Yidong Chen

92 papers C 2Misc 1Journal 52Unranked 36
YearRankTypeTitle / Venue / Authors
2026 J jnl
In Memoriam: Edward R. Dougherty [In Memoriam].
IEEE Signal Process. Mag.
Ulisses Braga-Neto, Yidong Chen
2024 J jnl
Predicting drug response through tumor deconvolution by cancer cell lines.
Patterns
Yu-Ching Hsu, Yu-Chiao Chiu, Tzu-Pin Lu, Tzu-Hung Hsiao, Yidong Chen
2024 J jnl
shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning.
Patterns
Li-Ju Wang, Michael Ning, Tapsya Nayak, Michael J. Kasper, Satdarshan P. Monga, Yufei Huang, Yidong Chen, Yu-Chiao Chiu
2022 J jnl
Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis.
Briefings Bioinform.
Mario Flores, Zhentao Liu, Tinghe Zhang, Md Musaddaqui Hasib, Yu-Chiao Chiu, Zhenqing Ye, Karla Paniagua, Sumin Jo, Jianqiu Zhang, Shou-Jiang Gao, Yu-Fang Jin, Yidong Chen, Yufei Huang
2022 J jnl
On the role of deep learning model complexity in adversarial robustness for medical images.
BMC Medical Informatics Decis. Mak.
David Rodriguez, Tapsya Nayak, Yidong Chen, Ram Krishnan, Yufei Huang
2021 J jnl
CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training.
BMC Bioinform.
Milad Mostavi, Yu-Chiao Chiu, Yidong Chen, Yufei Huang
2021 — ed.
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Houston, TX, USA, December 9-12, 2021
BIBM
Yufei Huang, Lukasz A. Kurgan, Feng Luo, Xiaohua Hu, Yidong Chen, Edward R. Dougherty, Andrzej Kloczkowski, Yaohang Li
2020 J jnl
Deep learning of pharmacogenomics resources: moving towards precision oncology.
Briefings Bioinform.
Yu-Chiao Chiu, Hung-I Harry Chen, Aparna Gorthi, Milad Mostavi, Siyuan Zheng, Yufei Huang, Yidong Chen
2019 J jnl
Convolutional neural network models for cancer type prediction based on gene expression.
CoRR
Milad Mostavi, Yu-Chiao Chiu, Yufei Huang, Yidong Chen
2019 J jnl
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods.
PLoS Comput. Biol.
Song-Yao Zhang, Shaowu Zhang, Xiaonan Fan, Jia Meng, Yidong Chen, Shou-Jiang Gao, Yufei Huang
2018 — conf
A Machine Learning Approach for Uncovering N6-methyladenosine-Disease Association.
BCB
Songyao Zhang, Shaowu Zhang, Xiaonan Fan, Jia Meng, Yidong Chen, Yufei Huang
2018 J jnl
Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen, Eric Y. Chuang
2018 J jnl
GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization.
CoRR
Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang, Yidong Chen
2018 J jnl
MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiaodong Cui, Lin Zhang, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang
2018 J jnl
Predicting drug response of tumors from integrated genomic profiles by deep neural networks.
CoRR
Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang, Songyao Zhang, Aparna Gorthi, Li-Ju Wang, Yufei Huang, Yidong Chen
2017 J jnl
Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net.
IEEE ACM Trans. Comput. Biol. Bioinform.
Lin Zhang, Hui Liu, Yufei Huang, Xuesong Wang, Yidong Chen, Jia Meng
2017 J jnl
Computational tools for genome-wide R-loops identification and characterisation.
Int. J. Comput. Biol. Drug Des.
Rongjie Liu, Aparna Gorthi, Yufang Jin, Alexander J. R. Bishop, Yidong Chen
2017 J jnl
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival.
BMC Bioinform.
Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu, Tzu-Hung Hsiao, Eric Y. Chuang, Yidong Chen
2017 J jnl
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.
BMC Bioinform.
Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson-Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodriguez, Yidong Chen
2016 J jnl
A novel algorithm for calling mRNA m
Bioinform.
Xiaodong Cui, Jia Meng, Shaowu Zhang, Yidong Chen, Yufei Huang
2016 J jnl
A simple gene set-based method accurately predicts the synergy of drug pairs.
BMC Syst. Biol.
Yu-Ching Hsu, Yu-Chiao Chiu, Yidong Chen, Tzu-Hung Hsiao, Eric Y. Chuang
2015 — conf
Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme.
