Publications written by members of ELIXIR Nodes. The papers are ordered by the surname of the first author.
- A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development.
Alexander SPH, Armstrong J, Davenport AP, et al. (2020) IUPHAR Review 29 [published online ahead of print, 2020 May 1].
Br J Pharmacol. 10.1111/bph.15094. (https://doi.org/10.1111/bph.15094) - Clinical population genetic analysis of variants in the SARS-CoV-2 receptor ACE2
Ardeshirdavani A, Zakeri P, Mehrtash A, Hosseini SM, Li G, et al. (2020)
medRxiv 2020.05.27.20115071 (https://doi.org/10.1101/2020.05.27.20115071) - Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic.
Blomberg, N, Lauer, KB (2020).
Eur J Hum Genet 28, 719–723. (https://doi.org/10.1038/s41431-020-0637-5) - The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor.
Brielle ES, Schneidman-Duhovny D, Linial M (2020).
Viruses 12 (5) 2020 (https://doi.org/10.1101/2020.03.10.986398). - Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2
Chiara M, Horner DS, Gissi C, Pesole G (2021).
Molecular Biology and Evolution, msab049 (https://doi.org/10.1093/molbev/msab049). - Comparative genomics provides an operational classification system and reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2
Chiara M, Horner DS, Gissi C, Pesole G (2020).
bioRxiv (https://doi.org/10.1101/2020.06.26.172924). - Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2
Chiara M, Horner DS, Gissi C, Pesole G (2020).
bioRxiv (https://doi.org/10.1101/2020.03.30.016790). - Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, et al. (2020).
Briefings in Bioinformatics, bbaa297 (https://doi.org/10.1093/bib/bbaa297). - CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
Chiara M, Zambelli F, Tangaro MA, Mandreoli P, Horner DS, Pesole G (2020).
Bioinformatics, btaa1047 (https://doi.org/10.1093/bioinformatics/btaa1047). - Comparative Genomics Reveals Early Emergence and BiasedSpatiotemporal Distribution of SARS-CoV-2
Chiara M, Horner DS, Gissi C, Pesole G (2021)
Molecular Biology and Evolution, Volume 38, Issue 6 (https://doi.org/10.1093/molbev/msab049) - A review on drug repurposing applicable to COVID-19
Dotolo S, Marabotti A, Facchiano A, Tagliaferri R (2020).
Briefings in Bioinformatics, bbaa288 (https://doi.org/10.1093/bib/bbaa288). - Translating Scientific Knowledge to Government Decision Makers Has Crucial Importance in the Management of the COVID-19 Pandemic.
Gombos K, Herczeg R, Erőss B, Kovács SZ, Uzzoli A, Nagy T, et al. (2021)
Popul Health Manag. Feb;24(1):35-45. (https://doi.org/10.1089/pop.2020.0159) - Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity
Graudenzi A, Maspero D, Angaroni F, Piazza R, Ramazzotti D (2021)
iScience 24, 102116 (https://doi.org/10.1016/j.isci.2021.102116) - Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix.
Kemenesi G, Zeghbib S, Somogyi BA, et al (2020).
Viruses 12(12):1401 (doi: https://doi.org/10.3390/v12121401). - SARS‑CoV‑2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.
Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen H, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM & Orengo (2020)
Nature Scientific Reports 10:16471 (https://doi.org/10.1038/s41598-020-71936-5) - Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Maier W, Bray S, van den Beek M, Bouvier D, Coraor N et al. (2021)
bioRxiv [Preprint]. 2021 Mar 25:2021.03.25.437046 (https://doi.org/10.1101/2021.03.25.437046). - Modeling COVID-19 pandemic using Bayesian analysis with application to Slovene data.
Manevski D, Gorenjec NR, Kejžar N, Blagus R (2020)
Mathematical Biosciences, Volume 329 (https://doi.org/10.1016/j.mbs.2020.108466). - SARS-CoV-2-Specific Antibody Profiles Distinguish Patients with Moderate from Severe COVID-19
Mata LC, Piñero J, Vaquero ST, Tachó-Piñot R, Kuksin M et al. (2020)
medRxiv 2020.12.18.20248461 (https://doi.org/10.1101/2020.12.18.20248461). - FAIR, ethical, and coordinated data sharing for COVID-19 response: a review of COVID-19 data sharing platforms and registries
Maxwell L, Shreedhar P, Dauga D, McQuilton P, Terry R et al. (2020)
Research Square (pre-print) (https://doi.org/10.21203/rs.3.rs-1045632/v1). - Characterization of accessory genes in coronavirus genomes.
