ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. - Yang Li 089; Pengyu Ni; Shaoqiang Zhang; Guojun Li; Zhengchang Su (Bioinform., 2019)

PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. - Pengyu Ni; Zhengchang Su (Database J. Biol. Databases Curation, 2022)

Natural Image Reconstruction from fMRI Based on Self-supervised Representation Learning and Latent Diffusion Model. - Pengyu Ni; Yifeng Zhang (ICDIP, 2023)

GENCODE: reference annotation for the human and mouse genomes in 2023. - Adam Frankish; Silvia Carbonell Sala; Mark Diekhans; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Carme Arnan; If Barnes; Abhimanyu Banerjee; Ruth Bennett; et al. (Nucleic Acids Res., 2023)