Estimation of optimal morphological τ-opening parameters based on independent observation of signal and noise pattern spectra. - Edward R. Dougherty; Robert M. Haralick; Yidong Chen 002; Carsten Agerskov; Ulrik Jacobi; Poul Henrik Sloth (Signal Process., 1992)

Adaptive Parameterized Openings. - Yidong Chen 002; Edward R. Dougherty (ISMM, 1994)

Optimal and Adaptive Design of Reconstructive Granulometric Filters. - Edward R. Dougherty; Yidong Chen 002 (ISMM, 1996)

Adaptive reconstructive tau-openings: convergence and the steady-state distribution. - Yidong Chen 002; Edward R. Dougherty (J. Electronic Imaging, 1996)

Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In situ hybridization. - Edward R. Dougherty; Yidong Chen 002; Amir Waks (Pattern Recognit., 1996)

Optimal and adaptive reconstructive granulometric bandpass filters. - Yidong Chen 002; Edward R. Dougherty (Signal Process., 1997)

Nonlinear filters in genomic control. - Edward R. Dougherty; Michael L. Bittner; Yidong Chen 002; Seungchan Kim; Krishnamoorthy Sivakumar; Junior Barrera; Paul S. Meltzer; Jeffrey M. Trent (NSIP, 1999)

Markovian Analysis of Adaptive Reconstructive Multiparameter tau-Openings. - Yidong Chen 002; Edward R. Dougherty (J. Math. Imaging Vis., 1999)

Coefficient of determination in nonlinear signal processing. - Edward R. Dougherty; Seungchan Kim; Yidong Chen 002 (Signal Process., 2000)

Robust optimal granulometric bandpass filters. - Edward R. Dougherty; Yidong Chen 002 (Signal Process., 2001)

E-CAST: A Data Mining Algorithm for Gene Expression Data. - Abdelghani Bellaachia; David Portnoy; Yidong Chen 002; Abdel G. Elkahloun (BIOKDD, 2002)

Ratio statistics of gene expression levels and applications to microarray data analysis. - Yidong Chen 002; Vishnu G. Kamat; Edward R. Dougherty; Michael L. Bittner; Paul S. Meltzer; Jeffrey M. Trent (Bioinform., 2002)

Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. - Mattias Wahde; Gregory T. Klus; Michael L. Bittner; Yidong Chen 002; Zoltan Szallasi (Bioinform., 2002)

Inference from Clustering with Application to Gene-Expression Microarrays. - Edward R. Dougherty; Junior Barrera; Marcel Brun; Seungchan Kim; Roberto Marcondes Cesar Junior; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (J. Comput. Biol., 2002)

Strong Feature Sets from Small Samples. - Seungchan Kim; Edward R. Dougherty; Junior Barrera; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (J. Comput. Biol., 2002)

Are We There Yet? Genomic Profiling and Mechanism in Cancer Research. - Paul S. Meltzer; Sean R. Davis; Kristin Baird; Yidong Chen 002 (CSB, 2004)

Which is better for cDNA-microarray-based classification: ratios or direct intensities. - Sanju Attoor; Edward R. Dougherty; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (Bioinform., 2004)

Editorial. - Xiaodong Wang 001; Edward R. Dougherty; Yidong Chen 002; Carsten O. Peterson (EURASIP J. Adv. Signal Process., 2004)

The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis. - Xiongwu Wu; Yidong Chen 002; Bernard R. Brooks; Yan A. Su (EURASIP J. Adv. Signal Process., 2004)

Optimal robust classifiers. - Edward R. Dougherty; Jianping Hua; Zixiang Xiong; Yidong Chen 002 (Pattern Recognit., 2005)

Normalization Benefits Microarray-Based Classification. - Jianping Hua; Yoganand Balagurunathan; Yidong Chen 002; James Lowey; Michael L. Bittner; Zixiang Xiong; Edward Suh; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2006)

