Online Microarray Laboratory Information Management System (M-LIMS): Linking Health Informatics and Bioinformatics. - Harpreet K. Monga; Adam L. Asare; Pearlly Yan; Tim Hui-Ming Huang; Charles William Caldwell (AMIA, 2001)

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)

Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands. - Wei Dai 006; Jens M. Teodoridis; Janet Graham; Constanze Zeller; Tim Hui-Ming Huang; Pearlly Yan; J. Keith Vass; Robert Brown 002; Jim Paul (BMC Bioinform., 2008)

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

Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. - Terry Camerlengo; Hatice Gulcin Ozer; Pearlly Yan; Jeffrey D. Parvin; Tim Hui-Ming Huang; Kun Huang 001; Mingxiang Teng; Lang Li 001; Yunlong Liu; Francisco Perez; Tahsin M. Kurç (BIBM, 2009)

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)

An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. - Huaxia Qin; Michael W. Y. Chan; Sandya Liyanarachchi; Curtis Balch; Dustin P. Potter; Irene J. Souriraj; Alfred S. L. Cheng; Francisco J. Agosto-Perez; Elena Nikonova; Pearlly Yan; Huey-Jen Lin; Kenneth P. Nephew; et al. (BMC Syst. Biol., 2009)

A scalable, flexible workflow for MethylCap-seq data analysis. - Benjamin Rodriguez; Hok-Hei Tam; David Frankhouser; Michael Trimarchi; Mark Murphy; Chris Kuo; Deval Parikh; Bryan Ball; Sebastian Schwind; John Curfman; William Blum; Guido Marcucci; et al. (GENSiPS, 2011)

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

A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. - Changyu Shen; Yi-Wen Huang; Yunlong Liu; Guohua Wang; Yuming Zhao; Zhiping Wang; Mingxiang Teng; Yadong Wang 001; David A. Flockhart; Todd C. Skaar; Pearlly Yan; Kenneth P. Nephew; et al. (BMC Syst. Biol., 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)

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)