​1) We published 10 papers since the last update. This includes three databases (protist.guru,  bacteria.guru and FINder), three reviews (1: on transcriptomic databases, 2: on kingdom-wide analyses of expression data, 3: on using machine learning to redesigning specialized metabolism), one spotlight with Ally Fernie (on ancestral genome reconstruction) and several collaborative papers. I am super happy to see Qiao Wen's study on how Marchantia responds to combined stresses in Nature Communications, and Irene's work on Oldenlandia in Journal of Integrative Plant Biology. Congrats to all involved!

​2) Funding-wise, we managed to pull in Tier 1 (to study biosynthesis of antibacterial metabolites), Tier 2 (to produce and study gene expression and metabolic atlases in the plant kingdom) and Tier 3 grant (to design new nanomaterials from pollen). We are also happy to be part of a consortium Nanyang Biologics comprising cancer researchers, chemists and machine learning scientists that aims to develop new sesquiterpene lactone drugs (https://www.ntu.edu.sg/nbnjl)

3) We are joined by: 1) Dr. Jiayi Cao (working on organ-specific stress responses), 2) Dr. Yanlin Li (elucidating gametophyte-spotophyte transitions in ferns),  3) Li Hui Peh (Project Officer studying abiotic stress programs in algae, bryophytes, lycophytes and flowering plants). In the coming months, we will be also joined by 4) Dr. Jiamin Lee (analyzing abiotic stress responses in local crops), 5) Jhing Yein Tan (PO: plant kingdom expression atlases), 6) Sabrina Tan (PO: producing novel triterpenes in yeast) and 7) Olivia Agatha (PhD student working on producing sesquiterpene lactones in yeast). Qiao Wen will stay with us as a research fellow after graduating (Aug-Sep this year). We are still looking for a postdoc and a project officer to join the exciting Tier 3 project on pollen exine biosynthesis. Drop me an email if you are interested.
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4) How left: I am super happy that Jonathan (now Dr. Ng) graduated and landed a nice job in an AI startup even before graduation. After productive two years, Jong Ching Goh (seen below in the brown sweater) received multiple offers and decided to study AI. After a productive year, Syahirah (first person, left row) started a Masters degree in bioinformatics, while Wee Han (last person, left row) started at Lonza to work on bioreactors. Good luck to you all and let's stay in touch!

Time for another update.
1) We published four papers this year so far. i) Riccardo's paper on structural landscape of viruses (a singular detour to virus land) was published in BMC Genomics. ii) Irene's comparative transcriptomic analysis of land plants was accepted in Nature Plants. iii) William's pipeline allowing construction of expression atlases for kingdoms of life landed in Bioinformatics. iv) Devendra's paper on removing auto-activators from yeast-two-hybrid assays found home in Scientific Reports.

2) Funding-wise, we managed to pull in three grants (out of six submitted proposals). We will (i) do a comparative study of stress responses in the plant kingdom, (ii) study how local crops modify their metabolism and transcriptome to stresses and different growth conditions and (iii) identify biosynthetic pathways of specialized metabolites in medicinal plants. Exciting times ahead!

3) We are joined by: i) Wee Han Poh (research fellow, joint appointment with Assoc. Prof. Scott Rice's lab), who will work on discovering the mode of action of antibacterial metabolites, ii) Syahirah Nur (project officer), who will work together with Wee Han, iii) Muhammad Zahin Bin Mohd Ali (Zahin Ali, project officer) , who will study gene expression in non-flowering plants and iv) Rajesh Gazara (research fellow), who will work on the local crops project (see above), v) Jong Ching ​Goh (project officer), who will work with Rajesh and vi) Peng Ken Lim (project officer), who is working on single cell transcriptomics and vii) Xinghai Zheng, who is working on omics analysis of heat stress acclimation in Brachypodium. We hope that COVID19 restrictions are lifted soon, as Rajesh is now waiting several months to join.

4) Riccardo left the group to pursue his passion on structural biology of viruses, while William finished his internship after publishing in Bioinformatics. Good luck guys!