A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. - Hung-I Harry Chen; Fang-Han Hsu; Yuan Jiang; Mong-Hsun Tsai; Pan-Chyr Yang; Paul S. Meltzer; Eric Y. Chuang; Yidong Chen 002 (Bioinform., 2008)

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. - Yuelin Zhu; Sean R. Davis; Robert M. Stephens; Paul S. Meltzer; Yidong Chen 002 (Bioinform., 2008)

A comprehensive study of a SVM-based miRNA target prediction algorithm. - Hui Liu 024; Dong Yue 002; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2009)

Mapping miRNA Regulation to Functional Gene Sets. - Yidong Chen 002; Hung-I Harry Chen; Yufei Huang 001 (IJCBS, 2009)

Constructing a compound mode-of-action network for personalized drug effectiveness prediction. - Chifeng Ma; Hung-I Harry Chen; Yufei Huang 001; Yidong Chen 002 (BCB, 2010)

A Bayesian decision fusion approach for microRNA target prediction. - Dong Yue 002; Hui Liu 024; Mingzhu Lu; Philip Chen 001; Yidong Chen 002; Yufei Huang 001 (BCB, 2010)

A computational framework for predicting drug Mode-of-Action. - Chifeng Ma; Hung-I Harry Chen; Yufei Huang 001; Yidong Chen 002 (BIBM Workshops, 2010)

An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks. - Jia Meng 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (BIBM, 2010)

Computational prediction of MicroRNA regulatory pathways. - Dong Yue 002; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (BIBM Workshops, 2010)

An iterated conditional mode solution for Bayesian factor modeling of transcriptional regulatory networks. - Jia Meng 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2010)

SysMicrO: A Novel Systems Approach for miRNA Target Prediction. - Hui Liu 024; Lin Zhang 015; Qilong Sun; Yidong Chen 002; Yufei Huang 001 (ICIC (2), 2010)

Improving performance of mammalian microRNA target prediction. - Hui Liu 024; Dong Yue 002; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (BMC Bioinform., 2010)

Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model. - Jia Meng 001; Jianqiu (Michelle) Zhang; Yuan (Alan) Qi; Yidong Chen 002; Yufei Huang 001 (EURASIP J. Adv. Signal Process., 2010)

Gene sets enrichment analysis of miRNA expression profile. - Tzu-Hung Hsiao; Hung-I Harry Chen; Patricia C. Sanchez-Diaz; Jaclyn Y. Hung; Yidong Chen 002; Yufei Huang 001 (BIBM Workshops, 2011)

Comprehensive investigation of connectivity map data-towards a drug mode of action network for personalized thnerapy. - Chifeng Ma; Yufei Huang 001; Huang-I Harry; Yidong Chen 002 (BIBM Workshops, 2011)

S-score: A novel scoring method of gene signatures for molecular classification. - Hung-I Harry Chen; Tzu-Hung Hsiao; Yidong Chen 002; Charles Keller (GENSiPS, 2011)

Multisource biological pathway consolidation. - Mark Doderer; Zachry Anguiano; Uthra Suresh; Ravi Dashnamoorthy; Alexander J. R. Bishop; Yidong Chen 002 (GENSiPS, 2011)

Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (GENSiPS, 2011)

Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles. - Fang-Han Hsu; Erchin Serpedin; Tzu-Hung Hsiao; Alexander J. R. Bishop; Edward R. Dougherty; Yidong Chen 002 (GENSiPS, 2011)

Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. - Jia Meng 001; Hung-I Chen 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (ICASSP, 2011)

Using gene sets to identify putative drugs for breast cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Yidong Chen 002; Yu-Heng Chen; Eric Y. Chuang (BIBM, 2012)

Identification of functional genomic regions with copy number alteration in liver cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Yidong Chen 002 (GENSiPS, 2012)

An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancer. - Lin Zhang 015; Hui Liu 024; Tzu-Hung Hsiao; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2012)

