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Cited by in F6Publishing
For: Borges V, Pinheiro M, Pechirra P, Guiomar R, Gomes JP. INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance. Genome Med 2018;10:46. [PMID: 29954441 DOI: 10.1186/s13073-018-0555-0] [Cited by in Crossref: 24] [Cited by in F6Publishing: 16] [Article Influence: 6.0] [Reference Citation Analysis]
Number Citing Articles
1 Simundza J. Infection and immunity: insights and therapeutic strategies through genomic analysis of the host, pathogen, and host-pathogen interaction. Genome Med 2018;10:72. [PMID: 30257712 DOI: 10.1186/s13073-018-0583-9] [Reference Citation Analysis]
2 Borges V, Isidro J, Cunha M, Cochicho D, Martins L, Banha L, Figueiredo M, Rebelo L, Trindade MC, Duarte S, Vieira L, Alves MJ, Costa I, Guiomar R, Santos M, Cortê-Real R, Dias A, Póvoas D, Cabo J, Figueiredo C, Manata MJ, Maltez F, Gomes da Silva M, Gomes JP. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere 2021;6:e0024421. [PMID: 34319130 DOI: 10.1128/mSphere.00244-21] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
3 Vilares A, Borges V, Sampaio D, Ferreira I, Martins S, Vieira L, Gargaté MJ, Gomes JP. Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii. Parasitol Res 2020;119:587-99. [PMID: 31897784 DOI: 10.1007/s00436-019-06523-3] [Reference Citation Analysis]
4 Van Goethem N, Robert A, Bossuyt N, Van Poelvoorde LAE, Quoilin S, De Keersmaecker SCJ, Devleesschauwer B, Thomas I, Vanneste K, Roosens NHC, Van Oyen H. Evaluation of the added value of viral genomic information for predicting severity of influenza infection. BMC Infect Dis 2021;21:785. [PMID: 34376182 DOI: 10.1186/s12879-021-06510-z] [Reference Citation Analysis]
5 Ghorbani A, Abundo MC, Ji H, Taylor KJM, Ngunjiri JM, Lee CW. Viral Subpopulation Screening Guides in Designing a High Interferon-Inducing Live Attenuated Influenza Vaccine by Targeting Rare Mutations in NS1 and PB2 Proteins. J Virol 2020;95:e01722-20. [PMID: 33115873 DOI: 10.1128/JVI.01722-20] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
6 Borges V, Isidro J, Macedo F, Neves J, Silva L, Paiva M, Barata J, Catarino J, Ciobanu L, Duarte S, Vieira L, Guiomar R, Gomes JP. Nosocomial Outbreak of SARS-CoV-2 in a "Non-COVID-19" Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses 2021;13:604. [PMID: 33916205 DOI: 10.3390/v13040604] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 4.0] [Reference Citation Analysis]
7 Borges V, Isidro J, Cortes-Martins H, Duarte S, Vieira L, Leite R, Gordo I, Caetano CP, Nunes B, Sá R, Oliveira A, Guiomar R, Gomes JP; Portuguese network for SARS-CoV-2 genomics. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerg Microbes Infect 2020;9:2488-96. [PMID: 33131453 DOI: 10.1080/22221751.2020.1844552] [Cited by in Crossref: 9] [Cited by in F6Publishing: 7] [Article Influence: 4.5] [Reference Citation Analysis]
8 Southgate JA, Bull MJ, Brown CM, Watkins J, Corden S, Southgate B, Moore C, Connor TR. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 2020;36:1681-8. [PMID: 31693070 DOI: 10.1093/bioinformatics/btz814] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 0.5] [Reference Citation Analysis]
9 Borges V, Isidro J, Trovão NS, Duarte S, Cortes-martins H, Martiniano H, Gordo I, Leite R, Vieira L, Lira AJS, Sousa Fernandes AM, Estrada A, Nunes A, Rodrigues A, Caldas A, Constança A, Henriques AM, Matos AM, Oliveira A, Dias AP, Pelerito A, Couto AR, Vilares A, Albuquerque A, Nunes B, Gouveia BR, de Fátima Rodrigues C, Feliciano C, Roque C, Cardoso C, Sousa C, Paulino C, Bettencourt CR, Branco CC, dos Santos CN, Godinho C, Caetano CP, Correia C, Toscano C, Veríssimo C, Silva D, da Silva DPP, Costa E, Pádua E, Martins F, Vale F, Vilarinho F, Branca F, Caldeira F, Lacerda F, Rocha F, Andrade G, Ribeiro H, Rodrigues H, Jesus H, Sousa H, Ferreira I, Baldaque I, Costa I, Gomes I, Slobidnyk I, Albergaria I, Dias I, Fernandes I, de Carvalho IL, Água-doce I, Armas JB, Ramos J, Sousa JC, Costa J, Dias J, Rodrigues J, Sobral J, Machado J, Meneses J, Alves J, Constantino JV, Brum L, Silveira L, Zé-zé L, Santos L, Freitas L, Silva L, Mota-vieira L, Lopes L, Monteiro L, Faria M, Farinha M, Vaz M, Pinto MA, Pessanha MA, Tomaz MB, Vellés MC, Maciel de Soveral MDG, Ramos MH, Veiga MI, Gargate MJ, Peres MJ, Borrego MJ, Figueiredo MM, Martins M, Viana M, Melim M, Jorreto MB, Fevereiro M, Pinheiro M, Oleastro M, Seixas N, Ventura N, Verdasca N, Costa O, Barros P, Fonseca P, Miguel P, Bajanca-lavado P, Branquinho P, Palminha P, Soares P, Valente P, Leandro P, Pereira P, Cardoso P, Pechirra P, Ramos P, Neves R, Rocha R, Rodrigues R, Sabino R, Sá R, Ferreira RFR, Rodrigues R, Veloso RC, Cordeiro R, Côrte-real R, de Sousa R, Gralha R, Macedo R, Matos R, Rodrigues R, Paulo S, Sousa S, Lopo S, Magalhães SMS, Rodrigues S, Silva S, Ladeiro S, Martins S, Silva S, Salvado T, Luís T, Alves V, Manageiro V, Guiomar R, Gomes JP; Portuguese network for SARS-CoV-2 genomics (Consortium). SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal. Commun Med 2022;2. [DOI: 10.1038/s43856-022-00072-0] [Reference Citation Analysis]
