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Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome.
Nucleic Acids Res. 2024 Feb 9;52(3):1207-1225. doi: 10.1093/nar/gkad1204.
Nucleic Acids Res. 2024.
PMID: 38117983
Free PMC article.
Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae.
Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Mehta ZH, Mouawad C, Storici F.
Kundnani DL, et al. Among authors: gombolay al.
bioRxiv [Preprint]. 2023 Oct 2:2023.10.02.560505. doi: 10.1101/2023.10.02.560505.
bioRxiv. 2023.
PMID: 37873120
Free PMC article.
Preprint.
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Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map.
Gombolay AL, Storici F.
Gombolay AL, et al.
Nat Protoc. 2021 Jul;16(7):3625-3638. doi: 10.1038/s41596-021-00553-x. Epub 2021 Jun 4.
Nat Protoc. 2021.
PMID: 34089018
Free PMC article.
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Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii.
El-Sayed WMM, Gombolay AL, Xu P, Yang T, Jeon Y, Balachander S, Newnam G, Tao S, Bowen NE, Brůna T, Borodovsky M, Schinazi RF, Kim B, Chen Y, Storici F.
El-Sayed WMM, et al. Among authors: gombolay al.
iScience. 2020 Dec 29;24(1):102005. doi: 10.1016/j.isci.2020.102005. eCollection 2021 Jan 22.
iScience. 2020.
PMID: 33490913
Free PMC article.
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Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ.
Meers C, Keskin H, Banyai G, Mazina O, Yang T, Gombolay AL, Mukherjee K, Kaparos EI, Newnam G, Mazin A, Storici F.
Meers C, et al. Among authors: gombolay al.
Mol Cell. 2020 Sep 17;79(6):1037-1050.e5. doi: 10.1016/j.molcel.2020.08.011. Epub 2020 Sep 2.
Mol Cell. 2020.
PMID: 32882183
Free PMC article.
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Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine.
Balachander S, Gombolay AL, Yang T, Xu P, Newnam G, Keskin H, El-Sayed WMM, Bryksin AV, Tao S, Bowen NE, Schinazi RF, Kim B, Koh KD, Vannberg FO, Storici F.
Balachander S, et al. Among authors: gombolay al.
Nat Commun. 2020 May 15;11(1):2447. doi: 10.1038/s41467-020-16152-5.
Nat Commun. 2020.
PMID: 32415081
Free PMC article.
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Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA.
Gombolay AL, Vannberg FO, Storici F.
Gombolay AL, et al.
Nucleic Acids Res. 2019 Jan 10;47(1):e5. doi: 10.1093/nar/gky874.
Nucleic Acids Res. 2019.
PMID: 30272244
Free PMC article.
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