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Penghao Xu
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Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine
S Balachander, AL Gombolay, T Yang, P Xu, G Newnam, H Keskin, ...
Nature communications 11 (1), 2447, 2020
242020
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases
P Xu, F Storici
Nucleic Acids Research 49 (18), 10542-10557, 2021
7*2021
Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii
WMM El-Sayed, AL Gombolay, P Xu, T Yang, Y Jeon, S Balachander, ...
Iscience 24 (1), 2021
72021
Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution
DY Song, Z Wang, ZJ Song, CC Zhou, PH Xu, J Yang, J Yang, BR Lu
Journal of systematics and evolution 55 (2), 149-157, 2017
52017
RESCOT: restriction enzyme set and combination optimization tools for rNMP capture techniques
P Xu, F Storici
Theoretical computer science 894, 203-213, 2021
32021
RibosePreferenceAnalysis: analyzing the preference of rNMPs embedded in genomic DNA
P Xu, F Storici
Software Impacts 10, 100149, 2021
32021
Enriched zones of embedded ribonucleotides are associated with DNA replication and coding sequences in the human mitochondrial genome
P Xu, T Yang, DL Kundnani, M Sun, S Marsili, AL Gombolay, Y Jeon, ...
bioRxiv, 2023.04. 05.535745, 2023
12023
Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome
P Xu, T Yang, DL Kundnani, M Sun, S Marsili, AL Gombolay, Y Jeon, ...
Nucleic Acids Research 52 (3), 1207-1225, 2024
2024
DSBplot: Indels in DNA Double-strand Break Repair Experiments
T Channagiri, MM Ferrari, Y Jeon, P Xu, F Storici, N Jonoska
arXiv preprint arXiv:2312.17590, 2023
2023
rNMPID: a database for riboNucleoside Mono-Phosphates In DNA
J Yang, M Sun, Z Ran, T Yang, DL Kundnani, F Storici, P Xu
bioRxiv, 2023.11. 16.567417, 2023
2023
RNA-mediated double-strand break repair in human cells
Y Jeon, MM Ferrari, T Channagiri, P Xu, S Balachander, VS Park, ...
bioRxiv, 2022.11. 01.514688, 2022
2022
RNA-Mediated DNA Double-Strand Break Repair
Y Jeon, P Xu, M Ferrari, T Channagiri, N Jonoska, F Storici
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 63, 39-40, 2022
2022
Ribonucleotide Incorporation Characteristics in Human Mitochondrial DNA and Relationship to Gene Size
P Xu, T Yang, D Kundnani, M Sun, F Storici
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 63, 149-149, 2022
2022
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