5) Irene's publication was covered by internal NTU news. Check the article out here: https://blogs.ntu.edu.sg/science/2021/09/08/plant-organs-evolve-by-reusing-old-genes/ . We also started a new tradition in the lab: publication mugs. Join us and get yours (eventually)!

6) We are looking for a project officer to work on the comparative stress responses in plants. Check out the openings section for more info!

7) Despite the COVID19 annoyance, we had a good time running BS1009, Introduction to Computational Thinking. The 289 students were taught Python and as their final project, they analyzed RNA sequencing data for protists. What worked really well this year was having the student and instructors join WhatsApp groups, allowing the students to ask questions and receive answers within minutes. Thanks to the great instructors (most who are BS1009 alumni from 2019/2020), who answered questions 24/7. 

8) Like last year, we run a two month long internship, where BS1009 alumni analyzed gene expression data. This year, ~40 students were split into two groups. One group analyzed gene expression of bacteria to make bacteria.guru, while the other group downloaded and processed gene expression data to make protist.guru. you can find the preprints here and here, respectively.  

9) Peng Ken Lim received a PhD scholarship and will join us as a PhD student in Jan 2022.  Great job!

2) Another batch of students graduated from BS1009 - Introduction to Computational Thinking, armed with a solid foundation in Python programming and algorithm development. This year, we had an unusual project for the students: to analyze >20,000 RNA sequencing experiments of pathogenic bacteria, and to identify novel genes that are putatively involved in protein synthesis. The results of the project were published in BMC Biology, and you can read more about our pedagogical adventure here: Strength in Numbers: Research Amidst a Pandemic. ​

After a very constructive peer review, the manuscript is out in Plant Cell. Thanks to all people involved!

Time flies and the the two PhD students did a good job defending their projects and work. Jonathan talked about his project that uses machine learning to identify genes involved in secondary metabolism, while Qiao Wen described her systems biology analysis of heat acclimation project. Good job!

It has been a while since the last update and a lot of good things happened. 

1) We had a pleasure to host four fantastic Final Year Project (FYP) students for three months.  Ying Kiat (nr. 1 from the left) and Vernice (3) were supervised by Dr. Devendra Shivhare (2) and Dr. Zhu Xinyi (SCELSE, not shown), and have identified many plant extracts that inhibit planktonic and biofilm growth of Pseudomonas ​aeruginosa and Staphylococcus aureus. Mun Yi (4) and Veronique (6) were supervised by Qiao Wen Tan (5) to study stress memory and cross-acclimation to multiple abiotic stresses in Arabidopsis thaliana​. 

2) The group expanded. Dr. Irene Julca and Dr. Riccardo Delli-Ponti joined to work on the Hedyotis genome project and on an online database capturing expression of biosynthetic pathways, respectively.

3) We finished coordinating the first run of Computational Thinking course (BS1009). Now ~230 students are (theoretically) able to write useful scripts in Python. It was a great experience and we look forward to do it again next year. ​

4) We got some papers out this year and produced two comparative transcriptomic databases: malaria.tools allows comparative genomic and transcriptomic analyses for Plasmodium species, while diurnal.tools can analyse diurnal gene expression in 17 members of Archaeplastida, including  algae and land plants. Diurnal.tools lands in research highlights in Plant Cell and Physiology. 

The year of the pig started well!

1. I am very proud to say that Camilla Ferrari, my Ph.D. student from Max Planck Institute of Molecular Plant Physiology, defended her Ph.D. thesis with a very strong magna cum laude. Congrats to Camilla!
2. Camilla's Ph.D. work culminated in a publication in Nature Communications (please check out the publications section). Further congrats, Camilla!
3. We have been successful in securing a Tier 2 grant to study the biosynthetic pathways of Hedyotis corymbosa, which as potent growth inhibition activity against several forms of cancer. We will sequence and assemble the genome, generate transcriptomic and metabolomic atlas and identify the active compound by a combination of biophysical and in vivo approaches.