CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure. - Pei Fen Kuan; Hyonho Chun; Sündüz Keles (Pacific Symposium on Biocomputing, 2008)

A statistical framework for Illumina DNA methylation arrays. - Pei Fen Kuan; Sijian Wang; Xin Zhou; Haitao Chu (Bioinform., 2010)

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. - Benedikt Zacher; Pei Fen Kuan; Achim Tresch (BMC Bioinform., 2010)

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. - Dongjun Chung; Pei Fen Kuan; Bo Li 015; Rajendran Sanalkumar; Kun Liang 001; Emery H. Bresnick; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2011)

methylDMV: Simultaneous Detection of Differential DNA Methylation and Variability with Confounder Adjustment. - Pei Fen Kuan; Junyan Song; Shuyao He (PSB, 2017)

A systematic evaluation of nucleotide properties for CRISPR sgRNA design. - Pei Fen Kuan; R. Scott Powers; Shuyao He; Kaiqiao Li; Xiaoyu Zhao; Bo Huang (BMC Bioinform., 2017)

methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. - Xu Ren; Pei Fen Kuan (Bioinform., 2019)

Multiple-kernel learning for genomic data mining and prediction. - Christopher M. Wilson; Kaiqiao Li; Xiaoqing Yu; Pei Fen Kuan; Xuefeng Wang (BMC Bioinform., 2019)

Negative binomial additive model for RNA-Seq data analysis. - Xu Ren; Pei Fen Kuan (BMC Bioinform., 2020)

Fenchel duality of Cox partial likelihood with an application in survival kernel learning. - Christopher M. Wilson; Kaiqiao Li; Qiang Sun; Pei Fen Kuan; Xuefeng Wang (Artif. Intell. Medicine, 2021)

A systematic assessment of cell type deconvolution algorithms for DNA methylation data. - Junyan Song; Pei Fen Kuan (Briefings Bioinform., 2022)

Efficient gradient boosting for prognostic biomarker discovery. - Kaiqiao Li; Sijie Yao; Zhenyu Zhang; Biwei Cao; Christopher M. Wilson; Denise Kalos; Pei Fen Kuan; Ruoqing Zhu; Xuefeng Wang (Bioinform., 2022)

A systematic evaluation of cell-type-specific differential methylation analysis in bulk tissue. - Shuo Li; Pei Fen Kuan (Briefings Bioinform., 2024)