16
Author(s): Chaturong Putaporntip, Jun Miao, Napaporn Kuamsab, Jetsumon Sattabongkot, Jeeraphat Sirichaisinthop, Somchai Jongwutiwes, Liwang Cui
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2019.02408

Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica
Cited by: 14
Author(s): Yang Li, Qian‐Qian Cha, Yan-Ru Dang, Xiu-Lan Chen, Min Wang, Andrew McMinn, Giannina Espina, Yuzhong Zhang, Jenny M. Blamey, Qi‐Long Qin
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.639995

Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae
Cited by: 2
Author(s): Rachana Banerjee, Narendrakumar M. Chaudhari, Abhishake Lahiri, Anupam Gautam, Debaleena Bhowmik, Chitra Dutta, Sujay Chattopadhyay, Daniel H. Huson, Sandip Paul
Software Mentions: 3
Published: almost 3 years ago

10.3389/fvets.2020.00176

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks
Cited by: 1
Author(s): Moh A. Alkhamis, Chong Li, Montserrat Torremorell
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2019.01708

Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene
Cited by: 14
Author(s): Yanzhi Mao, Xuhong Sun, Jianguo Shen, Fangluan Gao, Guangwei Qiu, Teng Wang, Xianzhou Nie, Wei Zhang, Yanling Gao, Yuling Bai
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12917-019-2035-1

Phylogenetic evidence of a novel lineage of canine pneumovirus and a naturally recombinant strain isolated from dogs with respiratory illness in Thailand
Cited by: 17
Author(s): Chutchai Piewbang, Somporn Techangamsuwan
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2014.00034

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN
Cited by: 88
Author(s): Marc G. Dumont, Claudia Lüke, Yangfan Deng, Peter Frenzel
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2021.633710

Viruses Without Borders: Global Analysis of the Population Structure, Haplotype Distribution, and Evolutionary Pattern of Iris Yellow Spot Orthotospovirus (Family Tospoviridae, Genus Orthotospovirus)
Cited by: 2
Author(s): Afsha Tabassum, S. V. Ramesh, Ying Zhai, Romana Iftikhar, Cristián Olaya
Software Mentions: 3
Published: over 2 years ago

10.7717/peerj.12000

Virulence effector SidJ evolution in <i>Legionella pneumophila</i> is driven by positive selection and intragenic recombination
Cited by: 1
Author(s): Xiao-Yong Zhan, Jin-Lei Yang, Xuefu Zhou, Yichao Qian, Ke Huang, Hongyan Sun, Huacheng Wang, Yang Leng, Bihui Huang, Yulong He
Software Mentions: 3
Published: almost 3 years ago

10.3390/v13071412

Phylogenetic Analysis of Massilia phlebovirus in Portugal
Cited by: 8
Author(s): Fátima Amaro, Líbia Zé-Zé, José Lourenço, Marta Giovanetti, Stefanie Becker, Maria João Alves
Software Mentions: 3
Published: almost 3 years ago

10.1111/eva.12515

A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America
Cited by: 37
Author(s): Jakob Trimpert, Nicole Groenke, Maria Jenckel, Shulin He, Dušan Kunec, Moriah L. Szpara, Stephen J. Spatz, Nikolaus Osterrieder, Dino P. McMahon
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2018.00359

Evidence for Introgression Among Three Species of the Anastrepha fraterculus Group, a Radiating Species Complex of Fruit Flies
Cited by: 14
Author(s): Fernando Dı́az, André Luís A. Lima, Aline Minali Nakamura, Felippe Fernandes, Iderval Sobrinho, Reinaldo Alves de Brito
Software Mentions: 3
Published: over 5 years ago

10.1111/j.1462-2920.2008.01706.x

probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity
Cited by: 175
Author(s): Alexander Loy, Roland Arnold, Patrick Tischler, Thomas Rattei, Michael Wagner, Matthias Horn
Software Mentions: 3
Published: over 15 years ago

10.1111/eva.12459

Adaptive evolution and demographic history contribute to the divergent population genetic structure of<i>Potato virus Y</i>between China and Japan
Cited by: 25
Author(s): Fangluan Gao, Wenchao Zou, Liji Xie, Jiasui Zhan
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2020.576738

In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides
Cited by: 8
Author(s): Yasmin Neves Vieira Sabino, Katialaine Corrêa de Araújo, Fábia Giovana do Val de Assis, Sofia Magalhães Moreira, Thaynara da Silva Lopes, Tiago Antônio de Oliveira Mendes, Sharon Huws, Hilário Cuquetto Mantovani
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2015.00746

