Author

Andrew Zhou

Harvard University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 2 Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2 Approach:machine learning (classical)· 2 Assay:bulk RNA-seq· 1 Research Focus:gene regulatory network inference· 1 Assay:protein sequence· 1 Assay:protein structure· 1

Frequent Co-Authors

Bree B. AldridgeiD· 2 shared James C. SacchettiniiD· 2 shared Maha Reda FarhatiD· 2 shared Marinka ŽitnikiD· 2 shared Yasha EktefaieiD· 2 shared Ada FangiD· 1 shared Andrew WhiteiD· 1 shared Armando Flores· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersBioinformatics

Bree B. AldridgeORCID

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4 papers

Recent·Most cited

Improving Generalizability in Whole-Cell Antibiotic Discovery Through Active Learning

Lia R. Serrano, Andrew Zhou, Ziming Wei, Kee-Lee K. Stocks, Yasha Ektefaie, Peter J. Gwynne, Eric Chen, Inna V. Krieger, James C. Sacchettini, Bree B. Aldridge, Linden T. Hu, Maha Reda Farhat

This paper evaluates active learning strategies for whole-cell antibiotic discovery, finding an optimal approach that significantly improves hit rates and generalizability across bacterial species.

bioRxiv · Jul 5, 2026 · PreprintBioinformatics

Expanding P-NET, a multi-purpose biologically informed deep learning framework

Marc Glettig, Andrew Zhou, Chenzhang Zhou, Giuseppe Tarantino, Tyler J. Aprati, Eliezer M. Van Allen, David Liu, Haitham Elmarakeby

The paper expands P-NET, a deep learning framework that uses biological pathways for genomic and transcriptomic predictions, showing competitive performance and interpretability.

bioRxiv · Apr 22, 2026 · PreprintBioinformatics

Learning Universal Representations of Intermolecular Interactions with ATOMICA

Ada Fang, Michael Desgagné, Zaixi Zhang, Andrew Zhou, Joseph Loscalzo, Bradley L. Pentelute, Marinka Žitnik

ATOMICA learns transferable representations of intermolecular interactions across diverse molecular types, enabling cross-modal comparisons and experimentally testable hypotheses.

bioRxiv · Apr 2, 2025 · PreprintBioinformatics

Fleming: An AI Agent for Antibiotic Discovery in Mycobacterium Tuberculosis

Ziming Wei, Yasha Ektefaie, Andrew Zhou, Dereje Abate Negatu, Bree B. Aldridge, Thomas Dick, Michael Skarlinski, Andrew White, Samuel G. Rodriques, Sepideh Hosseiniporgham, Maloy Parai, Armando Flores, Inna Krieger, Marinka Žitnik, James C. Sacchettini, Maha Reda Farhat

Fleming is an AI agent that identifies lead compounds for Mycobacterium tuberculosis by combining discriminative and generative models, achieving higher discrimination and hit rates than alternative approaches.

bioRxiv · Apr 1, 2025 · PreprintBioinformatics