Author

Yuda Munarko

University of AucklandORCID 0000-0002-9656-3945Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Research Focus:software / tool· 2 Approach:deep learning· 1 Approach:experimental assay· 1

Frequent Co-Authors

David Phillip NickersoniD· 4 shared Anand RampadarathiD· 3 shared Dewan Mahabub SarwariD· 2 shared John H. GennariiD· 2 shared Maxwell Lewis NealiD· 2 shared Herbert M. SauroiD· 1 shared Joseph L. HellersteiniD· 1 shared Koray AtalağiD· 1 shared

Activity by Year

2019-2023 · peak 1/yr

Co-Author Collaboration Network

9 top collaborators · 30 mutual co-author links

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4 shared papersBioinformatics

David Phillip NickersonORCID

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Author profile →

4 papers

Recent·Most cited

CASBERT: BERT-Based Retrieval for Compositely Annotated Biosimulation Model Entities

Yuda Munarko, Anand Rampadarath, David Phillip Nickerson

CASBERT improves entity retrieval in biosimulation models using BERT embeddings, outperforming bag-of-words methods in precision and recall.

Frontiers in Bioinformatics · Feb 14, 2023Peer-reviewedBioinformatics

NLIMED: Natural Language Interface for ModelEntity Discovery in Biosimulation ModelRepositories

Yuda Munarko, Dewan Mahabub Sarwar, Anand Rampadarath, Koray Atalağ, John H. Gennari, Maxwell Lewis Neal, David Phillip Nickerson

NLIMED converts natural language queries into SPARQL to discover model entities from biosimulation model repositories.

Frontiers in Physiology · Feb 24, 2022Peer-reviewedBioinformatics

SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

Woosub Shin, Joseph L. Hellerstein, Yuda Munarko, Maxwell Lewis Neal, David Phillip Nickerson, Anand Rampadarath, Herbert M. Sauro, John H. Gennari

SBMate evaluates annotation quality in systems biology models using coverage, consistency, and specificity metrics on 1,000 BioModels repository models.

bioRxiv · Oct 9, 2021 · PreprintSystems Biology

Epithelial Modelling Platform: A Tool for Model Discovery and Assembly with the Physiome Model Repository

Dewan Mahabub Sarwar, Yuda Munarko, David Phillip Nickerson

The paper introduces a web-based platform for constructing and assembling epithelial transport models using existing models from the Physiome Model Repository.

bioRxiv · May 8, 2019 · PreprintBioinformatics