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original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2025―Sep―19 |
Predicting the Trend of SARS-CoV-2 Mutation Frequencies Using Historical Data |
Xinyu Zhou, Yi Yan, Kevin Hu, Haixu Tang, Yijie Wang, Lu Wang, Chi Zhang, Sha Cao, Zhiyong Lu |
| 2 |
[GO] |
2025―Sep―19 |
Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows |
Rok Kogoj, Mauro Petrillo, Samo Zakotnik, Alen Suljič, Miša Korva, Gabriele Leoni, Inanc Birol |
| 3 |
[GO] |
2025―Sep―10 |
TransFactor-Prediction of pro-viral SARS-CoV-2 host factors using a protein language model |
Yang An, Valter Bergant, Samuele Firmani, Corinna Grünke, Batiste Bonnal, Alexander Henrici, Andreas Pichlmair, Benjamin Schubert, Annalisa Marsico, Jianlin Cheng |
| 4 |
[GO] |
2025―Jun―28 |
Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity specific gene networks |
Heewon Park, Seiya Imoto, Satory Miyano, Pier Luigi Martelli |
| 5 |
[GO] |
2025―Feb―08 |
APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19 |
George I Gavriilidis, Vasileios Vasileiou, Stella Dimitsaki, Georgios Karakatsoulis, Antonis Giannakakis, Georgios A Pavlopoulos, Fotis Psomopoulos, Pier Luigi Martelli |
| 6 |
[GO] |
2024―Nov―04 |
ViralPrimer: a Web Server to Monitor Viral Nucleic Acid Amplification Tests’ Primer Efficiency during Pandemics, with Emphasis on SARS-CoV-2 and Mpox |
Norbert Deutsch, Zsuzsanna Dosztányi, István Csabai, Anna Medgyes-Horváth, Orsolya Anna Pipek, József Stéger, Krisztián Papp, Dávid Visontai, Gábor Erdős, Anikó Mentes, Christina Kendziorski |
| 7 |
[GO] |
2024―Oct―27 |
Correction to: Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students |
|
| 8 |
[GO] |
2024―Sep―03 |
SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes |
William Boulton, Fatma Rabia Fidan, Hubert Denise, Nicola De Maio, Nick Goldman, Janet Kelso |
| 9 |
[GO] |
2024―Jun―28 |
Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions |
Daniel Platt, Aritra Bose, Kahn Rhrissorrakrai, Chaya Levovitz, Laxmi Parida |
| 10 |
[GO] |
2024―Apr―12 |
Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students |
Pavlin G Poličar, Martin Špendl, Tomaž Curk, Blaž Zupan |
| 11 |
[GO] |
2024―Feb―20 |
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment |
Zuher Jahshan, Leonid Yavits, Alfonso Valencia |
| 12 |
[GO] |
2023―Oct―17 |
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites |
Shihu Jiao, Xiucai Ye, Chunyan Ao, Tetsuya Sakurai, Quan Zou, Lei Xu, Janet Kelso |
| 13 |
[GO] |
2023―Aug―30 |
Tracking and curating putative SARS-CoV-2 recombinants with RIVET |
Kyle Smith, Cheng Ye, Yatish Turakhia, Janet Kelso |
| 14 |
[GO] |
2023―May―25 |
DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response |
Zhijian Huang, Pan Zhang, Lei Deng |
| 15 |
[GO] |
2022―Nov―16 |
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19 |
Henry Cousins, Taryn Hall, Yinglong Guo, Luke Tso, Kathy T H Tzeng, Le Cong, Russ B Altman, Alfonso Valencia |
| 16 |
[GO] |
2022―Oct―14 |
Common data model for COVID-19 datasets |
Philipp Wegner, Geena Mariya Jose, Vanessa Lage-Rupprecht, Sepehr Golriz Khatami, Bide Zhang, Stephan Springstubbe, Marc Jacobs, Thomas Linden, Cindy Ku, Bruce Schultz, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Alfonso Valencia |
| 17 |
[GO] |
2022―Aug―29 |
CovidGraph: A Graph to fight COVID-19 |
Lea Gütebier, Tim Bleimehl, Ron Henkel, Jamie Munro, Sebastian Müller, Axel Morgner, Jakob Laenge, Anke Pachauer, Alexander Erdl, Jens Weimar, Kirsten Walther Langendorf, Vincent Vialard, Thorsten Liebig, Martin Preusse, Dagmar Waltemath, Alexander Jarasch, Alfonso Valencia |
| 18 |
[GO] |
2022―Jul―21 |
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants |
Gabriel Cia, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci, Pier Luigi Martelli |
| 19 |
[GO] |