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils
Cited by: 19
Author(s): C. Ryan Penton, Derek St. Louis, Amanda Pham, James R. Cole, Liyou Wu, Yiqi Luo, E. A. G. Schuur, Jizhong Zhou, James M. Tiedje
Software Mentions: 3
Published: almost 9 years ago

10.1186/1752-0509-7-S4-S13

Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems
Cited by: 9
Author(s): Lei Shang, David P. Gardner, Wei Xu, Jamie J. Cannone, Daniel P. Miranker, Stuart Ozer, Robin R. Gutell
Software Mentions: 3
Published: over 10 years ago

10.1128/AEM.00134-18

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria
Cited by: 54
Author(s): Sander Wuyts, Wannes Van Beeck, Eline Oerlemans, Stijn Wittouck, Ingmar Claes, Ilke De Boeck, Stefan Weckx, Bart Lievens, Luc De Vuyst, Sarah Lebeer
Software Mentions: 3
Published: almost 6 years ago

10.3390/v7031454

Interaction Research on the Antiviral Molecule Dufulin Targeting on Southern Rice Black Streaked Dwarf Virus P9-1 Nonstructural Protein
Cited by: 23
Author(s): Zhenchao Wang, Xiangyang Li, Wenli Wang, Weiying Zhang, Yu Lu, Deyu Hu, Baoan Song
Software Mentions: 3
Published: about 9 years ago

10.3390/v8060153

Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
Cited by: 36
Author(s): Pedro Luis Ramos-González, Camila Chabi-Jesus, Orlene Guerra‐Peraza, Michèle Claire Breton, Gabriella Dias Arena, Maria Andréia Nunes, Elliot Watanabe Kitajima, Marcos Antônio Machado, Juliana Freitas-Astúa
Software Mentions: 3
Published: almost 8 years ago

10.1002/ece3.6800

Genetic diversity analysis of papaya leaf distortion mosaic virus isolates infecting transgenic papaya “Huanong No. 1” in South China
Cited by: 0
Author(s): Cuiping Mo, Zilin Wu, Hengping Xie, Shuguang Zhang, Huaping Li
Software Mentions: 3
Published: over 3 years ago

10.3390/v12101080

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd
Cited by: 10
Author(s): Alba Folgueiras-González, Robin van den Braak, Bartjan Simmelink, Martin Deijs, Lia van der Hoek, Ad de Groof
Software Mentions: 3
Published: over 3 years ago

10.3390/v13081476

Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches
Cited by: 6
Author(s): Lester J. Pérez, Gavin Cloherty, Michael G. Berg
Software Mentions: 3
Published: almost 3 years ago

10.1111/eva.12629

Evidence for intragenic recombination and selective sweep in an effector gene of <i>Phytophthora infestans</i>
Cited by: 27
Author(s): Lina Yang, Hai-Bing Ouyang, Zhi-Guo Fang, Weihua Zhu, E‐Jiao Wu, Guihuo Luo, Li‐Ping Shang, Jiasui Zhan
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.650

Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (<i>Phoxinus phoxinus</i>)
Cited by: 13
Author(s): Hélène Collin, Reto Burri, Fabien Comtesse, Luca Fumagalli
Software Mentions: 3
Published: almost 11 years ago

10.1002/ece3.2460

Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to <i>Bacillus thuringiensis</i>
Cited by: 23
Author(s): V. V. Martemyanov, І. A. Belousova, Sergey V. Pavlushin, Ivan M. Dubovskiy, Nikita I. Ershov, Tatyana Alikina, Мarsel R. Kabilov, В. В. Глупов
Software Mentions: 3
Published: over 7 years ago

10.1002/ece3.5373

Origin and evolution of the major histocompatibility complex class I region in eutherian mammals
Cited by: 19
Author(s): Shamshidin Abduriyim, Da Hu Zou, Huabin Zhao
Software Mentions: 3
Published: almost 5 years ago

10.1093/ve/veab020

The evolutionary dynamics of endemic human coronaviruses
Cited by: 37
Author(s): Wendy K Jo, Christian Drosten, Jan Felix Drexler
Software Mentions: 3
Published: over 3 years ago

10.1093/ve/veab060

Integrating animal movements with phylogeography to model the spread of PRRSV in the USA
Cited by: 13
Author(s): Dennis N. Makau, Moh A. Alkhamis, Igor Adolfo Dexheimer Paploski, Cesar Corzo, Samantha Lycett, Kimberly VanderWaal
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pone.0174765

