Jonathan GÖKE

RESEARCH

The Laboratory of Computational Transcriptomics (PI: Jonathan Göke) develops computational methods for high throughput, long read RNA sequencing data. The team combines machine learning, statistics, and algorithms to identify new RNAs, quantify RNA expression, and profile RNA modifications. We work together with experimental teams and clinicians to apply these methods to cell lines, model systems and patient samples to study the role of RNA expression and modifications in cancer and neurodegenerative diseases such as Alzheimer’s disease.

Dr Jonathan Göke is a group leader at the Genome Institute of Singapore and Adjunct Associate Professor at the Department of Statistics and Data Science at the National University of Singapore. He obtained his PhD in Computer Science and Mathematics from the Max Planck Institute for Molecular Genetics/Freie Universität Berlin (Germany). Dr Göke has received scholarships from the Max Planck Society and the German Academic Exchange Service (DAAD), he was selected as GIS Fellow (2014-2016) and A*STAR Fellow (2024-2027). In 2024, Dr Göke received the Young Scientist Award by the Singapore National Academy of Science and the National Research Foundation “for his pioneering work in developing computational methods for long read RNA sequencing data that have enabled the profiling of RNA transcription and modifications at unprecedented resolution and accuracy.”

➡️ To find out more about the Laboratory of Computational Transcriptomics, visit the lab website for latest news on publications, preprints, conference talks and job offers: https://www.jglab.org

➡️ Visit the GitHub page for code and documentation: https://github.com/goekelab

➡️ Follow news from the team on X, and Jonathan Göke on Bluesky, X, or Linkedin

Postdoc positions and PhD scholarships available! Please contact Jonathan Göke for details

• A*STAR Research (1/2025): 'Guiding stars at scientific frontiers'
• Straits Times (10/2024): '4 young scientists in Singapore receive award for pushing boundaries in their fields'
• Channel News Asia (10/2024): 'Young Scientist Award: Dr Daniel Ting and Dr Jonathan Göke on use of AI in ophthalmology, RNA research'
• National Research Foundation (10/2024): ‘The President’s Science and Technology Awards 2024: Young Scientist Awards (YSA)’
• A*STAR Research (6/2024):‘Charting activity in genetic cityscapes’
• Asian Scientist (03/2023): 'AI Can Help Identify Diseases Early'
• GenomeWeb (6/2021): ‘Nature Papers Present Method to Uncover Differential RNA Modifications, Neutrophils in Innate Immune Response’

Selected Publications

• Chen Y, Davidson NM, Wan YK, Patel H, Yao F, Low HM, Hendra C, Watten L, Sim A, [...], Love MI, Goh WSS, Ng SB, Oshlack A, Göke J+, SG-NEx consortium. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. Nature Methods (in press).
• Oomen E, Rodriguez-Terrones D, Simmet K, Zakhartchenko V, Mottes L, Kurome M, Noll C, Nakatani T, Mourra-Diaz M, Aksoy I,  Savatier P, Göke J, Wolf E , Kaessmann H and Torres-Padilla ME. Mapping transcription initiation across mammalian species using Smart-seq+5’ reveals regulatory principles of embryonic genome activation. Cell (2025)
• Sim AD, Ling MH, Chen Y, Lu H, See YX, Perrin A, Leng Agnes OB, Cao EY, Chia B, Liu J, Wüstefeld T., Shin J+,  Göke J+, Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump, bioRxiv. 2025:2024-12
• Karwacki-Neisius V, Jang A, Cukuroglu E, [...],Göke J, He X, Lehtinen M, Pomeroy S, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature (2024): 1-10.
• Pardo-Palacios, Francisco J., et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods (2024): 1-15.
• Chen Y*, Sim AD*, Wan YK, Yeo K, Lee JJX, Ling MH, Love MI and Göke J+,. Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu. Nature Methods (2023) 20.8: 1187-1195.
• Hendra C, Pratanwanich PN, Wan YK, Sho Goh WS, Thiery A+, Göke J+. Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Nature Methods (2022). https://doi.org/10.1038/s41592-022-01666-1
• Wan YK, Hendra C, Pratanwanich PN, Göke J+. Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. Trends in Genetics. (2022). doi:10.1016/j.tig.2021.09.001
• Davidson N M, Chen Y, Ryland GL, Blombery P, Göke J, & Oshlack A (2022). JAFFAL: Detecting fusion genes with long read transcriptome sequencing. Genome Biology 23.1 (2022): 1-20.
• Pratanwanich PN, Yao F, Chen Y, Koh CWQ, Wan YK, Hendra C, Poon P, Goh YT, Yap PML, Chooi JY, Chng WJ, Ng SB, Thiery A, Goh WSS+, Göke J+. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nature Biotechnology. 2021. doi:10.1038/s41587-021-00949-w
• Wratten L, Wilm A, Göke J+. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nature Methods. 2021;18(10):1161-1168.
• PCAWG Transcriptome Core Group (Calabrese C*, Davidson NR*, Demircioğlu D*, Fonseca NA*, He Y*, Kahles A*, Lehmann K-V*, Liu F*, Shiraishi Y*, Soulette CM*, Urban L*), [...], PCAWG Transcriptome Working Group, Brazma A+, Brooks AN+, Göke J+, Rätsch G+, Schwarz RF+, Stegle O+, Zhang Z+, PCAWG Consortium. Genomic basis for RNA alterations in cancer. Nature. 2020;578(7793):129-136.
• ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020;578(7793):82-93.
• Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann K-V, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J+. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell. 2019;178(6):1465-1477.e17.