Yang Dai

发表

Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures

Damian Roqueiro, Lei Huang, Yang Dai, 2011, Proteome Science.

A probabilistic meta-predictor for the MHC class II binding peptides

Lei Huang, Yang Dai, Oleksiy Karpenko, 2007, Immunogenetics.

On Simplified Global Nonlinear Function for Fitness Landscape: A Case Study of Inverse Protein Folding

Jie Liang, Yang Dai, Yun Xu, 2014, PloS one.

MiMeNet: Exploring microbiome-metabolome relationships using neural networks

Yang Dai, B. Layden, Derek Reiman, 2020, bioRxiv.

Correlative Analysis of miRNA Expression and Oncotype Dx Recurrence Score in Estrogen Receptor Positive Breast Carcinomas

J. Frasor, Yang Dai, E. Wiley, 2015, PloS one.

Computational methods for the identification of microRNA targets.

Yang Dai, Xiaofeng Zhou, 2010, Open access bioinformatics.

Predicting bacterial community assemblages using an artificial neural network approach.

Peter E. Larsen, Yang Dai, F. Collart, 2012, Methods in molecular biology.

Site-Specific Expression Pattern of PIWI-Interacting RNA in Skin and Oral Mucosal Wound Healing

Yang Dai, Zujian Chen, Xiaofeng Zhou, 2020, International journal of molecular sciences.

Structural learning of genetic regulatory networks based on prior biological knowledge and microarray gene expression measurements

Peter E. Larsen, Yang Dai, E. Almasri, 2009 .

A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments

Eyad Almasri, Yang Dai, Peter E. Larsen, 2007, BMC Bioinformatics.

Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction

Peter E. Larsen, Yang Dai, F. Collart, 2016, Front. Plant Sci..

A Local Genetic Algorithm for the Identification of Condition-Specific MicroRNA-Gene Modules

Damian Roqueiro, Yang Dai, Damian Roqueiro, 2013, TheScientificWorldJournal.

Intrinsic Differences between Oral and Skin Keratinocytes

Yang Dai, L. DiPietro, P. Marucha, 2014, PloS one.

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

Ahmed A. Metwally, Yang Dai, P. Finn, 2016, bioRxiv.

MeDEStrand: an improved method to infer genome-wide absolute methylation level from DNA enrichment experiment

Yang Dai, P. Yin, S. Bulun, 2017, bioRxiv.

Selection of Multiple SNPs in Case-Control Association Study Based on a Discretized Network Flow Approach ?

S. Dutt, Yang Dai, J. Fontanarosa, 2009 .

Patterns and Localization of Gene Expression During Intramembranous Bone Regeneration in the Rat Femoral Marrow Ablation Model

Yang Dai, S. Shott, S. Kuroda, 2005, Calcified Tissue International.

LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines

Yang Dai, Hong Hu, Jingting Xu, 2016, bioRxiv.

�ocal �enetic �lgorithm �or the Identi�cation o� �ondition��eci�c

Damian Roqueiro, Yang Dai, MicroR��eneModules, 2013 .

Correlated Discretized Expression Score: A Method for Identifying Gene Interaction Networks from Time Course Microarray Expression Data

Peter E. Larsen, Yang Dai, E. Almasri, 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

Sample Scale-Free Gene Regulatory Network Using Gene Ontology

Peter E. Larsen, Yang Dai, E. Almasri, 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

In Vivo Genome-Wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor

Yang Dai, P. Yin, Stacy A. Kujawa, 2022, Reproductive Sciences.

Modeling interaction networks between host, diet, and bacteria predicts obesogenesis in a mouse model

Peter E. Larsen, Yang Dai, 2022, Frontiers in Molecular Biosciences.

Local application of rhTGF-beta2 modulates dynamic gene expression in a rat implant model.

Yang Dai, S. Shott, S. Kuroda, 2005, Bone.

BindSDb: A binding-information spatial database

Damian Roqueiro, Yang Dai, J. Frasor, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Prioritizing predicted cis-regulatory elements for co-expressed gene sets based on Lasso regression models

Hong Hu, Yang Dai, Damian Roqueiro, 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

Patricia W. Finn, Yang Dai, Ahmed A. Metwally, 2016, bioRxiv.

A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes

Yang Dai, J. Rehman, Shang Gao, 2021, Genome research.

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells

Damian Roqueiro, Yang Dai, Serdar E. Bulun, 2012, PloS one.

PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolution Neural Networks for Metagenomic Data

Derek Reiman, Yang Dai, Ahmed A. Metwally, 2018, bioRxiv.