BIBM
Yu-Chiao Chiu, Kai-Wen Liang, Tzu-Hung Hsiao, Yidong Chen, Eric Y. Chuang
2015 J jnl
MeT-DB: a database of transcriptome methylation in mammalian cells.
Nucleic Acids Res.
Hui Liu, Mario A. Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet K. Rao, Yidong Chen, Yufei Huang
2015 — conf
Model-based and context-specific background correction and differential methylation testing for MBDCap-seq.
BIBM
Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
2015 — conf
Patho-finder - A fast and accurate program for pathogen identification through RNA-seq.
BIBM
Chin-Ting Wu, Tzu-Hung Hsiao, Yu-Chiao Chiu, Yu-Ching Hsu, Eric Y. Chuang, Yidong Chen
2014 J jnl
A novel significance score for gene selection and ranking.
Bioinform.
Yufei Xiao, Tzu-Hung Hsiao, Uthra Suresh, Hung-I Harry Chen, Xiaowu Wu, Steven E. Wolf, Yidong Chen
2014 J jnl
BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data.
BMC Bioinform.
Zijing Mao, Chifeng Ma, Tim Hui-Ming Huang, Yidong Chen, Yufei Huang
2014 — conf
Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test.
GlobalSIP
Lin Zhang, Jia Meng, Hui Liu, Xiaodong Cui, Shao-Wu Zhang, Yidong Chen, Yufei Huang
2014 J jnl
Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012).
IEEE ACM Trans. Comput. Biol. Bioinform.
Yufei Huang, Yidong Chen, Xiaoning Qian
2013 — conf
An HMM-based Exome Peak-finding package for RNA epigenome sequencing data.
GENSiPS
Xiaodong Cui, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang
2013 — conf
BIMMER: A Bi-layer hidden Markov model for differential methylation analysis.
BIBM
Zijing Mao, Tim Hui-Ming Huang, Yidong Chen, Yufei Huang
2013 J jnl
BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database.
BMC Syst. Biol.
Chifeng Ma, Hung-I Harry Chen, Mario Flores, Yufei Huang, Yidong Chen
2013 — conf
Characterization of conditions for competing endogenous RNA regulation in GBM.
GENSiPS
Yu-Chiao Chiu, Eric Y. Chuang, Tzu-Hung Hsiao, Yidong Chen
2013 — conf
Differential analysis of rna methylation sequencing data.
GlobalSIP
Xiaodong Cui, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang
2013 J jnl
Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy.
IEEE Trans. Biomed. Eng.
Fang-Han Hsu, Edward R. Dougherty, Yidong Chen, Erchin Serpedin
2013 J jnl
Exome-based analysis for RNA epigenome sequencing data.
Bioinform.
Jia Meng, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, Yufei Huang
2013 J jnl
Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis.
Adv. Bioinformatics
Mario Flores, Tzu-Hung Hsiao, Yu-Chiao Chiu, Eric Y. Chuang, Yufei Huang, Yidong Chen
2013 J jnl
Identification of genomic functional hotspots with copy number alteration in liver cancer.
EURASIP J. Bioinform. Syst. Biol.
Tzu-Hung Hsiao, Hung-I Harry Chen, Stephanie Roessler, Xin Wei Wang, Yidong Chen
2013 — conf
Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer.
BIBM
Lin Zhang, Hui Liu, Jia Meng, Xuesong Wang, Yidong Chen, Yufei Huang
2013 — conf
Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme.
BIBM
Yu-Chiao Chiu, Eric Y. Chuang, Tzu-Hung Hsiao, Yidong Chen
2013 — conf
NetceRNA: An algorithm for construction of phenotype-specific regulation networks via competing endogenous RNAs.
GENSiPS
Mario Flores, Yufei Huang, Yidong Chen
2013 — conf
Unveiling the dynamics in RNA epigenetic regulations.
BIBM
Jia Meng, Xiaodong Cui, Hui Liu, Lin Zhang, Shaowu Zhang, Manjeet K. Rao, Yidong Chen, Yufei Huang
2012 — conf
An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancer.
GENSiPS
Lin Zhang, Hui Liu, Tzu-Hung Hsiao, Yidong Chen, Yufei Huang
2012 J jnl
Evaluating Dynamic Effects of Copy Number Alterations on Gene Expression Using a Single Transcription Model.
IEEE Trans. Biomed. Eng.
Fang-Han Hsu, Erchin Serpedin, Yidong Chen, Edward R. Dougherty
2012 — conf
Identification of functional genomic regions with copy number alteration in liver cancer.