10 Pelerito A, Nunes A, Grilo T, Isidro J, Silva C, Ferreira AC, Valdezate S, Núncio MS, Georgi E, Gomes JP. Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles. Front Microbiol 2021;12:740068. [PMID: 34867857 DOI: 10.3389/fmicb.2021.740068] [Reference Citation Analysis]
11 Bakalos N, Kaselimi M, Doulamis N, Doulamis A, Kalogeras D, Bimpas M, Davradou A, Vlachostergiou A, Fotopoulos A, Plakia M, Karalis A, Tsekeridou S, Anagnostopoulos T, Despotopoulou AM, Bonavita I, Petersen K, Pelepes L, Voumvourakis L, Anagnostou A, Groen D, Mintram K, Saha A, Taylor SJE, Ham CVD, Kaleta P, Ignjatović D, Rossi L. STAMINA: Bioinformatics Platform for Monitoring and Mitigating Pandemic Outbreaks. Technologies 2022;10:63. [DOI: 10.3390/technologies10030063] [Reference Citation Analysis]
12 Zé-Zé L, Borges V, Osório HC, Machado J, Gomes JP, Alves MJ. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal. PLoS Negl Trop Dis 2020;14:e0008657. [PMID: 32997656 DOI: 10.1371/journal.pntd.0008657] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
13 Eckert EM, Di Cesare A, Fontaneto D, Berendonk TU, Bürgmann H, Cytryn E, Fatta-Kassinos D, Franzetti A, Larsson DGJ, Manaia CM, Pruden A, Singer AC, Udikovic-Kolic N, Corno G. Every fifth published metagenome is not available to science. PLoS Biol 2020;18:e3000698. [PMID: 32243442 DOI: 10.1371/journal.pbio.3000698] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 3.5] [Reference Citation Analysis]
14 Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PP, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Res 2021:gkab660. [PMID: 34379778 DOI: 10.1093/nar/gkab660] [Reference Citation Analysis]
15 Sansone M, Andersson M, Gustavsson L, Andersson LM, Nordén R, Westin J. Extensive Hospital In-Ward Clustering Revealed By Molecular Characterization of Influenza A Virus Infection. Clin Infect Dis 2020;71:e377-83. [PMID: 32011654 DOI: 10.1093/cid/ciaa108] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 5.0] [Reference Citation Analysis]
16 Sá R, Isidro J, Borges V, Duarte S, Vieira L, Gomes JP, Tedim S, Matias J, Leite A. Unravelling the hurdles of a large COVID-19 epidemiological investigation by viral genomics. Journal of Infection 2022. [DOI: 10.1016/j.jinf.2022.05.013] [Reference Citation Analysis]
17 Amicone M, Borges V, Alves MJ, Isidro J, Zé-Zé L, Duarte S, Vieira L, Guiomar R, Gomes JP, Gordo I. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol Med Public Health 2022;10:142-55. [PMID: 35419205 DOI: 10.1093/emph/eoac010] [Cited by in Crossref: 4] [Cited by in F6Publishing: 1] [Article Influence: 4.0] [Reference Citation Analysis]
18 Harilal D, Ramaswamy S, Loney T, Suwaidi HA, Khansaheb H, Alkhaja A, Varghese R, Deesi Z, Nowotny N, Alsheikh-Ali A, Abou Tayoun A. SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission. Clin Chem 2020;66:1450-8. [PMID: 32715310 DOI: 10.1093/clinchem/hvaa187] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 6.0] [Reference Citation Analysis]
19 Correia CR, Marçal M, Vieira F, Santos E, Novais C, Maria AT, Malveiro D, Prior AR, Aguiar M, Salazar A, Gouvêa Pinto C, Carvalho Rodrigues L, Pessanha MA, Borges V, Isidro J, Gomes JP, Duarte S, Vieira L, Costa I, Alves MJ, Calhau C, Guiomar R, Tuna ML. Congenital SARS-CoV-2 Infection in a Neonate With Severe Acute Respiratory Syndrome. Pediatr Infect Dis J 2020;39:e439-43. [PMID: 33060519 DOI: 10.1097/INF.0000000000002941] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
20 Mengual-Chuliá B, Alonso-Cordero A, Cano L, Mosquera MDM, de Molina P, Vendrell R, Reyes-Prieto M, Jané M, Torner N, Martínez AI, Vila J, Díez-Domingo J, Marcos MÁ, López-Labrador FX. Whole-Genome Analysis Surveillance of Influenza A Virus Resistance to Polymerase Complex Inhibitors in Eastern Spain from 2016 to 2019. Antimicrob Agents Chemother 2021;65:e02718-20. [PMID: 33782005 DOI: 10.1128/AAC.02718-20] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
21 Frost JR, Schulz H, McLachlan E, Hiebert J, Severini A. An enrichment method for capturing mumps virus whole genome sequences directly from clinical specimens. J Virol Methods 2021;294:114176. [PMID: 33957163 DOI: 10.1016/j.jviromet.2021.114176] [Cited by in F6Publishing: 1] [Reference Citation Analysis]