Author

Shan Chun Lim

Nanyang Technological University

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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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Research Focus:database / resource· 3 Assay:bulk RNA-seq· 2 Approach:statistical model· 2 Organism:Arabidopsis· 1 Research Focus:benchmarking· 1 Approach:deep learning· 1 Organism:fungi (other)· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Marek MutwiliD· 4 shared Manoj Itharajula· 2 shared Ann Don Low· 1 shared Cherlyn Xin’Er Chua· 1 shared Dhira Anindya Putri· 1 shared Edbert Edric Rodrigues· 1 shared Emilia Emmanuelle Davey· 1 shared Erielle Marie Fajardo Villanueva· 1 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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4 shared papersBioinformatics

Marek MutwilORCID

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Author profile →

4 papers

Recent·Most cited

Constructing Gene Co-functional and Co-regulatory Networks from Public Transcriptomes using Condition-Specific Ensemble Co-expression

Peng Ken Lim, Ruoxi Wang, Shan Chun Lim, Jenet Princy Antony Velankanni, Marek Mutwil

This paper introduces TEA-GCN, a method for constructing gene co-functional and co-regulatory networks from public RNA-seq data, showing improved performance and cross-species conservation.

Nature Communications · Apr 30, 2026Peer-reviewedBioinformatics

From Parametric Guessing to Graph-Grounded Answers: Building Reliable ChatGPT-like tools for Plant Science

Manoj Itharajula, Shan Chun Lim, Marek Mutwil

This paper evaluates LLMs for plant biology tasks, identifies their limitations, and proposes GraphRAG as a solution using structured knowledge graphs for reliable, reproducible answers.

bioRxiv · Apr 6, 2026 · PreprintBioinformatics

PlantConnectome: knowledge graph encompassing >70,000 plant articles

Shan Chun Lim, Manoj Itharajula, Mads Harder Møller, Rohan Shawn Sunil, Kevin Fo, Yu Song Chuah, Herman Foo, Emilia Emmanuelle Davey, Melissa J. Fullwood, Guillaume Thibault, Marek Mutwil

PlantConnectome extracts 5 million functional relationships from 71,000 plant biology abstracts using large language models and provides a database for gene-metabolite interactions and regulatory networks.

The Plant Cell · Jul 1, 2025Peer-reviewedBioinformatics

Fungi.guru: comparative genomic and transcriptomic database for the Fungi kingdom

Jolyn Jia Jia Lim, Jace Koh, Jia Rong Moo, Erielle Marie Fajardo Villanueva, Dhira Anindya Putri, Yuen Shan Lim, Wei Song Seetoh, Sriya Mulupuri, Janice Wan Zhen Ng, Nhi Le Uyen Nguyen, Rinta Reji, Margaret Xuan Zhao, Tong Ling Chan, Edbert Edric Rodrigues, Ryanjit Singh Kairon, , Marek Mutwil

The paper introduces fungi.guru, a database integrating genomic and transcriptomic data from 19 fungi to identify conserved pathways and gene functions, with examples of secondary metabolite and catabolic pathways.

bioRxiv · Jun 26, 2020 · PreprintBioinformatics