Armin Bayati, PhD

Drug Discovery, Target Validation & Machine Learning for Biology

Senior Scientist III in Neuroimmunology at Merck. I build human iPSC neuron, microglia, and astrocyte tricultures and take compounds through potency, target engagement, and multi-omics readouts. On the AI/ML side, I build open-source tools like AutoMorphoTrack, benchmark biology foundation models such as scGPT and Geneformer, and evaluate model-generated science against the primary literature. Behind that sit 10+ years of drug discovery, CRISPR functional genomics, and imaging across neurodegeneration, neuroinflammation, and infectious disease, plus iPSC work in cardiomyocytes and pancreatic β-cells.

Get in Touch View Publications AI/ML Work Open neurodigineration →

New: neurodigineration — interactive cross-disease network of 200+ neurodegeneration-relevant genes, AI-powered gene briefs grounded in UniProt/NCBI/Ensembl/Reactome, free-text Q&A about how any protein relates to neurodegeneration, and a human-in-the-loop training GUI for SME labeling.

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First-author, Nature Neuroscience
Developed novel iPSC-based Lewy body model for Parkinson's disease

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First to characterize SARS-CoV-2 cell entry
JBC Editors' Pick — clathrin-mediated endocytosis mechanism

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Led preclinical drug discovery programs
Novel therapeutics targeting neurodegeneration, viral entry & cancer

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25+ publications · 1,300+ citations
Harvard, McGill, Nature Neuroscience, Cell Reports, JBC, Lancet

About

Background

I'm a cellular and molecular biologist with a Ph.D. in Neuroscience from McGill University and 10+ years across drug discovery, multi-omics, and machine learning applied to biological data. I'm currently a Senior Scientist III in Neuroimmunology at Merck, working in preclinical discovery with human iPSC neuron, microglia, and astrocyte tricultures, and a fellow in AI/ML training at Aligned Labs, where I evaluate model-generated science against the primary literature (more on that work).

I have led projects that identified how pathogenic proteins enter and infect cells, uncovered mechanisms involved in neuronal degeneration, developed Python-based tools to analyze live-cell imaging, and helped advance novel small-molecule therapeutics targeting mitochondrial health, viral entry, and cellular aging.

25+

Peer-reviewed publications

1,300+

Citations

500K+

Paper downloads

With first- or corresponding-author studies in Nature Neuroscience, Cell Reports, and the Journal of Biological Chemistry (where I'm also an Early Career Reviewer), my research bridges fundamental discovery with translational drug development across neuroscience, immunology, infectious disease, and oncology.

Research at a Glance

Impact metrics & technical breadth across 10+ years in biomedical research

Research Impact

Publications

Nature Neurosci, Cell Reports, JBC

Total Citations

Google Scholar verified

First-Author Papers

Incl. Nature Neuroscience

Institutional Affiliations

Merck · Aligned Labs · Harvard · MGB · MNI · McGill · UVic

Technical Breadth

iPSC Lineages Differentiated

qPCR Primer Pairs

Flow Cytometry Panels

Assay Platforms

CRISPR · Viral · Protein · Imaging

Viral Vector Systems

Lenti · AAV · SARS-CoV-2

Differentiation Protocols

Neurons · Islets · Immune

Experience

Work Experience & Education

2026 – Present

Merck · Senior Scientist III, Neuroimmunology

Boston, MA. Preclinical drug discovery in neuroimmunology. I build and run human iPSC-derived neuron, microglia, and astrocyte tricultures and neuronal spheroids as disease-relevant screening systems, develop reporter and luminescence assays for pathway activity and cellular target engagement in 96- and 384-well high-content formats, and fold transcriptomic, proteomic, and imaging readouts into ML-supported analysis for target validation and mechanism of action. Findings go to program leads and cross-functional discovery teams as recommendations against defined acceptance criteria.

2026 – Present

Aligned Labs · Fellow, AI/ML Training in Cell Biology & Neuroscience

Remote. Evaluate model-generated scientific content in cell biology, neuroscience, and pharmacology, checking claims against primary literature and scoring accuracy, reasoning, and citation quality with structured rubrics. Write and grade expert reference responses, benchmark biology foundation models (scGPT, Geneformer), and audit curated datasets for contamination and labeling consistency. More on the AI/ML work →

2024 – 2026

Harvard Medical School & Mass General Brigham · Research Fellow, Department of Neurology

Led a small-molecule Parkin agonist program from target validation to in vivo proof of concept, integrating single-cell transcriptomics and LC-MS/MS pharmacokinetics. Built and published AutoMorphoTrack, an open-source Python framework for organelle morphology and motility, validated against expert annotation by Dice, IoU, and F1. Ran iPSC-derived neuronal, glial, and cardiomyocyte platforms for disease modeling, designed high-content imaging assays for cytotoxicity, mitophagy, and aggregation, and coordinated biopharma collaborations (Thermo Fisher, Nysnobio) and CRO deliverables (abmgood, Curia/Lake Pharma, Novogene). Mentored junior scientists.

2023 – 2024

Montreal Neurological Institute, McGill University · Research Associate

Established the first human iPSC-derived dopaminergic neuron model forming Lewy body-like inclusions through sequential α-synuclein fibril and proinflammatory cytokine exposure, the core of a first- and corresponding-author Nature Neuroscience paper. Used CRISPR knockout and siRNA knockdown of GBA and LAMP2 to pin lysosomal impairment as the driver of inclusion formation. Coordinated LC-MS/MS proteomics, high-content imaging, and bioinformatics across six institutions in the US and Canada, and built high-resolution EM and CD63/CD9 EV-transfer workflows along the way.

2018 – 2023

McGill University · Ph.D. in Neuroscience (Cell Biology), Doctoral Researcher

Doctoral work at the Montreal Neurological Institute. Authored the first study defining SARS-CoV-2 cell entry by clathrin-mediated endocytosis, using purified spike protein and pseudovirus infectivity assays in BSL-2 and BSL-3 settings. Worked with GSK, UNC Chapel Hill, and the Structural Genomics Consortium on antiviral discovery, identifying CSNK2 and PIKfyve as druggable host kinases. Found rapid macropinocytic transfer of α-synuclein to lysosomes, characterized by STED super-resolution and immunogold EM.

2018

University of Victoria · Undergraduate Researcher (USRA)

Tissue processing, sectioning, and sample preparation for electron microscopy in the Nahirney lab.

2013 – 2018

University of Victoria · B.Sc. in Biology & Psychology (Honours with Distinction)

Honours work exploring the neurodegenerative effects of stroke in mice using electron microscopy.

Research

Explore My Work

My research spans iPSC-based disease modeling, cellular and molecular assays, advanced microscopy, drug discovery, automation, and computational image analysis.

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iPSC-Derived Neurons

Dopaminergic, cortical, and glial differentiation. Lewy body disease modeling. MEA electrophysiology, calcium imaging, HPLC dopamine quantification.

Drug Discovery, Target Validation & Machine Learning for Biology

Background

Work Experience & Education

Explore My Work

Recent Activity

Thesis Documents

Core Expertise