Using convolutional neural networks to explore the microbiome. - Derek Reiman; Ahmed Metwally 002; Yang Dai (EMBC, 2017)

Using Autoencoders for Predicting Latent Microbiome Community Shifts Responding to Dietary Changes. - Derek Reiman; Yang Dai (BIBM, 2019)

Using Convolutional Neural Network to Study the Regulatory Relationship Between DNA Methylation and Gene Expression. - Jingting Xu; Derek Reiman; Shang Gao; Yang Dai (BIBM, 2019)

Integrating RNA expression and visual features for immune infiltrate prediction. - Derek Reiman; Lingdao Sha; Irvin Ho; Timothy Tan; Denise Lau; Aly A. Khan (PSB, 2019)

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks. - Ahmed A. Metwally; Philip S. Yu; Derek Reiman; Yang Dai; Patricia W. Finn; David L. Perkins (PLoS Comput. Biol., 2019)

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets. - Derek Reiman; Yang Dai (DeLTA, 2020)

PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data. - Derek Reiman; Ahmed A. Metwally; Jun Sun; Yang Dai (IEEE J. Biomed. Health Informatics, 2020)

Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach. - Derek Reiman; Ali M. Farhat; Yang Dai (Artificial Neural Networks, 3rd Edition, 2021)

Integrating microbiome and metabolome data for host disease prediction via deep neural networks. - Tina Khajeh; Derek Reiman; Ryan Morley; Yang Dai (BHI, 2021)

Meta-Signer: Metagenomic Signature Identifier based onrank aggregation of features. - Derek Reiman; Ahmed Metwally 002; Jun Sun; Yang Dai (F1000Research, 2021)

MiMeNet: Exploring microbiome-metabolome relationships using neural networks. - Derek Reiman; Brian T. Layden; Yang Dai (PLoS Comput. Biol., 2021)

Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. - Derek Reiman; Godhev Kumar Manakkat Vijay; Heping Xu; Andrew Sonin; Dianyu Chen; Nathan Salomonis; Harinder Singh; Aly A. Khan (PLoS Comput. Biol., 2021)

TRIBAL: Tree Inference of B Cell Clonal Lineages. - Leah L. Weber; Derek Reiman; Mrinmoy Saha Roddur; Yuanyuan Qi; Mohammed El-Kebir; Aly A. Khan (RECOMB, 2024)