Publications

Research Publications

Peer-reviewed papers, preprints, and technical reports from AI Biotechnologies researchers and funded collaborators.

Recent Publications

Drug Discovery
Generative Molecular Design at Billion-Compound Scale Using Transformer-Based Chemical Language Models
Chen Y, Patel R, Williams M, Nakamura T, et al. — AI Biotechnologies Research Division
Nature Chemical Biology · 2025 · DOI: 10.1038/s41589-025-00xxx

We present MolGen-2, a transformer-based generative model trained on 1.8 billion chemical structures that designs novel small molecules optimized simultaneously for target binding affinity, ADMET properties, and synthetic accessibility. In prospective validation across 14 oncology targets, 31% of generated candidates showed sub-nanomolar IC50 values.

Protein Science
De Novo Enzyme Design via Protein Language Model-Guided Backbone Generation Achieves Sub-Angstrom Accuracy
Rodriguez A, Kim S, Thompson L — AI Biotechnologies Protein Science Group
Science · 2025 · DOI: 10.1126/science.xxx

We describe a two-stage pipeline combining backbone diffusion with sequence design for the de novo engineering of enzymes with novel catalytic activities. Across 47 designed enzymes, 38 folded as predicted and 19 demonstrated measurable catalytic activity, with six achieving kcat/KM values within 10-fold of natural homologs.

Genomics
Population-Scale Polygenic Risk Score Modeling Identifies Novel Risk Loci for Rare Metabolic Diseases Across 12 Ancestry Groups
Okonkwo B, Martinez C, Singh P, Ito H — AI Biotechnologies Genomics Division
Nature Genetics · 2025 · DOI: 10.1038/s41588-025-00xxx

Analysis of whole-genome sequencing data from 87,000 individuals across 12 ancestral populations identified 344 novel genetic loci associated with rare metabolic disorders, with AI-derived polygenic risk scores demonstrating 3.2-fold improvement in predictive accuracy over existing models for non-European ancestry groups.

Lab Automation
A Self-Driving Laboratory Platform Achieves 40-Fold Acceleration in Hit-to-Lead Optimization via Closed-Loop Reinforcement Learning
Fischer J, Lee A, Pham T, Brown K — AI Biotechnologies Automation Group
ACS Central Science · 2025 · DOI: 10.1021/acscentsci.5cxxx

We describe AutoLab-1, a fully autonomous drug discovery platform that integrates AI experimental design, robotic liquid handling, in-line mass spectrometry, and reinforcement learning to iteratively optimize lead compounds. In a blinded comparison against parallel human teams, AutoLab-1 achieved equivalent lead quality 40-fold faster with 60% lower reagent consumption.

Drug Discovery
Multi-Target Drug Repurposing via Knowledge Graph Embedding Identifies 18 Candidates for Neglected Tropical Diseases
Adeyemi O, Kumar V, Zhang X — AI Biotechnologies, RepurposeAI Program
PLOS Computational Biology · 2025 · DOI: 10.1371/journal.pcbi.xxxxxxx

RepurposeAI, a heterogeneous knowledge graph combining FDA drug databases, proteome-scale interaction data, and clinical outcome records, identified 18 FDA-approved drugs with computational evidence for repositioning against neglected tropical diseases. Six candidates were confirmed active in cell-based assays at clinically achievable concentrations.

Genomics
AI-Guided Tumor Genomics Reduces Time to Matched Therapy in Advanced NSCLC by 73%
Park J, Hernandez M, Liu Y, Wallace D — AI Biotechnologies, PrecisionRx Program
Journal of Clinical Oncology · 2024 · DOI: 10.1200/JCO.24.xxxxx

A prospective multicenter study of 1,240 patients with advanced non-small cell lung cancer demonstrated that AI-guided tumor genomic analysis reduced median time to matched therapy selection from 21 days to 5.7 days, with the AI-recommended regimen concordant with multidisciplinary tumor board consensus in 89% of cases.

For full publication archives, preprints, and data repositories, contact our research office.

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