A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. - Wei Li 036; Clifford A. Meyer; Xiaole Shirley Liu (ISMB (Supplement of Bioinformatics), 2005)

CEAS: cis-regulatory element annotation system. - Xuwo Ji; Wei Li 036; Jun Song; Liping Wei; Xiaole Shirley Liu (Nucleic Acids Res., 2006)

xMAN: extreme MApping of oligoNucleotides. - Wei Li 036; Jason S. Carroll; Myles Brown; Xiaole Shirley Liu (BIOCOMP, 2007)

Microarray blob-defect removal improves array analysis. - Jun S. Song; Kaveh Maghsoudi; Wei Li 036; Edward Fox; John Quackenbush; Xiaole Shirley Liu (Bioinform., 2007)

BSMAP: whole genome bisulfite sequence MAPping program. - Yuanxin Xi; Wei Li 036 (BMC Bioinform., 2009)

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. - Bo Qin; Meng Zhou; Ying Ge; Len Taing; Tao Liu 022; Qian Wang; Su Wang; Junsheng Chen; Lingling Shen; Xikun Duan; Sheng'en Hu; Wei Li 036; et al. (Bioinform., 2012)

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. - Yuanxin Xi; Christoph Bock; Fabian Müller 001; Deqiang Sun; Alexander Meissner; Wei Li 036 (Bioinform., 2012)

BSeQC: quality control of bisulfite sequencing experiments. - Xueqiu Lin; Deqiang Sun; Benjamin Rodriguez; Qian Zhao; Hanfei Sun; Yong Zhang 006; Wei Li 036 (Bioinform., 2013)

From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-seq Data. - Ya Cui; Jason Sheng Li; Wei Li 036 (Genom. Proteom. Bioinform., 2021)

3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues. - Ya Cui; Fanglue Peng; Dan Wang; Yumei Li 010; Jason Sheng Li; Lei Li; Wei Li 036 (Nucleic Acids Res., 2022)

Population-scale genetic control of alternative polyadenylation and its association with human diseases. - Lei Li; Yumei Li 010; Xudong Zou; Fuduan Peng; Ya Cui; Eric J. Wagner; Wei Li 036 (Quant. Biol., 2022)