Matthew O'Meara

Assistant Professor Department of Computational Medicine and Bioinformatics, University of Michigan (Bioinformatics and computational biology not elsewhere classified; Infectious diseases; Pharmacology and pharmaceutical sciences not elsewhere classified; Biostatistics)

Ann Arbor, Michigan, United States

Developing statistical and machine learning models for pharmacology and biochemistry with applications in infectious disease and neurobiology


  • Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction
  • Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
  • A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
  • Reengineering biocatalysts: Computational redesign of chondroitinase ABC improves efficacy and stability
  • DeORFanizing Candida albicans Genes using Coexpression
  • Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2
  • Valproic Acid-Induced Changes of 4D Nuclear Morphology in Astrocyte Cells
  • Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo
  • Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2
  • A Multi-Omics Human Liver Organoid Screening Platform for DILI Risk Prediction
  • Structures of the σ2 receptor enable docking for bioactive ligand discovery
  • Scientific benchmarks for guiding macromolecular energy function improvement
  • Role of electrostatic repulsion in controlling pH-dependent conformational changes of viral fusion proteins.
  • The Cryptococcus neoformans Rim101 transcription factor directly regulates genes required for adaptation to the host.
  • Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.
  • A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.
  • The Recognition of Identical Ligands by Unrelated Proteins.
  • The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.
  • Prediction of enzymatic pathways by integrative pathway mapping.
  • High-Throughput Screening Identifies Genes Required for Candida albicans Induction of Macrophage Pyroptosis.
  • Local delivery of stabilized chondroitinase ABC degrades chondroitin sulfate proteoglycans in stroke-injured rat brains.
  • Ultra-large library docking for discovering new chemotypes.
  • A Unified Stochastic Gradient Approach to Designing Bayesian-Optimal Experiments
  • Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  • Property-Unmatched Decoys in Docking Benchmarks.
  • Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19.
  • Chondroitinase ABC Mutants and Methods of Manufacture and use Thereof
  • Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.
  • Prioritizing virtual screening with interpretable interaction fingerprints
  • In Vitro Evaluation and Mitigation of Niclosamide’s Liabilities as a COVID-19 Treatment
  • Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
  • Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential
  • Multiple ParA/MinD ATPases Coordinate the Positioning of Disparate Cargos in a Bacterial Cell
  • In Vitro Evaluation and Mitigation of Niclosamide's Liabilities as a COVID-19 Treatment.
  • Maximum geodesic routing in the plane with obstacles
  • Colour Patterns for Polychromatic Four-colourings of Rectangular Subdivisions
  • DeORFanizing Candida albicans Genes using Co-Expression
  • Development of an Automated Screen for Kv7.2 Potassium Channels and Discovery of a New Agonist Chemotype
  • Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell
  • Erratum: The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (J. Chem. Theory Comput. (2017) 13: 6 (3031-3048) DOI: 10.1021/acs.jctc.7b00125)
  • Development of an automated screen for Kv7.2 potassium channels and discovery of a new agonist chemotype
  • Valproic acid-induced changes of 4D nuclear morphology in astrocyte cells
  • The Rosetta all-atom energy function for macromolecular modeling and design
  • Morphological Cell Profiling of SARS-CoV-2 Infection Identifies Drug Repurposing Candidates for COVID-19.
  • Computational Redesign of Bacterial Chondroitinase ABC to Treat Spinal Cord Injury and Stroke
  • Phospholipidosis explains a plurality of SARS-CoV-2 Drug-repurposing hits
  • CADs as a target for chemoinformatic filtering in virtual screening libraries
  • Designer proteins for nerve regeneration
  • From Protein-Interactions to Organoids: Drug Repurposing for SARS-CoV-2
  • From millions of images of SARS-CoV-2 infected cells to drug mechanism of action
  • Property-unmatched decoys in docking benchmarks and bootstrapping on the ranked list to obtain confidence intervals
  • Machine Learning and Assay Development for Image-based Phenotypic Profiling of Drug Treatments
  • The life and times of endogenous opioid peptides: Updated understanding of synthesis, spatiotemporal dynamics, and the clinical impact in alcohol use disorder.
  • Morphological cell profiling of SARS-CoV-2 infection identifies lactoferrin as candidate for COVID-19
  • A metabolic code for polypharmacology
  • A Hydrogen Bonding Geometry Encyclopedia
  • A Hydrogen Bonding Geometry Encyclopedia
  • A metabolic code for polypharmacology
  • Testing the predictive limits of large scale virtual screening
  • Host-pathogen interactions of highly pathogenic coronaviruses reveal drug targets
  • A metabolic code for pharmacology
  • A Human Liver Organoid Screening Platform for DILI Risk Prediction
  • Virtual Phospholipidosis explains a plurality of SARS-CoV-2 Drug-repurposing hits
  • High-Content Screening to Identify Inhibitors of Dengue Virus Replication
  • Imaging-based screening identifies modulators of theeIF3translation initiation factor complex inCandida albicans
  • Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease.
  • Imaging-Based Screening Identifies Modulators of the eIF3 Translation Initiation Factor Complex in Candida albicans
  • CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair
  • Predicting the Structural Impact of Human Alternative Splicing

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Co-workers & collaborators

Jacob Steenwyk

Graduate student - Nashville, TN

Jacob Steenwyk

Matthew O'Meara's public data