Göke Lab

Computational Transcriptomics @ GIS


How can different cell types arise from the same genome? What discriminates a normal cell from a cancer cell? Will genomics data help to understand, model, and predict human disease progression?

Welcome to the website of Jonathan Göke’s team at the Genome Institute of Singapore!

We’re a computational genomics group searching for answers to these questions. We develop algorithms and investigate genomics and transcriptomics data to better understand human diseases such as cancer. Our group specifically works on third generation long read sequencing technology. We are located at the Genome Institute of Singapore. Read more about us, our research and publications, or available scholarships (PhD, internships) and positions. You can find more information about methods from the team on our github page.

Recent lab news

17/11/2022: Jonathan will present at the CSI-GIS RNA conference about computational methods for long read RNA-Seq data.

10/11/2022: m6Anet is published in Nature Methods! You can read the article here and a short summary here. Congratulations to PhD student Christopher Hendra! Here is the link to the method: https://github.com/GoekeLab/m6anet

08/08/2022: Jonathan Göke will give a talk at the 1st Thailand Symposium on Nanopore Technology on the topic of RNA modification detection.

23/07/2022: Christopher Hendra will present his work on the deteection of RNA modifications using machine learning at ICML 2022. Congratulation Chris!

11/07/2022: Andre Sim will present about Bambu at ISMB 2022. You can watch his talk in the RNA session or visit his poster!

29/06/2022: Updated team picture from lab event in east coast park!

13/05/2022: Jonathan Göke will give a talk on “AI meets nanopore: From sequencing to high dimensional genomics data” as part of the AI & Analytics Talk Series.

09/03/2022: Our review on machine learning methods for analysing Nanopore signal data is featured on the cover of Trends in Genetics! Congratulations Yuk Kei, Christopher, and Ploy! (open access: link)


06/01/2022: Congratulations to Chen Ying and collaborators Nadia Davdison and Alicia Oshlak for publishing JAFFAL, a method for fusion detection form long read RNA-Seq data in Genome Biology! (link)

25/10/2021: Congratulations PhD student Yuk Kei Wan on publishing this review about machine learning for Nanopore signal data published in Trends in Genetics! You can read the article here (open access link coming soon)

23/09/2021: New publication on bioinformatics workflow managers by visiting student Laura Wratten in Nature Methods. Congratulations Laura! You can read the article here

03/08/2021: Andre Sim and Joseph Lee will present their work on proActiv and bambu at BioC2020, you can still register!

21/07/2021: Our manuscript describing xPore is published in Nature Biotechnology! Congratulations Ploy Pratanwanich, Yuk Kei Wan, Chen Ying and all collaborators! xPore is available on github, with detailed documentation. You can read the paper here

22/04/2021: New preprints from our group is online! You can read about the Singapore Nanopore Expression project here, the data is available through github. Congratulations to first author Chen Ying!

28/08/2020: Jonathan will present at the Victoria Cancer Bioinformatics Meeting (Australia), you can see the program here

28/07/2020: Congratulations Chen Ying for receiving the Best Talk award in HiTSeq/ISMB 2020! Chen Ying presented about her method, bambu, for transcript discovery and quantification using Nanopore long read RNA-Seq data (https://github.com/GoekeLab/bambu)

26/06/2020: New Preprint from Ploy Pratanwanich about her method that enables the analysis of differential RNA modifications using direct RNA-Seq data: https://www.biorxiv.org/content/10.1101/2020.06.18.160010v1.full  xPore is available through github page: https://github.com/GoekeLab/xpore you can read the documentation here

18/06/2020: Chen Ying and Ploy Pratanwanich will present their work on RNA modifications and transcript quantification at London Calling 2020. You can test their software on out github page: https://github.com/GoekeLab

26/03/2020: The DREAM Challenge paper on multiple myeloma risk prediction is published (you can read it here). Congratulations again to Christine and Jiayi from our group for winning this challenge and contributing the best performing predictor!

05/02/2020: The Pan Cancer Analysis of Whole Genomes (PCAWG) is published! Congratulations to everyone involved from our group, GIS and all international collaborators (see publications)


31/01/2020: Congratulations for winning the Genome Institute of Singapore graduate student prize Deniz!Deniz_graduateStudentPrize

13/01/2020: Deniz has prepared detailed supplementary tables for his manuscript (Demircioglu et al. (2019)). You can find the additional information here

05/11/2019: Jonathan presents at the Frontiers in Cancer Science meeting in Singapore

05/09/2019: Our first paper is published on the cover of Cell! Congratulations to the first author Deniz Demircioglu and everyone else who has contributed! You can read the article here.Cell Cover 2019

01/07/2019: Postdoctoral positions are available for computational postdocs to work on long read direct RNA-Sequencing, you can contact Jonathan for more details.

28/2/2019: You can watch a webinar about the Singapore Nanopore-Expression project today

15/2/2019: Happy Chinese New Year! Some updates to the team site and new pictures from this year’s Lo Hei

Find more news in our News Archive.