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Current progress and open challenges for applying deep learning across the biosciences.
Sapoval N, Aghazadeh A, Nute MG, Antunes DA, Balaji A, Baraniuk R, Barberan CJ, Dannenfelser R, Dun C, Edrisi M, Elworth RAL, Kille B, Kyrillidis A, Nakhleh L, Wolfe CR, Yan Z, Yao V, Treangen TJ. Sapoval N, et al. Among authors: treangen tj. Nat Commun. 2022 Apr 1;13(1):1728. doi: 10.1038/s41467-022-29268-7. Nat Commun. 2022. PMID: 35365602 Free PMC article. Review.
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.
Curry KD, Yu FB, Vance SE, Segarra S, Bhaya D, Chikhi R, Rocha EPC, Treangen TJ. Curry KD, et al. Among authors: treangen tj. bioRxiv [Preprint]. 2024 Jan 30:2024.01.25.577285. doi: 10.1101/2024.01.25.577285. bioRxiv. 2024. Update in: Bioinformatics. 2024 Jun 28;40(Suppl 1):i58-i67. doi: 10.1093/bioinformatics/btae224. PMID: 38352454 Free PMC article. Updated. Preprint.
Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Sapoval N, et al. Among authors: treangen tj. bioRxiv [Preprint]. 2020 Jul 2:2020.07.02.184481. doi: 10.1101/2020.07.02.184481. bioRxiv. 2020. Update in: Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120. PMID: 32637955 Free PMC article. Updated. Preprint.
Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact.
da Silveira WA, Fazelinia H, Rosenthal SB, Laiakis EC, Kim MS, Meydan C, Kidane Y, Rathi KS, Smith SM, Stear B, Ying Y, Zhang Y, Foox J, Zanello S, Crucian B, Wang D, Nugent A, Costa HA, Zwart SR, Schrepfer S, Elworth RAL, Sapoval N, Treangen T, MacKay M, Gokhale NS, Horner SM, Singh LN, Wallace DC, Willey JS, Schisler JC, Meller R, McDonald JT, Fisch KM, Hardiman G, Taylor D, Mason CE, Costes SV, Beheshti A. da Silveira WA, et al. Cell. 2020 Nov 25;183(5):1185-1201.e20. doi: 10.1016/j.cell.2020.11.002. Cell. 2020. PMID: 33242417 Free PMC article.
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. Sapoval N, et al. Among authors: treangen tj. Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120. Epub 2021 Feb 18. Genome Res. 2021. PMID: 33602693 Free PMC article.
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.
Gallego-García P, Varela N, Estévez-Gómez N, De Chiara L, Fernández-Silva I, Valverde D, Sapoval N, Treangen TJ, Regueiro B, Cabrera-Alvargonzález JJ, Del Campo V, Pérez S, Posada D. Gallego-García P, et al. Among authors: treangen tj. Virus Evol. 2022 Feb 4;8(1):veac008. doi: 10.1093/ve/veac008. eCollection 2022. Virus Evol. 2022. PMID: 35242361 Free PMC article.
95 results