Yidong Chen
Affiliations:- University of Texas Health Science Center at San Antonio, Department of Epidemiology and Biostatistics, TX, USA
- National Institutes of Health, Cancer Genetic Branch, Bethesda, MD, USA (former)
- Rochester Institute of Technology, NY, USA (PhD)
According to our database1,
Yidong Chen
authored at least 87 papers
between 1992 and 2024.
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Bibliography
2024
shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning.
Patterns, 2024
Patterns, 2024
2022
On the role of deep learning model complexity in adversarial robustness for medical images.
BMC Medical Informatics Decis. Mak., 2022
Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis.
Briefings Bioinform., 2022
2021
CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training.
BMC Bioinform., 2021
2020
Briefings Bioinform., 2020
2019
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods.
PLoS Comput. Biol., 2019
Convolutional neural network models for cancer type prediction based on gene expression.
CoRR, 2019
2018
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization.
CoRR, 2018
Predicting drug response of tumors from integrated genomic profiles by deep neural networks.
CoRR, 2018
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
2017
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Int. J. Comput. Biol. Drug Des., 2017
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.
BMC Bioinform., 2017
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival.
BMC Bioinform., 2017
2016
BMC Syst. Biol., 2016
A novel algorithm for calling mRNA m<sup>6</sup>A peaks by modeling biological variances in MeRIP-seq data.
Bioinform., 2016
2015
Nucleic Acids Res., 2015
Patho-finder - A fast and accurate program for pathogen identification through RNA-seq.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
Model-based and context-specific background correction and differential methylation testing for MBDCap-seq.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012).
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data.
BMC Bioinform., 2014
Proceedings of the 2014 IEEE Global Conference on Signal and Information Processing, 2014
2013
Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy.
IEEE Trans. Biomed. Eng., 2013
Identification of genomic functional hotspots with copy number alteration in liver cancer.
EURASIP J. Bioinform. Syst. Biol., 2013
BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database.
BMC Syst. Biol., 2013
Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis.
Adv. Bioinformatics, 2013
Proceedings of the IEEE Global Conference on Signal and Information Processing, 2013
NetceRNA: An algorithm for construction of phenotype-specific regulation networks via competing endogenous RNAs.
Proceedings of the 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, 2013
Proceedings of the 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, 2013
Proceedings of the 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, 2013
Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
Evaluating Dynamic Effects of Copy Number Alterations on Gene Expression Using a Single Transcription Model.
IEEE Trans. Biomed. Eng., 2012
Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic.
IEEE Trans. Biomed. Eng., 2012
Int. J. Funct. Informatics Pers. Medicine, 2012
An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancer.
Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012
Identification of functional genomic regions with copy number alteration in liver cancer.
Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012
2011
Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model.
Proceedings of the IEEE International Conference on Acoustics, 2011
Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Comprehensive investigation of connectivity map data-towards a drug mode of action network for personalized thnerapy.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
2010
EURASIP J. Adv. Signal Process., 2010
Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2010
An iterated conditional mode solution for Bayesian factor modeling of transcriptional regulatory networks.
Proceedings of the 2010 IEEE International Workshop on Genomic Signal Processing and Statistics, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
Constructing a compound mode-of-action network for personalized drug effectiveness prediction.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
2009
Proceedings of the International Joint Conferences on Bioinformatics, 2009
Proceedings of the 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 2009
2008
Bioinform., 2008
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
Bioinform., 2008
2006
EURASIP J. Bioinform. Syst. Biol., 2006
2005
2004
The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis.
EURASIP J. Adv. Signal Process., 2004
Which is better for cDNA-microarray-based classification: ratios or direct intensities.
Bioinform., 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2002
J. Comput. Biol., 2002
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.
Bioinform., 2002
Ratio statistics of gene expression levels and applications to microarray data analysis.
Bioinform., 2002
Proceedings of the 2nd ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2002), 2002
2001
2000
1999
J. Math. Imaging Vis., 1999
Nonlinear filters in genomic control.
Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999
1997
Signal Process., 1997
1996
Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In <i>situ</i> hybridization.
Pattern Recognit., 1996
J. Electronic Imaging, 1996
Proceedings of the 3th International Symposium on Mathematical Morphology and its Applications to Image and Signal Processing, 1996
1994
Proceedings of the 2nd International Symposium on Mathematical Morphology and Its Applications to Image Processing, 1994
1992
Estimation of optimal morphological τ-opening parameters based on independent observation of signal and noise pattern spectra.
Signal Process., 1992