Publications

Scientific publications, preprints, and technical reports related to the PhenoGenX platform and HIV drug resistance research.

Primary Platform Manuscript

PhenoGenX: A Data-Driven Platform for HIV-1 Drug Resistance Interpretation Integrating Ensemble Machine Learning with Extended Clinical Rule-Based Algorithms

Authors:

Yimam G.1,2, Belete W.2, Kidist Z.2, Minilik D.2, Gemechu L.2, Yenew K.3, Lingjie L.4, Yiming S.4

Affiliations:

1PhenoGenX AI Research
2Ethiopian Public Health Institute
3African Center for Disease Control and Prevention
4Chinese Center for Disease Control and Prevention

Manuscript Status

Submitted for peer review to a leading computational biology/journal (December 2025).

Preprint expected Q1 2026. Citation details will be updated upon acceptance.

Key Contributions
  • Integrated rule-based + ML resistance interpretation
  • CRPS-optimized ensemble ML models
  • 45,000+ genotype-phenotype training dataset
  • Subtype-aware mutation scoring
  • Side-by-side clinical + ML outputs
  • Web-based platform for research/clinical use
HIV-1 Drug Resistance Machine Learning Ensemble Models Clinical Decision Support Subtypes
Published Research Papers
GenBank2PubMed: bridging viral genomic data and the scientific literature with AI-assisted curation

Authors: Tao, K., Zhou, J., Getaneh, Y., & Shafer, R.W.

Journal: Scientific Reports, Article number: (2025)

DOI/PMID: Link pending

AI-assisted curation tool linking viral genomic data in GenBank with PubMed literature.

Evaluation of HIV-1 drug resistance among patients failing first-line antiretroviral therapy in Ethiopia

Authors: Getaneh, Y., He, Q., Rashid, A., Kassa, D., Kang, L., Yi, F., et al.

Journal: Journal of Global Antimicrobial Resistance, 30, 418–427 (2022)

DOI: 10.1016/j.jgar.2022.07.019

HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy

Authors: Getaneh, Y., Getnet, F., Ning, F., Rashid, A., Liao, L., & Yi, F.

Journal: Biomedicines, 11(2) (2023)

DOI: 10.3390/biomedicines11020510

HIV drug resistance early warning indicators in Ethiopia: Variability at regional and health facility levels and trend over time

Authors: Getaneh, Y., Zealyas, K., Adugna, F., Kursha, K., Atsbeha, G., Kassa, D., et al.

Journal: International Journal of Infectious Diseases, 95, 90–97 (2020)

DOI: 10.1016/j.ijid.2020.02.031

Human Immunodeficiency Virus Type-1 Genetic Diversity and Drugs Resistance Mutations among People Living with HIV in Karachi, Pakistan

Authors: Rashid, A., Kang, L., Yi, F., Getaneh, Y., Wei, M., Chang, S., Abidi, S.H., et al.

Journal: Viruses, 16(6) (2024)

DOI: 10.3390/v16060962

Related Publications & Preprints
Benchmarking Ensemble Methods for HIV-1 Phenotypic Resistance Prediction

Authors: Yimam G., Li Kang, Belete W.

Status: In preparation (Target: Bioinformatics, 2026)

Comparative analysis of ElasticNet, LightGBM, XGBoost, and Random Forest for fold-change prediction.

Subtype-Specific Mutation Signatures in Ethiopian HIV-1 Isolates

Authors: Belete W., Yimam, G., Yiming S. et al.

Status: Manuscript in revision (Journal of Clinical Microbiology)

Analysis of HIV-1 subtypes mutation patterns from Ethiopian clinical samples.

CRPS Optimization for Clinical ML Model Selection

Authors: Yimam, G., Kidist Z., Minilik D.

Status: Technical report (PhenoGenX, 2025)

Methodology for using Continuous Ranked Probability Score in ensemble HIV resistance models.

Conference Presentations & Abstracts
International Conference on Bioinformatics (InCoB, September 2025)

November 2025 | Virtual

Title: "PhenoGenX: An Open Platform for HIV Drug Resistance Interpretation in Resource-Limited Settings"

EPHI Annual Research Symposium

October 2025 | Addis Ababa

Title: "Integrating Machine Learning with Clinical Guidelines for HIV Resistance Monitoring in Ethiopia"

Publication Policy

Preprint Availability: All PhenoGenX-related manuscripts will be made available as preprints on bioRxiv or medRxiv prior to journal submission.

Open Access: We are committed to open science. Final versions will be published in open-access journals or deposited in institutional repositories.

Citation Request: Please cite the PhenoGenX platform and related publications when using this tool for research purposes.

How to Cite PhenoGenX
Getaneh Y., Woldesemyat B., Kidist, Z. et al.(2025). PhenoGenX: A Data-Driven Platform for HIV-1 Drug Resistance Interpretation Integrating Ensemble Machine Learning with Extended Clinical Rule-Based Algorithms. [Manuscript submitted for publication]. The Intergrated Computational Viromics and Digital Analytics & Ethiopian Public Health Institute.

Formal citation will be updated upon journal acceptance. For now, please use this provisional citation.