Lab Highlights
1 November 2023
Another successful conduct of the module GMS6907: Applied Bioinformatics and Omics Data Analysis for the year 2023. This is the second year we are running the module, and it was an overwhelming response from students, post-docs, clinicians and even professors! At the end of the module, most of the students were able to use Python to solve medical problems and were able to create simple webtools to facilitate data science analysis. Once again, I sincerely thank Justin and Clara for helping with the practical sessions. Hopefully the knowledge they have gained would help them a long way in the future career development and advancement!
30 October 2023
Perfect time for Justin Ooi to showcase his research study on the relationship between humoral and T cell responses to vaccination. His work highlights the need to understand both arms of adaptive responses to gain a full understanding on the correlates of protection for vaccines. Proud of his achievements and hope he will continue to advance our understanding on vaccination responses and protection!
24-25 October 2023
What a great opportunity to be able to attend a Duke/Duke-NUS Joint Symposium at the Duke University! It was great time learning from the Duke University professors, and to be able to bond with the students, post-docs and PIs from the department. It was also great fun visiting the chapel and the lemur center.
11 October 2023
We are very happy to be able to share our knowledge of vaccines and data science on the conference "Update on Vaccine Science" sponsored by GSK and Takaeda, held in Duke-NUS Medical School on the 11th-13th October. Justin Ooi shared on his knowledge of transcriptional correlates of protection for vaccines, and shared his data on the transcriptomics profile performed with the Shingles vaccines on the elderly subjects. On the other hand, I shared my knowledge on systems vaccinology and conducted a team-based learning session for the attendees to ensure that the participants had time to interact.
11 June 2023
We are super excited to be able to conduct a workshop at The Federal University of Espírito Santo in Vitoria, Brazil. This is a 6 day workshop where we will topics related to Python and R programming, covering from fundamentals to the more advanced topics. We hope these efforts will empower the students to use Python and R for big data analysis and improve their data analysis for their research. The topics covered can be found here.
Meanwhile, we are extremely grateful to Rachel and Bruno for bringing us around Vitoria. Thank you for their kind hospitality, it means a lot to us!
11 June 2023
It has been an exciting year for the lab, as we have published 4 papers since the start of the year 2023! In one paper published in Med, we show the potential involvement of RNase2 in mRNA vaccine-associated cardiac complication. In another paper we published in Sci Rep, we developed a web-tool called STAGEs that allows users to analyse gene expression studies. A paper also involved the experimental design of a clinical trial to understand the importance of T cells in vaccine protection published in Frontiers Immunol. Finally, we are proud of our publication in eBioMedicine where we identified MCEMP1 and HLA-DRA expression as early prognostic markers for severe COVID-19
11 May 2023
I am very honoured to be featured on Straits Times based on our findings that RNase2 could be involved in mRNA vaccine-associated cardiac complications. Full article can be found here. Hopefully these efforts will help in mRNA vaccine development!
I also had the opportunity to be interviewed by Channel 8, where I talked about the isolation policies for COVID-19. Full interview can be found here. These publicity comments should help people understand more about COVID-19 and COVID-19 management
27 December 2022
In the midst of fighting against COVID-19, do not forget about dengue. Privileged to be able to contribute to a commentary article in Straits Times detailing the efforts that have been done and how each of us can contribute in the battle against dengue. To read the full article, you may access the article here.
5 December 2022
Proud to highlight that Clara Koh has been nominated as the best research assistant award in the department and the Bunsen Burner award in the SingHealth Duke-NUS AMC Research Staff Day for the year 2022. What a great way to end the year! I am very privileged to be able to work with her on multiple projects, utilising omics data to understand human biology. Hope to be able to see her shine even more in the years to come!
