Author

Matthew Murphy

Indiana University Bloomington

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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Bioengineering· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:DNA methylation· 1 Organism:E. coli· 1 Approach:experimental assay· 1 Approach:machine learning (classical)· 1 Research Focus:software / tool· 1 Research Focus:variant effect prediction· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Bea YuiD· 1 shared Ben S. DugganiD· 1 shared Brandon Fischer· 1 shared John MetzcariD· 1 shared Paul MackliniD· 1 shared Peter A. Carr· 1 shared Randy W. HeilandiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

7 top collaborators · 11 mutual co-author links

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1 shared paperBioengineering

Bea YuORCID

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2 papers

Recent·Most cited

A simple framework for agent-based modeling with extracellular matrix

John Metzcar, Ben S. Duggan, Brandon Fischer, Matthew Murphy, Randy W. Heiland, Paul Macklin

The paper introduces a simplified agent-based framework for modeling cell-ECM interactions using PhysiCell, demonstrating its utility in various biological processes.

Bulletin of Mathematical Biology · Feb 12, 2025Peer-reviewedSystems Biology

A Framework for Predicting Design Failures in Engineered Genetic Codes

Bea Yu, Matthew Murphy, Peter A. Carr

The paper develops a machine learning framework to predict genetic code design failures by analyzing codon usage effects on E. coli viability.

bioRxiv · Jul 6, 2018 · PreprintBioengineering