An Algorithm for Haplotype Analysis. - Shili Lin; Terence P. Speed (J. Comput. Biol., 1997)

Class discovery and classification of tumor samples using mixture modeling of gene expression data - a unified approach. - Roxana Alexandridis; Shili Lin; Mark Irwin (Bioinform., 2004)

Genome-Wide Tagging SNPs with Entropy-Based Monte Carlo Method. - Zhenqiu Liu; Shili Lin; Ming Tan (J. Comput. Biol., 2006)

Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data. - Zailong Wang; Pearlly Yan; Dustin P. Potter; Charis Eng; Tim Hui-Ming Huang; Shili Lin (BMC Bioinform., 2007)

Probe signal correction for differential methylation hybridization experiments. - Dustin P. Potter; Pearlly Yan; Tim Hui-Ming Huang; Shili Lin (BMC Bioinform., 2008)

Comparative study on ChIP-seq data: normalization and binding pattern characterization. - Cenny Taslim; Jiejun Wu; Pearlly Yan; Greg Singer; Jeffrey D. Parvin; Tim Hui-Ming Huang; Shili Lin; Kun Huang 001 (Bioinform., 2009)

Identifying differentially methylated genes using mixed effect and generalized least square models. - Shuying Sun; Pearlly Yan; Tim Hui-Ming Huang; Shili Lin (BMC Bioinform., 2009)

A robust unified approach to analyzing methylation and gene expression data. - Abbas Khalili; Tim Hui-Ming Huang; Shili Lin (Comput. Stat. Data Anal., 2009)

Sparse Support Vector Machines with L_{p} Penalty for Biomarker Identification. - Zhenqiu Liu; Shili Lin; Ming Tan (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model. - Cenny Taslim; Shili Lin; Kun Huang 001; Tim Hui-Ming Huang (GENSiPS, 2011)

Preprocessing differential methylation hybridization microarray data. - Shuying Sun; Yi-Wen Huang; Pearlly Yan; Tim Hui-Ming Huang; Shili Lin (BioData Min., 2011)

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models. - Cenny Taslim; Tim Hui-Ming Huang; Shili Lin (Bioinform., 2011)

Identifying hypermethylated CpG islands using a quantile regression model. - Shuying Sun; Zhengyi Chen; Pearlly Yan; Yi-Wen Huang; Tim Hui-Ming Huang; Shili Lin (BMC Bioinform., 2011)

PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data. - David E. Frankhouser; Mark Murphy; James S. Blachly; Jincheol Park; Mike W. Zoller; Javkhlan-Ochir Ganbat; John Curfman; John C. Byrd; Shili Lin; Guido Marcucci; Pearlly Yan; Ralf Bundschuh (Bioinform., 2014)

FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads. - Meng Wang 059; Shili Lin (Bioinform., 2014)

A Mixture Modeling Framework for Differential Analysis of High-Throughput Data. - Cenny Taslim; Shili Lin (Comput. Math. Methods Medicine, 2014)

Detecting associations of rare variants with common diseases: collapsing or haplotyping? - Meng Wang 059; Shili Lin (Briefings Bioinform., 2015)

Network construction and structure detection with metagenomic count data. - Zhenqiu Liu; Shili Lin; Steven T. Piantadosi (BioData Min., 2015)

GrammR: graphical representation and modeling of count data with application in metagenomics. - Deepak Nag Ayyala; Shili Lin (Bioinform., 2015)

Statistical methods for detecting differentially methylated regions based on MethylCap-seq data. - Deepak Nag Ayyala; David E. Frankhouser; Javkhlan-Ochir Ganbat; Guido Marcucci; Ralf Bundschuh; Pearlly Yan; Shili Lin (Briefings Bioinform., 2016)

Impact of data resolution on three-dimensional structure inference methods. - Jincheol Park; Shili Lin (BMC Bioinform., 2016)

Sparse Inverse Covariance Estimation with L0 Penalty for Network Construction with Omics Data. - Zhenqiu Liu; Shili Lin; Nan Deng; Dermot P. B. McGovern; Steven T. Piantadosi (J. Comput. Biol., 2016)

Investigation on dynamic equalisation performance of lithium battery pack management. - Jie Lv; Wenji Song; Shili Lin; Ziping Feng; Yulong Ding; Yongliang Li (IET Circuits Devices Syst., 2017)

Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures. - Jincheol Park; Shili Lin (Briefings Bioinform., 2019)

Are dropout imputation methods for scRNA-seq effective for scHi-C data? - Chenggong Han; Qing Xie; Shili Lin (Briefings Bioinform., 2021)

A Novel Pigeon-Inspired Optimized RBF Model for Parallel Battery Branch Forecasting. - Yanhui Zhang; Shili Lin; Haiping Ma; Yuanjun Guo; Wei Feng 009 (Complex., 2021)

HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data. - Qing Xie; Chenggong Han; Victor Jin; Shili Lin (PLoS Comput. Biol., 2022)

Hybrid energy storage system and its hardware-in-loop platform for 1500-V metro DC power supply system based on voltage droop control. - Shili Lin; Cheng Chen; Gaoju Liang; Xianyong Zhang; Sheng Li (Int. J. Circuit Theory Appl., 2024)

scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data. - Qing Xie; Wang Meng; Shili Lin (BMC Bioinform., 2025)