Ecosyste.ms: Papers

10.1371/journal.pone.0255169

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts
Cited by: 25
Author(s): Rafail Nikolaos Tasakis, Georgios Samaras, Anna Jamison, Michelle Lee, Alexandra Paulus, Gabrielle Whitehouse, Laurent Verkoczy, F. Nina Papavasiliou, Marilyn Diaz
Software Mentions: 8
Published: over 3 years ago

10.3389/fgene.2021.711437

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
Cited by: 23
Author(s): Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
Software Mentions: 5
Published: over 3 years ago

10.12688/wellcomeopenres.16661.2

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
Cited by: 120
Author(s): Áine O’Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Isaac I Bogoch, Kamran Khan, Jane P. Messina, Houriiyah Tegally, Richard Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse A. Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo I. Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita Desai, Vasanthapuram Ravi, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Antonio Parisi, Angelica Bianco, Darı́o Garcı́a de Viedma, Sergio Buenestado‐Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William D. Rawlinson, Ira W. Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward C. Holmes, Kirsten St. George, Erica Lasek‐Nesselquist, Reina S. Sikkema, Bas B. Oude Munnink, Marion Koopmans, Mia Brytting, Vannavada Sudha Rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin K. Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine V. F. Carrington, Nikita Sahadeo, Michael J. Carr, Gabo Gonzalez, Search Alliance San Diego, SeqCOVID-Spain, Túlio de Oliveira, Nuno Rodrigues Faria, Andrew Rambaut, Moritz U. G. Kraemer
Software Mentions: 5
Published: over 3 years ago

10.1093/bib/bbaa232

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Cited by: 99
Author(s): Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Alex Bateman, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F Löchel, Marı́a Jesús Martı́n, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine O’Toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
Software Mentions: 4
Published: about 4 years ago

10.1093/database/baw063

PGD: a pangolin genome hub for the research community
Cited by: 4
Author(s): Tze King Tan, Ka Yun Tan, Riitta Hari, Aini Mohamed Yusoff, George T.F. Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mikhail Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O’Brien, Siew Woh Choo
Software Mentions: 4
Published: almost 9 years ago

10.1016/j.patter.2021.100212

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Cited by: 26
Author(s): Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti‐Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
Software Mentions: 4
Published: almost 4 years ago

10.1093/molbev/msaa316

Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny
Cited by: 36
Author(s): Lenore Pipes, Hongru Wang, John P. Huelsenbeck, Rasmus Nielsen
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-021-04294-2

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
Cited by: 22
Author(s): Phuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura
Software Mentions: 3
Published: over 3 years ago

10.1093/ve/veab064

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
Cited by: 649
Author(s): Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abudahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W. Attwood, David M. Aanensen, Edward C. Holmes, Oliver G. Pybus, Andrew Rambaut
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0258019

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh
Cited by: 12
Author(s): Ishtiaque Ahammad, Mohammad Uzzal Hossain, Ashikur Rahman, Zeshan Mahmud Chowdhury, Arittra Bhattacharjee, Keshob Chandra Das, Chaman Ara Keya, Md. Salimullah
Software Mentions: 3
Published: about 3 years ago

10.1093/infdis/jiab368

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion
Cited by: 122
Author(s): Isabella Ferreira, Steven Kemp, Rawlings P. Datir, Akatsuki Saito, Bo Meng, Partha Rakshit, Akifumi Takaori‐Kondo, Yusuke Kosugi, Keiya Uriu, Izumi Kimura, Kotaro Shirakawa, Adam Abdullahi, Anurag Agarwal, Seiya Ozono, Kenzo Tokunaga, Kei Sato, Gupta Rk
Software Mentions: 3
Published: over 3 years ago

10.1016/j.isci.2021.102116

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity
Cited by: 60
Author(s): Alex Graudenzi, Davide Maspero, Fabrizio Angaroni, Rocco Piazza, Daniele Ramazzotti
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.665041

A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity
Cited by: 19
Author(s): Carlos Farkas, Andy Mella, Maxime Turgeon, Jody J. Haigh
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12091428