Michel CJ, Mayer C, Poch O, Thompson JD (2020)
Virology Journal volume 17, Article number: 131 (https://doi.org/10.1186/s12985-020-01402-1). - The landscape of SARS-CoV-2 RNA modifications.
Milad M, Fuchs J, Maier W, Weigang S, Díaz i Pedrosa N, Weiss L, Lother A, Nekrutenko A, Ruzsics Z, Panning M, Kochs G, Gilsbach R, Grüning B (2020)
bioRxiv 2020.07.18.204362 (https://doi.org/10.1101/2020.07.18.204362) - Detailed disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic: An exploratory analysis
Modrák M, Bürkner P, Sieger T, Slisz T, Vašáková M, et al. (2020)
medRxiv 2020.12.03.20239863 (https://doi.org/10.1101/2020.12.03.20239863) - Different mutations in SARS-CoV-2 associate with severe and mild outcome.
Nagy Á, Pongor S, Győrffy B. (2021)
Int J Antimicrob Agents 57(2):106272. (https://doi.org/10.1016/j.ijantimicag.2020.106272). - From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance
Ortuño FM, Loucera C, Casimiro-Soriguer CS, Lepe JA, Martinez PC, Diaz LM et al. (2021)
bioRxiv 2021.04.13.439668 (https://doi.org/10.1101/2021.04.13.439668) - Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece
Pechlivanis N, Tsagiopoulou M, Maniou M, Togkousidis A, Mouchtaropoulou E et al. (2021)
Scientific Reports (https://doi.org/10.21203/rs.3.rs-677811/v1) - Detection of A-to-I RNA Editing in SARS-COV-2
Picardi E, Mansi L, Pesole G (2021)
Genes (Basel) Dec 23;13(1):41. (https://doi.org/10.3390/genes13010041). - Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion
Russell YN, Nikos CK, Christos AO (2021).
mBio Jan 2021, 12 (1) e03014-20. (https://doi.org/10.1128/mBio.03014-20) - Galaxy and HyPhy developments teams. No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics.
Nekrutenko A, Pond SLK (2020).
bioRxiv 2020.02.21.959973 (https://doi.org/10.1101/2020.02.21.959973) - COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski, M, Mazein, A, Gillespie, ME et al. (2020).
Sci Data 7, 136. (https://doi.org/10.1038/s41597-020-0477-8) - Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece
Pechlivanis N, Tsagiopoulou M, Maniou MC, Tougkousidis A, Laidou S et al. (2021)
medRxiv 2021.03.17.21252673 (https://doi.org/10.1101/2021.03.17.21252673) - A-to-I RNA editing in SARS-COV-2: real or artifact?
Picardi E, Mansi L, Pesole G. (2020)
bioRxiv. (https://doi.org/10.1101/2020.07.27.223172). - VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Ramazzotti D, Angaroni F, Maspero D, Antoniotti M, Graudenzi G, Piazza R (2021)
Patterns 2 (https://doi.org/10.1016/j.patter.2021.100212). - A-to-I RNA editing in SARS-COV-2: real or artifact?
Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J (2020)
bioRxiv. (https://doi.org/10.1101/2020.04.12.025577). - Mechanistic modeling of the SARS-CoV-2 disease map
Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J (2021)
BioData Mining volume 14, Article number: 5 (https://doi.org/10.1186/s13040-021-00234-1). - Role of the early secretory pathway in SARS-CoV-2 infection.
Sicari D, Chatziioannou A, Koutsandreas T, Sitia R, Chevet E. (2020)
The Journal of Cell Biology Sep;219(9). (https://doi.org/10.1083/jcb.202006005). - Prevalence of SARS-CoV-2 infection in the Luxembourgish population – the CON-VINCE study
Snoeck CJ, Vaillant M, Abdelrahman T, Satagopam VP, Turner JD, Beaumont K et al. (2020)
medRxiv. (https://doi.org/10.1101/2020.05.11.20092916). - Recombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein S.
Tagliamonte MS, Abid N, Ostrov DA, et al. (2020)
bioRxiv. (https://doi.org/10.1101/2020.03.30.015685). - BIP4COVID19: Impact metrics and indicators for coronavirus related publications (Version 0.1) [Data set]
Vergoulis T, Kanellos I, Chatzopoulos S, Karidi DP Dalamagas T (2020).
Zenodo (https://doi.org/10.5281/zenodo.3723282) - Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy
Voigt A, Omholt S, Almaas E (2022).
PLOS One (https://doi.org/10.1371/journal.pone.0263155)