Temporal clustering of gene expression patterns using short-time segments. - Nguyen T. Nguyen; Ying Ann Chiao; Yufei Huang 001; Shou-Jiang Gao; Merry Lindsey; Yidong Chen 002; Yufang Jin (Int. J. Funct. Informatics Pers. Medicine, 2012)

Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2012)

Evaluating Dynamic Effects of Copy Number Alterations on Gene Expression Using a Single Transcription Model. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2012)

Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme. - Yu-Chiao Chiu; Eric Y. Chuang; Tzu-Hung Hsiao; Yidong Chen 002 (BIBM, 2013)

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)

Unveiling the dynamics in RNA epigenetic regulations. - Jia Meng 001; Xiaodong Cui; Hui Liu 024; Lin Zhang 015; Shaowu Zhang 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer. - Lin Zhang 015; Hui Liu 024; Jia Meng 001; Xuesong Wang 001; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Characterization of conditions for competing endogenous RNA regulation in GBM. - Yu-Chiao Chiu; Eric Y. Chuang; Tzu-Hung Hsiao; Yidong Chen 002 (GENSiPS, 2013)

An HMM-based Exome Peak-finding package for RNA epigenome sequencing data. - Xiaodong Cui; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2013)

NetceRNA: An algorithm for construction of phenotype-specific regulation networks via competing endogenous RNAs. - Mario Flores; Yufei Huang 001; Yidong Chen 002 (GENSiPS, 2013)

Differential analysis of rna methylation sequencing data. - Xiaodong Cui; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2013)

Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis. - Mario Flores; Tzu-Hung Hsiao; Yu-Chiao Chiu; Eric Y. Chuang; Yufei Huang 001; Yidong Chen 002 (Adv. Bioinformatics, 2013)

Exome-based analysis for RNA epigenome sequencing data. - Jia Meng 001; Xiaodong Cui; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (Bioinform., 2013)

BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database. - Chifeng Ma; Hung-I Harry Chen; Mario Flores; Yufei Huang 001; Yidong Chen 002 (BMC Syst. Biol., 2013)

Identification of genomic functional hotspots with copy number alteration in liver cancer. - Tzu-Hung Hsiao; Hung-I Harry Chen; Stephanie Roessler; Xin Wei Wang 001; Yidong Chen 002 (EURASIP J. Bioinform. Syst. Biol., 2013)

Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy. - Fang-Han Hsu; Edward R. Dougherty; Yidong Chen 002; Erchin Serpedin (IEEE Trans. Biomed. Eng., 2013)

Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Xiaodong Cui; Shao-Wu Zhang 001; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2014)

A novel significance score for gene selection and ranking. - Yufei Xiao; Tzu-Hung Hsiao; Uthra Suresh; Hung-I Harry Chen; Xiaowu Wu; Steven E. Wolf; Yidong Chen 002 (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)

Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012). - Yufei Huang 001; Yidong Chen 002; Xiaoning Qian (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. - Yu-Chiao Chiu; Kai-Wen Liang; Tzu-Hung Hsiao; Yidong Chen 002; Eric Y. Chuang (BIBM, 2015)

Model-based and context-specific background correction and differential methylation testing for MBDCap-seq. - Yuanhang Liu; Desiree Wilson; Robin J. Leach; Yidong Chen 002 (BIBM, 2015)

Patho-finder - A fast and accurate program for pathogen identification through RNA-seq. - Chin-Ting Wu; Tzu-Hung Hsiao; Yu-Chiao Chiu; Yu-Ching Hsu; Eric Y. Chuang; Yidong Chen 002 (BIBM, 2015)

MeT-DB: a database of transcriptome methylation in mammalian cells. - Hui Liu 024; Mario A. Flores; Jia Meng 001; Lin Zhang 015; Xinyu Zhao; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (Nucleic Acids Res., 2015)

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data. - Xiaodong Cui; Jia Meng 001; Shaowu Zhang 001; Yidong Chen 002; Yufei Huang 001 (Bioinform., 2016)

