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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB; Yale SARS-CoV-2 Genomic Surveillance Initiative; Hanage WP, Grubaugh ND, Peccia J, Baym M. Baaijens JA, et al. Among authors: imakaev m. Genome Biol. 2022 Nov 8;23(1):236. doi: 10.1186/s13059-022-02805-9. Genome Biol. 2022. PMID: 36348471 Free PMC article.
Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States.
Duvallet C, Wu F, McElroy KA, Imakaev M, Endo N, Xiao A, Zhang J, Floyd-O'Sullivan R, Powell MM, Mendola S, Wilson ST, Cruz F, Melman T, Sathyanarayana CL, Olesen SW, Erickson TB, Ghaeli N, Chai P, Alm EJ, Matus M. Duvallet C, et al. Among authors: imakaev m. ACS ES T Water. 2022 Nov 11;2(11):1899-1909. doi: 10.1021/acsestwater.1c00434. Epub 2022 May 3. ACS ES T Water. 2022. PMID: 36380771 Free PMC article.
Cooltools: Enabling high-resolution Hi-C analysis in Python.
Open2C; Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Open2C, et al. Among authors: imakaev m. PLoS Comput Biol. 2024 May 6;20(5):e1012067. doi: 10.1371/journal.pcbi.1012067. eCollection 2024 May. PLoS Comput Biol. 2024. PMID: 38709825 Free PMC article.
Bioframe: operations on genomic intervals in Pandas dataframes.
Open2C; Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev S. Open2C, et al. Among authors: imakaev m. Bioinformatics. 2024 Feb 1;40(2):btae088. doi: 10.1093/bioinformatics/btae088. Bioinformatics. 2024. PMID: 38402507 Free PMC article.
Pairtools: from sequencing data to chromosome contacts.
Open2C; Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Open2C, et al. Among authors: imakaev m. bioRxiv [Preprint]. 2023 Feb 15:2023.02.13.528389. doi: 10.1101/2023.02.13.528389. bioRxiv. 2023. PMID: 36824968 Free PMC article. Preprint.
Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.
Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. Reiff SB, et al. Among authors: imakaev m. Nat Commun. 2022 Nov 2;13(1):6561. doi: 10.1038/s41467-022-34458-4. Nat Commun. 2022. PMID: 36323678 Free PMC article. No abstract available.
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.
Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. Reiff SB, et al. Among authors: imakaev m. Nat Commun. 2022 May 2;13(1):2365. doi: 10.1038/s41467-022-29697-4. Nat Commun. 2022. PMID: 35501320 Free PMC article.
Metrics to relate COVID-19 wastewater data to clinical testing dynamics.
Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJ. Xiao A, et al. Among authors: imakaev m. Water Res. 2022 Apr 1;212:118070. doi: 10.1016/j.watres.2022.118070. Epub 2022 Jan 14. Water Res. 2022. PMID: 35101695 Free PMC article.
42 results