Different Strategies for the Identification of SARS-CoV-2 Variants in the Laboratory Practice
Cited by: 7
Author(s): Federico Anaclerio, Rossella Ferrante, Domitilla Mandatori, Ivana Antonucci, Matteo Capanna, Verena Damiani, Pamela Di Tomo, Rossella Ferrante, Marianna Ranaudo, Vincenzo De Laurenzi, Liborio Stuppia, Simone De Fabritiis
Software Mentions: 2
Published: over 3 years ago

10.1101/2021.04.23.441209

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring
Cited by: 5
Author(s): Sofiya K Garushyants, Igor B. Rogozin, Eugene V. Koonin
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.01610-20

Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2
Cited by: 203
Author(s): Yvonne C. F. Su, Danielle E. Anderson, Barnaby Edward Young, Martin Linster, Feng Zhu, Jayanthi Jayakumar, Zhuang Yan, Shirin Kalimuddin, Jenny Low, Chee Wah Tan, Wan Ni Chia, Tze Minn Mak, Sophie Octavia, Jean‐Marc Chavatte, Raphael Tze Chuen Lee, Surinder Pada, Seow Yen Tan, Louisa Sun, Gabriel Yan, Sebastian Maurer‐Stroh, Ian H. Mendenhall, Yee‐Sin Leo, David C. Lye, Lin‐Fa Wang, Gavin Smith
Software Mentions: 2
Published: over 4 years ago

10.1101/2021.08.31.21262938

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
Cited by: 18
Author(s): Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Petrone Me, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, Chantal B.F. Vogels, Mallery I. Breban, Claire Duvallet, Kyle A. McElroy, Newsha Ghaeli, Maxim Imakaev, Malaika F. Mckenzie-Bennett, Keith Robison, Alex Plocik, Rebecca Schilling, M Pierson, Rebecca Littlefield, Michelle Spencer, Birgitte B. Simen, Yale SARS-CoV Genomic Surveillance Initiative, William P. Hanage, Nathan D. Grubaugh, Jordan Peccia, Michael Baym
Software Mentions: 2
Published: over 3 years ago

10.3390/v13081510

Severe SARS-CoV-2 Infection in a Cat with Hypertrophic Cardiomyopathy
Cited by: 28
Author(s): Francisco R. Carvallo, Mathias Martins, Lok R. Joshi, Leonardo Cardia Caserta, Patrick K. Mitchell, Thomas E. Cecere, Sandy Hancock, Erin L. Goodrich, Julia Murphy, Diego G. Diel
Software Mentions: 2
Published: over 3 years ago

10.1038/srep28199

De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin
Cited by: 13
Author(s): Aini Mohamed Yusoff, Tze King Tan, Riitta Hari, Klaus Peter Koepfli, Wei Yee Wee, Agostinho Antunes, Frankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Kayal Vizi Karuppannan, George T.F. Wong, Leonard Lipovich, Wesley C. Warren, Stephen J. O’Brien, Siew Woh Choo
Software Mentions: 1
Published: over 8 years ago

10.1101/2020.09.23.310565

COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest
Cited by: 13
Author(s): Albert T. Chen, Kevin Altschuler, Shing Hei Zhan, Yujia Alina Chan, Benjamin E. Deverman
Software Mentions: 1
Published: about 4 years ago

10.1128/JVI.00711-20

An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)
Cited by: 112
Author(s): La Rinda A. Holland, Emily A Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue, Matthew Scotch, Efrem S. Lim
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.63409

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest
Cited by: 86
Author(s): Albert T. Chen, Kevin Altschuler, Shing Hei Zhan, Yujia Alina Chan, Benjamin E. Deverman
Software Mentions: 1
Published: almost 4 years ago

