Ecosyste.ms: Papers

10.1186/s40168-018-0507-3

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses
Cited by: 64
Author(s): Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez, Alberto López-Bueno
Software Mentions: 6
Published: over 6 years ago

10.12688/f1000research.13934.2

shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data
Cited by: 0
Author(s): Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 6 years ago

10.3390/v11060484

Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Cited by: 24
Author(s): René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John C. Anders, Antonis Chatzinotas
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0171333

Error baseline rates of five sample preparation methods used to characterize RNA virus populations
Cited by: 20
Author(s): Jeffrey R. Kugelman, Michael R. Wiley, Elyse R. Nagle, Daniel Reyes, B Pfeffer, Jens H. Kuhn, Mariano Sánchez-Lockhart, Gustavo Palacios
Software Mentions: 2
Published: over 7 years ago

10.3390/v8020042

Viruses Causing Gastroenteritis: The Known, The New and Those Beyond
Cited by: 65
Author(s): Bas B. Oude Munnink, Lia van der Hoek
Software Mentions: 1
Published: over 8 years ago

10.3390/v12080897

Rabbit Hemorrhagic Disease Virus Isolated from Diseased Alpine Musk Deer (Moschus sifanicus)
Cited by: 5
Author(s): Shijun Bao, Kai Nan An, Chunguo Liu, Xiaoyong Xing, Xiang Fu, Huiwen Xue, Wen Fang, Xijun He, Jingfei Wang
Software Mentions: 1
Published: about 4 years ago

10.3390/v13020203

Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens
Cited by: 5
Author(s): Annika Brinkmann, Steven Uddin, Eva Krause, Rebecca Surtees, Ender Dinçer, Sırrı Kar, Sabri Hacıoğlu, Aykut Özkul, Koray Ergünay, Andreas Nitsche
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pntd.0006576

A comparative genome analysis of Rift Valley Fever virus isolates from foci of the disease outbreak in South Africa in 2008-2010
Cited by: 11
Author(s): Moabi R. Maluleke, Maanda Noaxe Phosiwa, Antoinette van Schalkwyk, George Michuki, Baratang A. Lubisi, Phemelo S. Kegakilwe, Stephen J. Kemp, Phelix A.O. Majiwa
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0027483

Astrovirus Infection in Hospitalized Infants with Severe Combined Immunodeficiency after Allogeneic Hematopoietic Stem Cell Transplantation
Cited by: 108
Author(s): Werner Wunderli, Astrid Meerbach, Tayfun Guengoer, Christoph Berger, Oliver Greiner, Rosmarie Caduff, Alexandra Trkola, Walter Bossart, Daniel Gerlach, Manuel Schibler, Samuel Cordey, Thomas Alexander Mckee, Sandra Van Belle, Laurent Kaiser, Caroline Tapparel
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0076144

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing
Cited by: 44
Author(s): Toon Rosseel, Steven Van Borm, Frank Vandenbussche, Bernd Hoffmann, Thierry van den Berg, Dirk W. Höper
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0199714

An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates
Cited by: 26
Author(s): Stephanie Goya, Laura Valinotto, Estefanía Tittarelli, Gabriel Lihue Rojo, Mercedes Soledad Nabaes Jodar, Alexander L. Greninger, Jonathan Zaiat, Marcelo A. Martí, Alicia Mistchenko, Mariana Viegas
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0178433

Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics
Cited by: 30
Author(s): Paloma S Moreno, Josef Wagner, Caroline Mansfield, Matthew P. Stevens, James R. Gilkerson, Carl D. Kirkwood
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0013583

Identification and Nearly Full-Length Genome Characterization of Novel Porcine Bocaviruses
Cited by: 98
Author(s): Wei Cheng, Jin Song Li, Can Ping Huang, Dong ping Yao, Na Liu, Shu xian Cui, Jin Yu, Zhao Jun Duan
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0187780

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)
Cited by: 12
Author(s): Mette Myrmel, Veslemøy Sunniva Oma, Mamata Khatri, Hanne Hellerud Hansen, Maria Stokstad, Mikael Berg, Anne-Lie Blomström
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcimb.2020.565591

Amplicon-Based, Next-Generation Sequencing Approaches to Characterize Single Nucleotide Polymorphisms of Orthohantavirus Species
Cited by: 11
Author(s): Martha J. Taylor, Evan P. Williams, Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew, Colleen B. Jonsson
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2021.621719

High Throughput Sequencing for the Detection and Characterization of RNA Viruses
Cited by: 25
Author(s): Amy Fitzpatrick, Agnieszka Rupnik, Helen O’Shea, Fiona Crispie, Sinéad Keaveney, Paul D. Cotter
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-53043-2

Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues
Cited by: 20
Author(s): Jin Sun No, Won Keun Kim, Seungchan Cho, Seung Ho Lee, Jeong Ah Kim, Dae-Sang Lee, Dong Hyun Song, Se Hun Gu, Seong Tae Jeong, Michael R. Wiley, Gustavo Palacios, Jin Won Song
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-9-5

Viral genome sequencing by random priming methods
Cited by: 277
Author(s): Appolinaire Djikeng, Rebecca Halpin, Ryan Kuzmickas, Jay V. DePasse, Jeremy I. Feldblyum, Naomi Sengamalay, Claudio L. Afonso, Xinsheng Zhang, Norman G. Anderson, Elodie Ghedin, David Spiro
Software Mentions: 1
Published: almost 17 years ago

10.1128/mSystems.00039-15

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
Cited by: 27
Author(s): Lindsey A. Moser, Lisbeth Ramírez-Carvajal, Vinita Puri, Steven J. Pauszek, Krystal Matthews, Kari A. Dilley, Clancy Mullan, Jennifer McGraw, Michael M. Khayat, Karen Beeri, Anthony Yee, Vivien G. Dugan, Mark T. Heise, Matthew B. Frieman, Luis L. Rodrı́guez, Kristen A. Bernard, David E. Wentworth, Timothy B. Stockwell, Reed S. Shabman
Software Mentions: 1
Published: over 8 years ago

10.1186/1743-422X-10-181

Sequencing viral genomes from a single isolated plaque
Cited by: 16
Author(s): Jessica DePew, Bin Zhou, Jamison McCorrison, David E. Wentworth, Janaki Purushe, G. I. Koroleva, Derrick E. Fouts
Software Mentions: 1
Published: over 11 years ago

10.1186/s12985-014-0203-2

Identification and genomic characterization of a novel porcine parvovirus (PPV6) in china
Cited by: 54
Author(s): Jielei Ni, Caixia Qiao, Xue Han, Tao Han, Wenhua Kang, Zhanchao Zi, Zhen Cao, Xinyan Zhai, Cai Xue-peng
Software Mentions: 1
Published: almost 10 years ago

10.3390/v1020084

Molecular Characterization of Viruses from Clinical Respiratory Samples Producing Unidentified Cytopathic Effects in Cell Culture
Cited by: 6
Author(s): Yacine Abed, Guy Boivin
Software Mentions: 1
Published: over 15 years ago