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.