Microbiome Dynamics as Predictors of Lung Transplant Rejection. - Ahmed Metwally 002; Christian Ascoli; Kalista Andropolis; Ravi Ranjan; Yang Dai; Thomas Ferkol; Patricia W. Finn; David L. Perkins (BCB, 2017)

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA. - Ahmed A. Metwally; Patricia W. Finn; Yang Dai; David L. Perkins (BCB, 2017)

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

Cloud-based solution for improving usability and interactivity of metagenomic ensemble taxonomic classification methods. - Asem Alaa; Ahmed A. Metwally (BHI, 2018)

A review on probabilistic models used in microbiome studies. - Ahmed A. Metwally; Hani Aldirawi; Jie Yang 058 (Commun. Inf. Syst., 2018)

Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learning. - Jianguo Chen 001; Kenli Li 001; Kashif Bilal; Ahmed A. Metwally; Keqin Li 001; Philip S. Yu (CoRR, 2018)

Identifying Appropriate Probabilistic Models for Sparse Discrete Omics Data. - Hani Aldirawi; Jie Yang 058; Ahmed A. Metwally (BHI, 2019)

Taxonomic Classification at the Strain Level using a Species-of-Interest $ boldsymbol{k}$-mer Database. - Mladen R. Rasic; Ahmed A. Metwally; Patricia W. Finn; David L. Perkins (BHI, 2019)

Protein Subcellular Localization Prediction Based on Internal Micro-similarities of Markov Chains. - Asem Alaa; Ayman M. Eldeib; Ahmed A. Metwally (EMBC, 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)

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)

Learning Personal Food Preferences via Food Logs Embedding. - Ahmed A. Metwally; Ariel K. Leong; Aman Desai; Anvith Nagarjuna; Dalia Perelman; Michael Snyder 001 (BIBM, 2021)

Predicting upper limb disability progression in primary progressive multiple sclerosis using machine learning and statistical methods. - Sally Mostafa; Isabel Hyo Jung Song; Ahmed A. Metwally; Nicolas Strauli; Nehemiah Sewde; Michel Friesenhahn; Maxime Usdin; Xiaoming Jia (BIBM, 2021)

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

Robust identification of temporal biomarkers in longitudinal omics studies. - Ahmed A. Metwally; Tom Zhang; Si Wu; Ryan Kellogg; Wenyu Zhou; Kévin Contrepois; Hua Tang; Michael Snyder 001 (Bioinform., 2022)

Lifestyle-Informed Personalized Blood Biomarker Prediction via Novel Representation Learning. - A. Ali Heydari; Naghmeh Rezaei; Javier L. Prieto; Shwetak N. Patel; Ahmed A. Metwally (BHI, 2024)

High-resolution lifestyle profiling and metabolic subphenotypes of type 2 diabetes. - Heyjun Park; Ahmed A. Metwally; Alireza Delfarah; Yue Wu; Dalia Perelman; Caleb Mayer; Curtis McGinity; Majid Rodgar; Alessandra Celli; Tracey McLaughlin; Emmanuel Mignot; Michael Snyder 001 (npj Digit. Medicine, 2025)

Guest Editorial: Deep Medicine and AI for Health. - María Fernanda Cabrera-Umpiérrez; Tayo Obafemi-Ajayi; Ahmed Metwally 002; Bobak J. Mortazavi (IEEE J. Biomed. Health Informatics, 2025)

A Scalable Framework for Evaluating Health Language Models. - Neil Mallinar; A. Ali Heydari; Xin Liu 034; Anthony Z. Faranesh; Brent Winslow; Nova Hammerquist; Benjamin Graef; Cathy Speed; Mark Malhotra; Shwetak N. Patel; Javier L. Prieto; Daniel McDuff; et al. (CoRR, 2025)

Insulin Resistance Prediction From Wearables and Routine Blood Biomarkers. - Ahmed A. Metwally; A. Ali Heydari; Daniel McDuff; Alexandru Solot; Zeinab Esmaeilpour; Anthony Z. Faranesh; Menglian Zhou; David B. Savage; Conor Heneghan; Shwetak N. Patel; Cathy Speed; Javier L. Prieto (CoRR, 2025)

LSM-2: Learning from Incomplete Wearable Sensor Data. - Maxwell A. Xu; Girish Narayanswamy; Kumar Ayush; Dimitris Spathis; Shun Liao; Shyam A. Tailor; Ahmed Metwally 002; A. Ali Heydari; Yuwei Zhang; Jake Garrison; Samy Abdel-Ghaffar; Xuhai Xu; et al. (CoRR, 2025)

SensorLM: Learning the Language of Wearable Sensors. - Yuwei Zhang; Kumar Ayush; Siyuan Qiao; A. Ali Heydari; Girish Narayanswamy; Maxwell A. Xu; Ahmed A. Metwally; Shawn Xu; Jake Garrison; Xuhai Xu; Tim Althoff; Yun Liu 013; et al. (CoRR, 2025)

The Human-AI Hybrid Delphi Model: A Structured Framework for Context-Rich, Expert Consensus in Complex Domains. - Cathy Speed; Ahmed A. Metwally (CoRR, 2025)