Penghao Xu

LucaCell is a sequence-centric foundation model that improves cross-species single-cell analysis by using mRNA sequence embeddings instead of fixed gene identifiers.

The paper maps DNA-embedded ribonucleotides (rNMPs) across human cell types, revealing their non-random distribution and role as a novel epigenetic mark affecting gene expression.

The paper introduces rNMPID, a database that compiles rNMP-embedment data across species, providing insights into their genomic characteristics and potential roles in disease.

This study shows that transcript RNA facilitates DSB repair in human cells through NHEJ and MMEJ, promoting repair or mediating RNA-templated repair based on sequence complementarity.

The paper analyzes rNMP incorporation patterns around yeast ARSs to show differences in rNMP incorporation between leading and lagging strands, reflecting the labor division between Pol δ and Pol ε.

The paper identifies a disproportionate incorporation of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii compared to nuclear DNA, linked to elevated ATP levels.