GENSiPS
Tzu-Hung Hsiao, Hung-I Harry Chen, Yidong Chen
2012 J jnl
Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic.
IEEE Trans. Biomed. Eng.
Fang-Han Hsu, Erchin Serpedin, Yidong Chen, Edward R. Dougherty
2012 J jnl
Temporal clustering of gene expression patterns using short-time segments.
Int. J. Funct. Informatics Pers. Medicine
Nguyen T. Nguyen, Ying Ann Chiao, Yufei Huang, Shou-Jiang Gao, Merry Lindsey, Yidong Chen, Yufang Jin
2012 — conf
Using gene sets to identify putative drugs for breast cancer.
BIBM
Tzu-Hung Hsiao, Hung-I Harry Chen, Yidong Chen, Yu-Heng Chen, Eric Y. Chuang
2011 — conf
Comprehensive investigation of connectivity map data-towards a drug mode of action network for personalized thnerapy.
BIBM Workshops
Chifeng Ma, Yufei Huang, Huang-I Harry, Yidong Chen
2011 — conf
Computational prediction of microRNA regulatory pathways.
GENSiPS
Dong Yue, Yidong Chen, Shou-Jiang Gao, Yufei Huang
2011 — conf
Gene sets enrichment analysis of miRNA expression profile.
BIBM Workshops
Tzu-Hung Hsiao, Hung-I Harry Chen, Patricia C. Sanchez-Diaz, Jaclyn Y. Hung, Yidong Chen, Yufei Huang
2011 — conf
Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles.
GENSiPS
Fang-Han Hsu, Erchin Serpedin, Tzu-Hung Hsiao, Alexander J. R. Bishop, Edward R. Dougherty, Yidong Chen
2011 — conf
Multisource biological pathway consolidation.
GENSiPS
Mark Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander J. R. Bishop, Yidong Chen
2011 — conf
S-score: A novel scoring method of gene signatures for molecular classification.
GENSiPS
Hung-I Harry Chen, Tzu-Hung Hsiao, Yidong Chen, Charles Keller
2011 — conf
Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels.
GENSiPS
Fang-Han Hsu, Erchin Serpedin, Yidong Chen, Edward R. Dougherty
2011 Misc conf
Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model.
ICASSP
Jia Meng, Hung-I Chen, Jianqiu Zhang, Yidong Chen, Yufei Huang
2010 — conf
A Bayesian decision fusion approach for microRNA target prediction.
BCB
Dong Yue, Hui Liu, Mingzhu Lu, Philip Chen, Yidong Chen, Yufei Huang
2010 — conf
A computational framework for predicting drug Mode-of-Action.
BIBM Workshops
Chifeng Ma, Hung-I Harry Chen, Yufei Huang, Yidong Chen
2010 — conf
An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks.
BIBM
Jia Meng, Jianqiu Zhang, Yidong Chen, Yufei Huang
2010 — conf
An iterated conditional mode solution for Bayesian factor modeling of transcriptional regulatory networks.
GENSiPS
Jia Meng, Jianqiu Zhang, Yidong Chen, Yufei Huang
2010 — conf
Computational prediction of MicroRNA regulatory pathways.
BIBM Workshops
Dong Yue, Yidong Chen, Shou-Jiang Gao, Yufei Huang
2010 — conf
Constructing a compound mode-of-action network for personalized drug effectiveness prediction.
BCB
Chifeng Ma, Hung-I Harry Chen, Yufei Huang, Yidong Chen
2010 J jnl
Improving performance of mammalian microRNA target prediction.
BMC Bioinform.
Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao, Yufei Huang
2010 — conf
SysMicrO: A Novel Systems Approach for miRNA Target Prediction.
ICIC (2)
Hui Liu, Lin Zhang, Qilong Sun, Yidong Chen, Yufei Huang
2010 — conf
Temporal clustering of gene expression patterns using short-time segments.
BIBM Workshops
Nguyen T. Nguyen, Yufang Jin, Yufei Huang, Ying Ann Chiao, Shou-Jiang Gao, Merry Lindsey, Yidong Chen
2010 J jnl
Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model.
EURASIP J. Adv. Signal Process.
Jia Meng, Jianqiu (Michelle) Zhang, Yuan (Alan) Qi, Yidong Chen, Yufei Huang
2009 — conf
A comprehensive study of a SVM-based miRNA target prediction algorithm.