10.1128/mSphere.00180-21

Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020
Cited by: 7
Author(s): Evangelia Georgia Kostaki, Georgios A. Pavlopoulos, Kleio‐Maria Verrou, Giannis Ampatziadis-Michailidis, Vaggelis Harokopos, Pantelis Hatzis, Panagiotis Moulos, Nikolaos Siafakas, Spyridon Pournaras, Christos Hadjichristodoulou, Fani Chatzopoulou, Dimitrios Chatzidimitriou, Periklis Panagopoulos, Panagiota Lourida, Aikaterini Argyraki, Theodoros Lytras, Spyros Sapounas, Gerasimos Gerolymatos, Georgios Panagiotakopoulos, Panagiotis Prezerakos, Sotirios Tsiodras, Vana Sypsa, Angelos Hatzakis, Cleo Anastassopoulou, Nikolaos Spanakis, Athanasios Tsakris, Meletios A. Dimopoulos, Αναστασία Κοτανίδου, Petros P. Sfikakis, Γεώργιος Κόλλιας, Gkikas Magiorkinis, Dimitrios Paraskevis
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00410-21

Genome Sequences of SARS-CoV-2 P.1 (Variant of Concern) and P.2 (Variant of Interest) Identified in Uruguay
Cited by: 7
Author(s): Yanina Panzera, Natalia Goñi, Lucía Calleros, Natália Ramos, Sandra Frabasile, Ana Marandino, Gonzalo Tomás, Claudia Techera, Sofía Grecco, Eddie Fuques, Viviana Ramas, Leticia Cóppola, María Rosa Flieller, Noelia Morel, Maria-Noel Cortinas, Cristina Mogdasy, Juan Arbiza, Adriana Delfraro, Ruben Pérez, Héctor Chiparelli
Software Mentions: 1
Published: over 3 years ago

10.2807/1560-7917.ES.2021.26.30.2100673

Vaccine breakthrough infection and onward transmission of SARS-CoV-2 Beta (B.1.351) variant, Bavaria, Germany, February to March 2021
Cited by: 21
Author(s): Inge Kroidl, Ingo Mecklenburg, Peter Schneiderat, Katharina Müller, Philipp Girl, Roman Wölfel, Andreas Sing, Alexandra Dangel, Andreas Wieser, Michael Höelscher
Software Mentions: 1
Published: over 3 years ago

10.1590/0074-02760200310

Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil
Cited by: 42
Author(s): Valdinete Alves do Nascimento, André de Lima Guerra Corado, Fernanda Nascimento, Ana Carolina Carioca da Costa, Débora Duarte, Sérgio Luíz Bessa Luz, Luciana Mara Fé-Gonçalves, Michele Silva de Jesus, Cristiano Fernandes da Costa, Edson Delatorre, Felipe Gomes Naveca
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2021.653986

Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan–Brazilian Border
Cited by: 13
Author(s): Daiana Mir, Natalia Rego, Paola Cristina Resende, Fernando López Tort, Tamara Fernández-Calero, Verónica Noya, Mariana Brandes, Tania Possi, Mailén Arleo, Natalia Reyes, Matías Victoria, Andrés Lizasoain, Matías Castells, Leticia Maya, Matías Salvo, Tatiana Schäffer Gregianini, Marilda Tereza Mar da Rosa, Letícia Garay Martins, Cecilia Alonso, Yasser Vega, Cecilia Salazar, Ignacio Ferrés, Pablo Smircich, José Sotelo Silveira, Rafael Sebastián Fort, Cecilia Mathó, Ighor Arantes, Luciana Appolinario, Ana Carolina da Fonseca Mendonça, María José Benítez-Galeano, Camila Simoes, Martín Graña, Fernando do Couto Motta, Marilda Mendonça Siqueira, Gonzalo Bello, Rodney Colina, Lucía Spangenberg
Software Mentions: 1
Published: over 3 years ago

10.1101/2020.04.17.20069641

An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)
Cited by: 15
Author(s): LaRinda A Holland, Emily A Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue, Matthew Scotch, Efrem S. Lim
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.11015

Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon
Cited by: 16
Author(s): Rita Feghali, Georgi Merhi, Aurélia Kwasiborski, Véronique Hourdel, Nada Ghosn, Sima Tokajian
Software Mentions: 1
Published: almost 4 years ago