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Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit Iii R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O'Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Timme RE, et al. Among authors: karsch mizrachi i. Microb Genom. 2023 Dec;9(12):001145. doi: 10.1099/mgen.0.001145. Microb Genom. 2023. PMID: 38085797 Free PMC article.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
GenBank 2024 Update.
Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Sherry ST, Yankie L, Karsch-Mizrachi I. Sayers EW, et al. Among authors: karsch mizrachi i. Nucleic Acids Res. 2024 Jan 5;52(D1):D134-D137. doi: 10.1093/nar/gkad903. Nucleic Acids Res. 2024. PMID: 37889039 Free PMC article.
Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.
Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Adriaenssens EM, et al. Among authors: karsch mizrachi i. Nat Biotechnol. 2023 Sep;41(9):1346. doi: 10.1038/s41587-023-01952-z. Nat Biotechnol. 2023. PMID: 37608068 No abstract available.
Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.
Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Adriaenssens EM, et al. Among authors: karsch mizrachi i. Nat Biotechnol. 2023 Jul;41(7):898-902. doi: 10.1038/s41587-023-01844-2. Nat Biotechnol. 2023. PMID: 37430074 Free PMC article. No abstract available.
GenBank 2023 update.
Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Sherry ST, Yankie L, Karsch-Mizrachi I. Sayers EW, et al. Among authors: karsch mizrachi i. Nucleic Acids Res. 2023 Jan 6;51(D1):D141-D144. doi: 10.1093/nar/gkac1012. Nucleic Acids Res. 2023. PMID: 36350640 Free PMC article.
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank.
Underwood BA, Yankie L, Nawrocki EP, Palanigobu V, Gotvyanskyy S, Calhoun VC, Kornbluh M, Smith TG, Fleischmann L, Sinyakov D, Bollin CJ, Karsch-Mizrachi I. Underwood BA, et al. Among authors: karsch mizrachi i. Database (Oxford). 2022 Mar 1;2022:baac006. doi: 10.1093/database/baac006. Database (Oxford). 2022. PMID: 35230423 Free PMC article.
Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation.
Scholz AH, Freitag J, Lyal CHC, Sara R, Cepeda ML, Cancio I, Sett S, Hufton AL, Abebaw Y, Bansal K, Benbouza H, Boga HI, Brisse S, Bruford MW, Clissold H, Cochrane G, Coddington JA, Deletoille AC, García-Cardona F, Hamer M, Hurtado-Ortiz R, Miano DW, Nicholson D, Oliveira G, Bravo CO, Rohden F, Seberg O, Segelbacher G, Shouche Y, Sierra A, Karsch-Mizrachi I, da Silva J, Hautea DM, da Silva M, Suzuki M, Tesfaye K, Tiambo CK, Tolley KA, Varshney R, Zambrano MM, Overmann J. Scholz AH, et al. Among authors: karsch mizrachi i. Nat Commun. 2022 Feb 23;13(1):1086. doi: 10.1038/s41467-022-28594-0. Nat Commun. 2022. PMID: 35197464 Free PMC article.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Griffiths EJ, et al. Among authors: karsch mizrachi i. Gigascience. 2022 Feb 16;11:giac003. doi: 10.1093/gigascience/giac003. Gigascience. 2022. PMID: 35169842 Free PMC article.
Using GenBank and SRA.
Sayers EW, O'Sullivan C, Karsch-Mizrachi I. Sayers EW, et al. Among authors: karsch mizrachi i. Methods Mol Biol. 2022;2443:1-25. doi: 10.1007/978-1-0716-2067-0_1. Methods Mol Biol. 2022. PMID: 35037198
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