A Fuzzy Logic Rule-Based System for Chromosome Recognition. - James M. Keller; Paul D. Gader; Ozy Sjahputera; Charles William Caldwell; Tim Hui-Ming Huang (CBMS, 1995)

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)

Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System. - Lang Li 001; Huidong Shi; Constantin T. Yiannoutsos; Tim Hui-Ming Huang; Kenneth P. Nephew (J. Comput. Biol., 2005)

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. - Lang Li 001; Alfred S. L. Cheng; Victor X. Jin; Henry H. Paik; Meiyun Fan; Xiaoman Li; Wei Zhang; Jason Robarge; Curtis Balch; Ramana V. Davuluri; Sun Kim; Tim Hui-Ming Huang; et al. (Bioinform., 2006)

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. - Hao Sun 001; Saranyan K. Palaniswamy; Twyla T. Pohar; Victor X. Jin; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 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)

Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. - Sun Kim; Meng Li 013; Hyun-il Henry Paik; Kenneth P. Nephew; Huidong Shi; Robin Kramer; Dong Xu; Tim Hui-Ming Huang (Pacific Symposium on Biocomputing, 2008)

Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. - Meng Li 013; Hyun-il Henry Paik; Curtis Balch; Yoosung Kim; Lang Li 001; Tim Hui-Ming Huang; Kenneth P. Nephew; Sun Kim (Bioinform., 2008)

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)

A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments. - Hatice Gulcin Ozer; Doruk Bozdag; Terry Camerlengo; Jiejun Wu; Yi-Wen Huang; Timothy D. R. Hartley; Jeffrey D. Parvin; Tim Hui-Ming Huang; Ümit V. Çatalyürek; Kun Huang 001 (BICoB, 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 robust unified approach to analyzing methylation and gene expression data. - Abbas Khalili; Tim Hui-Ming Huang; Shili Lin (Comput. Stat. Data Anal., 2009)

Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines. - Leng Han; Siyuan Zheng; Shuying Sun; Tim Hui-Ming Huang; Zhongming Zhao (ICIC (1), 2010)

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. - Fei Gu; Hang-Kai Hsu; Pei-Yin Hsu; Jiejun Wu; Yilin Ma; Jeffrey D. Parvin; Tim Hui-Ming Huang; Victor X. Jin (BMC Syst. Biol., 2010)

HRTBLDb: an informative data resource for hormone receptors target binding loci. - Brian A. Kennedy; Wenqing Gao; Tim Hui-Ming Huang; Victor X. Jin (Nucleic Acids Res., 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)

An ERα/modulator regulatory network in the breast cancer cells. - Heng-Yi Wu; Yu Wang; Pengyue Zheng; Guanglong Jiang; Yunlong Liu; Tim Hui-Ming Huang; Kenneth P. Nephew; Lang Li 001 (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)

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)

Comparing Multiple Chip-Sequencing Experiments. - Hatice Gulcin Ozer; Yi-Wen Huang; Jiejun Wu; Jeffrey D. Parvin; Tim Hui-Ming Huang; Kun Huang 001 (J. Bioinform. Comput. Biol., 2011)

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. - Hao Sun 001; Jiejun Wu; Priyankara Wikramasinghe; Sharmistha Pal; Ravi Gupta; Anirban Bhattacharyya; Francisco J. Agosto-Perez; Louise C. Showe; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 2011)

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data. - Jianhua Ruan; Md. Jamiul Jahid; Fei Gu; Chengwei Lei; Yi-Wen Huang; Ya-Ting Hsu; David G. Mutch; Chun-Liang Chen; Nameer B. Kirma; Tim Hui-Ming Huang (BCB, 2012)

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data. - Zhi Han; Lu Tian; Thierry Pécot; Tim Hui-Ming Huang; Raghu Machiraju; Kun Huang 001 (BMC Bioinform., 2012)

A dynamic time order network for time-series gene expression data analysis. - Pengyue Zhang; Raphaël Mourad; Yang Xiang; Kun Huang 001; Tim Hui-Ming Huang; Kenneth P. Nephew; Yunlong Liu; Lang Li 001 (BMC Syst. Biol., 2012)

BIMMER: A Bi-layer hidden Markov model for differential methylation analysis. - Zijing Mao; Tim Hui-Ming Huang; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

A personalized committee classification approach to improving prediction of breast cancer metastasis. - Md. Jamiul Jahid; Tim Hui-Ming Huang; Jianhua Ruan (Bioinform., 2014)

BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data. - Zijing Mao; Chifeng Ma; Tim Hui-Ming Huang; Yidong Chen 002; Yufei Huang 001 (BMC Bioinform., 2014)

Construction and Evaluation of Robust Interpretation Models for Breast Cancer Metastasis Prediction. - Nahim Adnan; Maryam Zand; Tim Hui-Ming Huang; Jianhua Ruan (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)