28 November 2022
Finally our work on transcriptomic responses to self-amplifying mRNA vaccines is out! In this piece of work, we examined the transcriptomic responses that are most strongly associated with antibody and T-cell responses. We also compared the responses to other successful vaccines, which highlighted the potential of the use of self-amplifying mRNA for future viral pandemics. More information can be found at: https://www.nature.com/articles/s41541-022-00573-y
3 Novemember 2022
Privileged to be able to present in the ProImmune Mastering Immunity 2022, where I will be presenting Justin Ooi's work on: "Characterisation of host immune variations that influence live-attenuated Yellow Fever vaccine adaptive immune responses." He has also presented this work in the 16th Vaccine Congress in Italy 2022, and was well received. More details can be found at https://www.proimmune.com/proimmune-mastering-immunity-2022/
1 0 August 2022
Big congratulations to Meisam, who published his story on how TMEM41B and VMP-1 modulates multiple cellular pathways, including lipid mobilization, mitochondrial beta-oxidation, and global metabolic regulations, to facilitate the replication of flaviviruses and coronaviruses. We are happy to have helped in the metabolic profiling and mitochondria phenotyping of the knock-out cells. The GitHub address for the mass spectrometry data can be found here. For more details, the manuscript can be found here.
1 August 2022
A great privilege to be interviewed by Nanostring with Eugenia Ong from ViREMiCs to discuss about the roles of multi-omics platforms and bioinformatics in shaping vaccines and therapeutics development. To hear the podcast, please visit: https://podcasts.apple.com/sg/podcast/viremics-a-lab-for-vaccine-development-against/id1613104197?i=1000574536392
Enjoy!
28 July 2022
Congratulations to Clara Koh and Justin Ooi who are the co-first authors of a publication in Scientific Reports, where they developed a web tool using Streamlit that auto-corrects and converts old gene names and dates into the updated gene names, as recommended by the HUGO Gene Nomenclature Committee. These conversions make the genes more resilient to Excel auto-conversion, ensuring accuracy and integrity of gene expression data. Click on the hyperlinks to access to publication, GitHub, data files and blog for more details.
29 April 2022
Privileged to be invited as a speaker for an onsite conference in Singapore. Finally, a conference on dengue! Excited to share my recent research findings, which is on "Global analysis of baseline human immune variations that influence yellow fever live-attenuated vaccine immunogenicity." Hope to see all of you there and network with all of you.
Check out Justin Ooi's poster as well, to know more information about the project!
6 April 2022
I am privileged to be invited as one of the panelists to discuss about how COVID-19 has shaped the local environment and how we can potentially alter our surroundings to cope with the COVID-19 pandemic. Many thanks to Jian Hong for coordinating these activities and help increase our public awareness on these topics. It was a fun session!
15 December 2021
Big congratulations to Clement Yau and John Low for successfully publishing their work entitled "Dysregulated metabolism underpins Zika-virus-infection-associated impairment in fetal development," in Cell Reports. We integrated transcriptomics, metabolomics and cellular bioenergetics methods to uncover the molecular mechanisms how a single substitution in the Membrane protein of Zika virus (M-F37L) leads to dysregulated metabolism that promoted to zika pathogenesis. The effects of dysregulated metabolism can be potentially reversed by supplementing with pyruvate, suggesting a potential therapeutic avenue for Zika treatment.
6 December 2021
We are incredibly excited to share our first streamlit web tool developed by Clara Koh and Justin Ooi. Gene Updater auto-corrects and converts old gene names and dates into the updated gene names, as recommended by the HUGO Gene Nomenclature Committee. These conversions make the genes more resilient to Excel auto-conversion.
26 November 2021
Congratulations to one of our lab members, Justin Ooi, who was selected to give an oral presentation at the DUNES symposium. He gave an amazing talk on how transcriptomics datasets can be useful to accelerate vaccine research. Looking forward to see more of his discoveries in the field of omics research!
16 November 2021
It is a privilege to be an invited speaker at IVBDHC, where our lab showcased how our web tools can potentially accelerate systems vaccinology research.
Happy to hear that Meisam Yousefi, a PhD student whom I work very closely with, was awarded the best oral presenter. Looking forward for more discoveries from him and his mentor, Yaw Shin Ooi