A simple gene set-based method accurately predicts the synergy of drug pairs. - Yu-Ching Hsu; Yu-Chiao Chiu; Yidong Chen 002; Tzu-Hung Hsiao; Eric Y. Chuang (BMC Syst. Biol., 2016)

Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. - Yu-Chiao Chiu; Li-Ju Wang; Tzu-Pin Lu; Tzu-Hung Hsiao; Eric Y. Chuang; Yidong Chen 002 (BMC Bioinform., 2017)

XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. - Yuanhang Liu; Ping Wu; Jingqi Zhou; Teresa L. Johnson-Pais; Zhao Lai; Wasim H. Chowdhury; Ronald Rodriguez; Yidong Chen 002 (BMC Bioinform., 2017)

Computational tools for genome-wide R-loops identification and characterisation. - Rongjie Liu; Aparna Gorthi; Yufang Jin; Alexander J. R. Bishop; Yidong Chen 002 (Int. J. Comput. Biol. Drug Des., 2017)

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. - Lin Zhang 015; Hui Liu 024; Yufei Huang 001; Xuesong Wang 001; Yidong Chen 002; Jia Meng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

A Machine Learning Approach for Uncovering N6-methyladenosine-Disease Association. - Songyao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Yufei Huang 001 (BCB, 2018)

Predicting drug response of tumors from integrated genomic profiles by deep neural networks. - Yu-Chiao Chiu; Hung-I Harry Chen; Tinghe Zhang; Songyao Zhang; Aparna Gorthi; Li-Ju Wang; Yufei Huang 001; Yidong Chen 002 (CoRR, 2018)

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization. - Hung-I Harry Chen; Yu-Chiao Chiu; Tinghe Zhang; Songyao Zhang; Yufei Huang 001; Yidong Chen 002 (CoRR, 2018)

Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. - Yu-Chiao Chiu; Tzu-Hung Hsiao; Li-Ju Wang; Yidong Chen 002; Eric Y. Chuang (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. - Xiaodong Cui; Lin Zhang 015; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Convolutional neural network models for cancer type prediction based on gene expression. - Milad Mostavi; Yu-Chiao Chiu; Yufei Huang 001; Yidong Chen 002 (CoRR, 2019)

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Song-Yao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (PLoS Comput. Biol., 2019)

Deep learning of pharmacogenomics resources: moving towards precision oncology. - Yu-Chiao Chiu; Hung-I Harry Chen; Aparna Gorthi; Milad Mostavi; Siyuan Zheng; Yufei Huang 001; Yidong Chen 002 (Briefings Bioinform., 2020)

CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training. - Milad Mostavi; Yu-Chiao Chiu; Yidong Chen 002; Yufei Huang 001 (BMC Bioinform., 2021)

Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis. - Mario Flores; Zhentao Liu; Tinghe Zhang; Md Musaddaqui Hasib; Yu-Chiao Chiu; Zhenqing Ye; Karla Paniagua; Sumin Jo; Jianqiu Zhang 002; Shou-Jiang Gao; Yu-Fang Jin; Yidong Chen 002; et al. (Briefings Bioinform., 2022)

On the role of deep learning model complexity in adversarial robustness for medical images. - David Rodriguez; Tapsya Nayak; Yidong Chen 002; Ram Krishnan; Yufei Huang 001 (BMC Medical Informatics Decis. Mak., 2022)

Predicting drug response through tumor deconvolution by cancer cell lines. - Yu-Ching Hsu; Yu-Chiao Chiu; Tzu-Pin Lu; Tzu-Hung Hsiao; Yidong Chen 002 (Patterns, 2024)

shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. - Li-Ju Wang; Michael Ning; Tapsya Nayak; Michael J. Kasper; Satdarshan P. Monga; Yufei Huang 001; Yidong Chen 002; Yu-Chiao Chiu (Patterns, 2024)