Matthew O'Meara

Publications

• https://maomlab.github.io/
• 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