Using Convolutional Neural Network to Study the Regulatory Relationship Between DNA Methylation and Gene Expression

Derek Reiman, Yang Dai, Jingting Xu, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Ping Yin, Yang Dai, Jingting Xu, 2018, BMC Bioinformatics.

Regulatory Elements in Low-Methylated Regions Predict Directional Change of Gene Expression

Hong Hu, Yang Dai, Jingting Xu, 2015, IEEE Journal of Biomedical and Health Informatics.

Exploring regulatory elements in low-methylated regions for gene expression prediction

Hong Hu, Yang Dai, Yang Dai, 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Exploration of microRNA Genomic Variation Associated with Common Human Diseases

Yang Dai, J. Fontanarosa, 2013 .

Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction

Yang Dai, Zhengdeng Lei, Yang Dai, 2006, BMC Bioinformatics.

An SVM-based system for predicting protein subnuclear localizations

Yang Dai, Zhengdeng Lei, Yang Dai, 2005, BMC Bioinformatics.

A New Kernel Based on High-Scored Pairs of Tri-peptides and Its Application in Prediction of Protein Subcellular Localization

Yang Dai, Zhengdeng Lei, Yang Dai, 2005, International Conference on Computational Science.

A Class of New Kernels Based on High-Scored Pairs of k-Peptides for SVMs and Its Application for Prediction of Protein Subcellular Localization

Yang Dai, Zhengdeng Lei, Yang Dai, 2005, Trans. Comp. Sys. Biology.

A Novel Approach for Prediction of Protein Subcellular Localization from Sequence Using Fourier Analysis and Support Vector Machines

Yang Dai, Zhengdeng Lei, Yang Dai, 2004, BIOKDD.

Genome-Wide DNA Methylation Analysis Predicts an Epigenetic Switch for GATA Factor Expression in Endometriosis

Damian Roqueiro, Yang Dai, N. Jafari, 2014, PLoS genetics.

Overexpression of the Oral Mucosa-Specific microRNA-31 Promotes Skin Wound Closure

Yang Dai, Yan Zhao, Zujian Chen, 2019, International journal of molecular sciences.

Gene Expression Patterns in the Human Breast after Pregnancy

Yang Dai, C. Beam, E. Wiley, 2010, Cancer Prevention Research.

Prioritize Transcription Factor Binding Sites for Multiple Co-Expressed Gene Sets Based on Lasso Multinomial Regression Models

Yang Dai, Yang Dai, Hong Hu, 2019, Biotechnology.

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

Patricia W. Finn, Yang Dai, Ahmed A. Metwally, 2017, BCB.

In Vivo Genome-Wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor

Yang Dai, P. Yin, Stacy A. Kujawa, 2022, Reproductive Sciences.

Metabolome of human gut microbiome is predictive of host dysbiosis

Yang Dai, Peter E. Larsen, Yang Dai, 2015, GigaScience.

Incorporating Network Topology Improves Prediction of Protein Interaction Networks from Transcriptomic Data

Yang Dai, Frank Collart, Peter E. Larsen, 2010, Int. J. Knowl. Discov. Bioinform..

Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks

Yang Dai, Peter E. Larsen, Yang Dai, 2009, ISBRA.

Rank-based edge reconstruction for scale-free genetic regulatory networks

Eyad Almasri, Yang Dai, Peter E. Larsen, 2008, BMC Bioinformatics.

A Model-based approach to transcription regulatory network reconstruction from time-course gene expression data

Hong Hu, Yang Dai, Yang Dai, 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Prediction of MHC class II binders using the ant colony search strategy

Jianming Shi, Yang Dai, Oleksiy Karpenko, 2005, Artif. Intell. Medicine.

Using LASSO regression to detect predictive aggregate effects in genetic studies

Yang Dai, J. Fontanarosa, 2011, BMC proceedings.

Understanding Tamoxifen Resistance of Breast Cancer Based on Integrative Bioinformatics Approaches

Yang Dai, L. Huang, L. Huang, 2013 .

Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes

LEI HUANG, YANG DAI, Lei Huang, 2006, J. Bioinform. Comput. Biol..

PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data

Derek Reiman, Jun Sun, Yang Dai, 2020, IEEE Journal of Biomedical and Health Informatics.

Prediction of MHC class II binding peptides based on an iterative learning model

Yang Dai, Naveen Murugan, Yang Dai, 2005, Immunome research.

Building a meta-predictor for MHC class II-binding peptides.

Lei Huang, Yang Dai, Oleksiy Karpenko, 2007, Methods in molecular biology.

Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach

Derek Reiman, Yang Dai, Ali M Farhat, 2021, Artificial Neural Networks, 3rd Edition.

Meta-Signer: Metagenomic Signature Identifier based on Rank Aggregation of Features

Jun Sun, Derek Reiman, Yang Dai, 2020, bioRxiv.

Association of Aldosterone Concentration and Mineralocorticoid Receptor Genotype with Potassium Response to Spironolactone in Patients with Heart Failure

Yang Dai, L. Cavallari, S. Patel, 2010, Pharmacotherapy.

Using Autoencoders for Predicting Latent Microbiome Community Shifts Responding to Dietary Changes

Derek Reiman, Yang Dai, Yang Dai, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Targeting DNA Methylation Depletes Uterine Leiomyoma Stem Cell–enriched Population by Stimulating Their Differentiation

A. Shilatifard, Yang Dai, P. Yin, 2020, Endocrinology.

Meta-Signer: Metagenomic Signature Identifier based onrank aggregation of features [version 1; peer review: 1 approved with reservations, 1 not approved]

Ahmed A. Metwally, Yang Dai, Jun Sun, 2022 .

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets

Yang Dai, Derek Reiman, 2020, bioRxiv.

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

Ahmed A. Metwally, Yang Dai, P. Finn, 2018, Microbiome.

Title : 2 Identification of organ-specific transcriptomic shifts in the vasculature during 3 systemic inflammation using TrendCatcher 4

Yang Dai, J. Rehman, Xinge Wang, 2022 .

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling

Yang Dai, Peter E. Larsen, Frank R. Collart, 2015, PloS one.

Progesterone receptor-DNA methylation crosstalk regulates depletion of uterine leiomyoma stem cells: A potential therapeutic target

Yang Dai, P. Yin, Stacy A. Kujawa, 2021, Stem cell reports.

MicroRNA-Based Engineering of Mesenchymal Stem Cell Extracellular Vesicles for Treatment of Retinal Ischemic Disorders: Short Title: Engineered extracellular vesiclesand retinal ischemia.

Yang Dai, S. Kalinin, D. Feinstein, 2023, Acta biomaterialia.

Polycomb group protein EZH2‐mediated E‐cadherin repression promotes metastasis of oral tongue squamous cell carcinoma

A. Kolokythas, Yang Dai, Xiqiang Liu, 2013, Molecular carcinogenesis.

Using convolutional neural networks to explore the microbiome

Derek Reiman, Yang Dai, Ahmed Metwally, 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks

Philip S. Yu, Derek Reiman, Philip S Yu, 2019, PLoS Comput. Biol..

A prototype tobacco-associated oral squamous cell carcinoma classifier using RNA from brush cytology.

A. Kolokythas, J. Schwartz, Yang Dai, 2013, Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology.

An Integrated Bioinformatics Approach Identifies Elevated Cyclin E2 Expression and E2F Activity as Distinct Features of Tamoxifen Resistant Breast Tumors

Shuangping Zhao, Yang Dai, J. Frasor, 2011, PloS one.

Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections

Yang Dai, Peter E. Larsen, Frank R. Collart, 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Relational database index choices for genome annotation data

Yang Dai, Oleksiy Karpenko, Yang Dai, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks

Yang Dai, Zhigang Hong, Ankit Jambusaria, 2018, BMC Bioinformatics.

Differential microRNA profile underlies the divergent healing responses in skin and oral mucosal wounds

Yang Dai, Yan Zhao, Zujian Chen, 2019, Scientific Reports.

Improved protein fold assignment using support vector machines

Hui Lu, Robert E. Langlois, Yang Dai, 2005, Int. J. Bioinform. Res. Appl..

A block-based evolutionary optimization strategy to investigate gene-gene interactions in genetic association studies

Yang Dai, Joel Fontanarosa, Yang Dai, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

A new distance measurement for clustering time-course gene expression data

G. Chen, Yang Dai, Yang Dai, 2004, The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Reducing large diagonals in kernel matrices through semidefinite programming

Sumeet Gupta, Yang Dai, Hsiao-Mei Lu, 2003, BIOKDD.

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

Yang Dai, Christian Ascoli, Ahmed A. Metwally, 2018, Microbiome.

Gene Expression Patterns in the Human Breast after Pregnancy

Yang Dai, C. Beam, E. Wiley, 2010, Cancer Prevention Research.

Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information

Yang Dai, Peter E. Larsen, Frank R. Collart, 2018, mSystems.

An SVM-based system for predicting protein subnuclear localizations

Yang Dai, Zhengdeng Lei, 2005, BMC Bioinformatics.