GENSiPS
Hui Liu, Dong Yue, Yidong Chen, Yufei Huang
2009 — conf
Mapping miRNA Regulation to Functional Gene Sets.
IJCBS
Yidong Chen, Hung-I Harry Chen, Yufei Huang
2008 J jnl
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
Bioinform.
Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen
2008 J jnl
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
Bioinform.
Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen
2008 J jnl
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Bioinform.
Yuelin Zhu, Sean R. Davis, Robert M. Stephens, Paul S. Meltzer, Yidong Chen
2006 J jnl
Normalization Benefits Microarray-Based Classification.
EURASIP J. Bioinform. Syst. Biol.
Jianping Hua, Yoganand Balagurunathan, Yidong Chen, James Lowey, Michael L. Bittner, Zixiang Xiong, Edward Suh, Edward R. Dougherty
2005 J jnl
Optimal robust classifiers.
Pattern Recognit.
Edward R. Dougherty, Jianping Hua, Zixiang Xiong, Yidong Chen
2004 — conf
Are We There Yet? Genomic Profiling and Mechanism in Cancer Research.
CSB
Paul S. Meltzer, Sean R. Davis, Kristin Baird, Yidong Chen
2004 J jnl
Editorial.
EURASIP J. Adv. Signal Process.
Xiaodong Wang, Edward R. Dougherty, Yidong Chen, Carsten O. Peterson
2004 J jnl
The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis.
EURASIP J. Adv. Signal Process.
Xiongwu Wu, Yidong Chen, Bernard R. Brooks, Yan A. Su
2004 J jnl
Which is better for cDNA-microarray-based classification: ratios or direct intensities.
Bioinform.
Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent
2002 J jnl
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.
Bioinform.
Mattias Wahde, Gregory T. Klus, Michael L. Bittner, Yidong Chen, Zoltan Szallasi
2002 — conf
E-CAST: A Data Mining Algorithm for Gene Expression Data.
BIOKDD
Abdelghani Bellaachia, David Portnoy, Yidong Chen, Abdel G. Elkahloun
2002 J jnl
Inference from Clustering with Application to Gene-Expression Microarrays.
J. Comput. Biol.
Edward R. Dougherty, Junior Barrera, Marcel Brun, Seungchan Kim, Roberto Marcondes Cesar Junior, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent
2002 J jnl
Ratio statistics of gene expression levels and applications to microarray data analysis.
Bioinform.
Yidong Chen, Vishnu G. Kamat, Edward R. Dougherty, Michael L. Bittner, Paul S. Meltzer, Jeffrey M. Trent
2002 J jnl
Strong Feature Sets from Small Samples.
J. Comput. Biol.
Seungchan Kim, Edward R. Dougherty, Junior Barrera, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent
2001 J jnl
Robust optimal granulometric bandpass filters.
Signal Process.
Edward R. Dougherty, Yidong Chen
2000 J jnl
Coefficient of determination in nonlinear signal processing.
Signal Process.
Edward R. Dougherty, Seungchan Kim, Yidong Chen
1999 J jnl
Markovian Analysis of Adaptive Reconstructive Multiparameter tau-Openings.
J. Math. Imaging Vis.
Yidong Chen, Edward R. Dougherty
1999 — conf
Nonlinear filters in genomic control.
NSIP
Edward R. Dougherty, Michael L. Bittner, Yidong Chen, Seungchan Kim, Krishnamoorthy Sivakumar, Junior Barrera, Paul S. Meltzer, Jeffrey M. Trent
1997 J jnl
Optimal and adaptive reconstructive granulometric bandpass filters.
Signal Process.
Yidong Chen, Edward R. Dougherty
1996 J jnl
Adaptive reconstructive tau-openings: convergence and the steady-state distribution.
J. Electronic Imaging
Yidong Chen, Edward R. Dougherty
1996 J jnl
Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In
Pattern Recognit.
Edward R. Dougherty, Yidong Chen, Amir Waks
1996 C conf
Optimal and Adaptive Design of Reconstructive Granulometric Filters.
ISMM
Edward R. Dougherty, Yidong Chen
1994 C conf
Adaptive Parameterized Openings.
ISMM
Yidong Chen, Edward R. Dougherty
1992 J jnl
Estimation of optimal morphological τ-opening parameters based on independent observation of signal and noise pattern spectra.
Signal Process.
Edward R. Dougherty, Robert M. Haralick, Yidong Chen, Carsten Agerskov, Ulrik Jacobi, Poul Henrik Sloth