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Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Hufsky F, et al. Among authors: reyes a. Brief Bioinform. 2021 Mar 22;22(2):642-663. doi: 10.1093/bib/bbaa232. Brief Bioinform. 2021. PMID: 33147627 Free PMC article. Review.
Computational Tools for the Analysis of Uncultivated Phage Genomes.
Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Andrade-Martínez JS, et al. Among authors: reyes a. Microbiol Mol Biol Rev. 2022 Jun 15;86(2):e0000421. doi: 10.1128/mmbr.00004-21. Epub 2022 Mar 21. Microbiol Mol Biol Rev. 2022. PMID: 35311574 Free PMC article. Review.
From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.
Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MRJ, Sicheritz-Pontén T. Rangel-Pineros G, et al. Among authors: reyes a. Phage (New Rochelle). 2021 Dec 1;2(4):194-203. doi: 10.1089/phage.2021.0008. Epub 2021 Dec 16. Phage (New Rochelle). 2021. PMID: 36147515 Free PMC article.
Informative Regions In Viral Genomes.
Moreno-Gallego JL, Reyes A. Moreno-Gallego JL, et al. Among authors: reyes a. Viruses. 2021 Jun 18;13(6):1164. doi: 10.3390/v13061164. Viruses. 2021. PMID: 34207030 Free PMC article.
Minimum Information about an Uncultivated Virus Genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Roux S, et al. Among authors: reyes a. Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17. Nat Biotechnol. 2019. PMID: 30556814 Free PMC article.
Isolation and Characterization of vB_MsmS_Celfi: A New Mycobacterium tuberculosis Bacteriophage.
Payaslian F, Gradaschi V, Rondón Salazar L, Dieterle ME, Urdániz E, Di Paola M, Peña Cárcamo J, Zon F, Sosa E, Fernandez Do Porto D, Dunne M, Goeller P, Klumpp J, Raya RR, Reyes A, Piuri M. Payaslian F, et al. Among authors: reyes a. Phage (New Rochelle). 2021 Mar 1;2(1):43-49. doi: 10.1089/phage.2020.0030. Epub 2021 Mar 17. Phage (New Rochelle). 2021. PMID: 36148439 Free PMC article.
1,884 results