A comparison of sampling methods for examining the laryngeal microbiome
Cited by: 7
Author(s): Alissa S. Hanshew, Marie E. Jetté, Stephanie N. Tadayon, Susan L. Thibeault
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2180-12-S1-S13

Diversity and recombination in Wolbachia and Cardinium from Bryobia spider mites
Cited by: 49
Author(s): V.I.D. Ros, Vicki M. Fleming, Edward J. Feil, Johannes A. J. Breeuwer
Software Mentions: 3
Published: over 12 years ago

10.1093/ve/veaa056

The evolutionary history and global spatio-temporal dynamics of potato virus Y
Cited by: 14
Author(s): Fangluan Gao, Shusuke Kawakubo, Simon Y. W. Ho, Kazusato Ohshima
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0060116

Insight into the Evolution of the Histidine Triad Protein (HTP) Family in Streptococcus
Cited by: 20
Author(s): Zhu‐Qing Shao, Yanmei Zhang, Xiuzhen Pan, Bin Wang, Jian-Qun Chen
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0157046

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules
Cited by: 29
Author(s): James E. McDonald, Niels Larsen, Andrea Pennington, John Connolly, Corrin Wallis, David J. Rooks, Neil Hall, Alan J. McCarthy, Heather E. Allison
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0093945

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments
Cited by: 52
Author(s): Daniel P. R. Herlemann, Marcus Manecki, Christian Meeske, Falk Pollehne, Matthias Labrenz, Detlef E. Schulz‐Bull, Thorsten Dittmar, Klaus Jürgens
Software Mentions: 3
Published: about 10 years ago

10.1186/1743-422X-6-208

Genetic diversity and phylogeography of Seewis virus in the Eurasian common shrew in Finland and Hungary
Cited by: 46
Author(s): Hae Ji Kang, Satoru Arai, Andrew G. Hope, Jin Won Song, Joseph A. Cook, Richard Yanagihara
Software Mentions: 3
Published: over 14 years ago

10.1093/ve/vez020

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015
Cited by: 13
Author(s): Sean M. Bialosuknia, Yi Tan, Steven D. Zink, Cheri A. Koetzner, Joseph G. Maffei, Rebecca Halpin, Emmi A Mueller, M. A. Novotny, Meghan H. Shilts, Nadia Fedorova, Paolo Amedeo, Suman Das, Brett E. Pickett, Laura D. Kramer, Alexander T. Ciota
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0035216

Phylogeography of Rift Valley Fever Virus in Africa Reveals Multiple Introductions in Senegal and Mauritania
Cited by: 26
Author(s): Peinda O. Ly Soumaré, Caio Castro Freire, Ousmane Faye, Mawlouth Diallo, Juliana Velasco Castro de Oliveira, Paolo Marinho de Andrade Zanotto, Amadou Alpha Sall
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0132248

Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts
Cited by: 22
Author(s): Will A. Overholt, Rodrigo Díaz, Erin N. Rosskopf, Stefan J. Green, William A. Overholt
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0071565

Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses
Cited by: 5
Author(s): Hsiang-Iu Wang, Chih-Hung Chang, Po‐Hung Lin, Hui-Chuan Fu, Chuan‐Yi Tang, Hsin-Hung Yeh
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0175416

Homologous recombination is a force in the evolution of canine distemper virus
Cited by: 27
Author(s): Chaowen Yuan, Wenxin Liu, Yingbo Wang, Jin-Long Hou, Liguo Zhang, Guoqing Wang
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pntd.0002411

Phylogeography of Japanese Encephalitis Virus: Genotype Is Associated with Climate
Cited by: 95
Author(s): Amy J. Schuh, Melissa J. Ward, Andrew J. Leigh Brown, Alan D.T. Barrett
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0116230

Evaluation of Simultaneous Nutrient and COD Removal with Polyhydroxybutyrate (PHB) Accumulation Using Mixed Microbial Consortia under Anoxic Condition and Their Bioinformatics Analysis
Cited by: 10
Author(s): Jyotsnarani Jena, Ravindra Kumar, Anshuman Dixit, Satish Kumar Pandey, Trupti Das
Software Mentions: 3
Published: over 9 years ago

10.3390/vaccines9091019

The Importance of Quality Control of LSDV Live Attenuated Vaccines for Its Safe Application in the Field
Cited by: 16
Author(s): Andy Haegeman, Ilse De Leeuw, Meruyert A. Saduakassova, Willem Van Campe, Laetitia Aerts, Wannes Philips, Akhmetzhan A. Sultanov, Laurent Mostin, Kris De Clercq
Software Mentions: 3
Published: over 2 years ago