2022―Jul―08 |
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance |
Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M Bartoszewicz, Sebastian Beyvers, Marius A Dieckmann, Ulrich Genske, Sven H Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y Renard, Stephan Fuchs, Janet Kelso |
| 20 |
[GO] |
2022―Jun―30 |
Ab-CoV: a curated database for binding affinity and neutralization profiles of coronavirus related antibodies |
Puneet Rawat, Divya Sharma, R Prabakaran, Fathima Ridha, Mugdha Mohkhedkar, Vani Janakiraman, M Michael Gromiha, Peter Robinson |
| 21 |
[GO] |
2022―Jun―22 |
matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 |
Cheng Ye, Bryan Thornlow, Angie Hinrichs, Alexander Kramer, Cade Mirchandani, Devika Torvi, Robert Lanfear, Russell Corbett-Detig, Yatish Turakhia, Russell Schwartz |
| 22 |
[GO] |
2022―Jun―01 |
VOC-alarm: Mutation-based prediction of SARS-CoV-2 variants of concern |
Hongyu Zhao, Kun Han, Chao Gao, Vithal Madhira, Umit Topaloglu, Yong Lu, Guangxu Jin, Alfonso Valencia |
| 23 |
[GO] |
2022―May―10 |
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
Martin Hunt, Jeremy Swann, Bede Constantinides, Philip W Fowler, Zamin Iqbal, Can Alkan |
| 24 |
[GO] |
2022―Mar―24 |
EDGE COVID-19: A Web Platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts |
Chien-Chi Lo, Migun Shakya, Ryan Connor, Karen Davenport, Mark Flynn, Adán Myers y Gutiérrez, Bin Hu, Po-E Li, Elais Player Jackson, Yan Xu, Patrick S G Chain, Can Alkan |
| 25 |
[GO] |
2022―Mar―02 |
COVID-19 Spread Mapper: A multi-resolution, unified framework and open-source tool |
Andy Shi, Sheila M Gaynor, Rounak Dey, Haoyu Zhang, Corbin Quick, Xihong Lin, Jonathan Wren |
| 26 |
[GO] |
2022―Jan―13 |
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time |
Luca Cilibrasi, Pietro Pinoli, Anna Bernasconi, Arif Canakoglu, Matteo Chiara, Stefano Ceri, Jonathan Wren |
| 27 |
[GO] |
2021―Dec―13 |
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses |
James M Ferguson, Hasindu Gamaarachchi, Thanh Nguyen, Alyne Gollon, Stephanie Tong, Chiara Aquilina-Reid, Rachel Bowen-James, Ira W Deveson, Can Alkan |
| 28 |
[GO] |
2021―Oct―06 |
COVID-19 knowledge graph from semantic integration of biomedical literature and databases |
Chuming Chen, Karen E Ross, Sachin Gavali, Julie E Cowart, Cathy H Wu, Zhiyong Lu |
| 29 |
[GO] |
2021―May―26 |
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family |
Chen Wang, Daniel M Konecki, David C Marciano, Harikumar Govindarajan, Amanda M Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge, Alfonso Valencia |
| 30 |
[GO] |
2021―May―19 |
3DBionotes COVID-19 Edition |
Jose Ramon Macias, Ruben Sanchez-Garcia, Pablo Conesa, Erney Ramirez-Aportela, Marta Martinez Gonzalez, Carlos Wert-Carvajal, Alberto M Parra-Perez, Joan Segura Mora, Sam Horrell, Andrea Thorn, Carlos O S Sorzano, Jose Maria Carazo, Yann Ponty |
| 31 |
[GO] |
2021―Feb―05 |
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour |
Denisa Bojkova, Jake E McGreig, Katie-May McLaughlin, Stuart G Masterson, Magdalena Antczak, Marek Widera, Verena Krähling, Sandra Ciesek, Mark N Wass, Martin Michaelis, Jindrich Cinatl, Janet Kelso |
| 32 |
[GO] |
2020―Nov―10 |
COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database |
Daniel Korn, Tesia Bobrowski, Michael Li, Yaphet Kebede, Patrick Wang, Phillips Owen, Gaurav Vaidya, Eugene Muratov, Rada Chirkova, Chris Bizon, Alexander Tropsha, Jonathan Wren |
| 33 |
[GO] |
2020―Mar―26 |
Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus |
Sen Liu, Qiang Zheng, Zhiying Wang, Arne Elofsson |
| 34 |
[GO] |
2020―Feb―25 |
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes |
Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, Tulio de Oliveira, Pier Luigi Martelli |
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