Author

Tung V. N. Nguyen

European Bioinformatics InstituteORCID 0000-0002-2876-6046Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 4 Bioinformatics· 1

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Research Focus:benchmarking· 4 Approach:statistical model· 4 Approach:benchmark study· 2 Research Focus:software / tool· 2 Research Focus:database / resource· 1 Approach:large language model· 1

Frequent Co-Authors

Henning HermjakobiD· 5 shared Rahuman S. Malik‐SheriffiD· 5 shared Karthik RamaniD· 2 shared Krishna Kumar TiwariiD· 2 shared Ahmad Wisnu MulyadiiD· 1 shared Ahmad ZyoudiD· 1 shared Alexander A. PatrieiD· 1 shared Alexandre OliveiraiD· 1 shared

Activity by Year

2021-2025 · peak 2/yr

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10 top collaborators · 28 mutual co-author links

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5 shared papersSystems Biology

Henning HermjakobORCID

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Author profile →

5 papers

Recent·Most cited

Verification and reproducible curation of the BioModels repository

Lucian P. Smith, Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R. Karr, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David Phillip Nickerson, , Herbert M. Sauro

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

PLoS Computational Biology · Dec 4, 2025Peer-reviewedSystems Biology

Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models

Lilija Wehling, Gurdeep Singh, Ahmad Wisnu Mulyadi, Rakesh Hadne Sreenath, Henning Hermjakob, Tung V. N. Nguyen, Thomas Rückle, Mohammed H. Mosa, Henrik Cordes, Tommaso Andreani, Thomas Klabunde, Rahuman S. Malik‐Sheriff, Douglas McCloskey

Talk2Biomodels provides an AI platform for interacting with biological models using natural language, enhancing accessibility and FAIR principles.

BMC Bioinformatics · Nov 18, 2025Peer-reviewedSystems Biology

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung V. N. Nguyen, Daniel Lobo, St. Elmo Wilken, Krishna Kumar Tiwari, Aswathy K. Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, , Rahuman S. Malik‐Sheriff

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

bioRxiv · Sep 24, 2024 · PreprintSystems Biology

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

Divyang Deep Tiwari, Nils Hoffmann, Kieran Didi, Sumukh Deshpande, Sucheta Ghosh, Tung V. N. Nguyen, Karthik Raman, Henning Hermjakob, Rahuman S. Malik‐Sheriff

This paper introduces a protocol to create a FAIR collection of machine learning models in life sciences and medicine, aiming to improve reproducibility and reuse through community curation.

bioRxiv · May 22, 2023 · PreprintBioinformatics

Reproducibility in systems biology modelling

Krishna Kumar Tiwari, Sarubini Kananathan, Matthew G. Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V. N. Nguyen, Mihai Glont, Henning Hermjakob, Rahuman S. Malik‐Sheriff

The paper investigates reproducibility of systems biology models, finding that 49% of 455 models could not be reproduced due to missing data or inconsistencies.

Molecular Systems Biology · Feb 1, 2021Peer-reviewedSystems Biology