Plant Systems Biology and Evolution
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Welcome to the Mutwil Lab!
​The Mutwil lab is located within the School of Biological Sciences at Nanyang Technological University, Singapore.
We use systems biology to elucidate the function of genes in the plant kingdom. Today, knowledge of gene function is mostly confined to Arabidopsis thaliana, the main model organism in plant research, which limits our understanding of the plant kingdom. To remedy this, we are characterising also other plant species in terms of genomics, gene expression, metabolomics and protein-protein interaction networks. Based on this biological data we can then predict gene function with state-of-the-art network ensemble methods and other dry-lab techniques. This knowledge is important to understand plants and to tailor them to our needs.

September 27th, 2021

27/9/2021

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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.
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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)!
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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.  
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9) Peng Ken Lim received a PhD scholarship and will join us as a PhD student in Jan 2022.  Great job!
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End of 2020!

2/1/2021

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Finally, this bizarre year is coming to an end. The lockdown and staggered working hours have thrown a wrench into our daily routine, but thanks to the computational aspect of our work, we still managed to do research. Here is what happened in 2020:
1) Despite the lockdown (April-June), our lab managed to produce six papers (2 reviews and 4 original research) this year.
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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. ​
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3) 23 of the BS1009 undergrads did a two month-long internship in our lab to construct an online database www.fungi.guru. The project is building upon the BMC Bio paper, as the students analyzed >40,000 RNA sequencing samples from the fungi kingdom, and collectively wrote and published a paper. The results have been published in Computational and Structural Biotechnology Journal and our journey is described in this article:  Approaching New Frontiers in Fungi Research.
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4) Devendra got a lucrative offer from ACM Biolabs Pte Ltd, working there now as a Scientist since September, while IngTsyr moved to Yongui Gao’s lab to continue as Project Officer. Well done, both, and see you around the campus!
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5) The lockdown restlessness caused Marek to build ChuckNorris, a very cost-efficient (<4000$) workstation with 64 cores (128 threads), 256 GB RAM and 16 TB storage. You can read more about the assembly process here.
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6) Marek served as a main PhD opponent for Dr. Chanaka Mannapperuma (11.06.2020) and Dr. Bastian Schiffthaler (12.06.2020). Swedish PhD defenses are quite different from the German or Singaporean defenses, as i) the ‘opponent’ needs to make a small presentation introducing the thesis and ii) the ‘opponent’ and ‘defendant’ should discuss for 1 hour in front of the audience. Pretty hardcore! 

7) Three URECA students joined our lab: Erielle Villanueva, Dhira Putri and Wu Jingyuan, to work on organ-specific co-expression, soil metagenomics and a new search engine for scientific articles, respectively. 
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8) Together with Asst. Prof. Adriana Lopes dos Santos, we obtained a collaborative research award to work in single-cell transcriptomics of algae. We are looking for a motivated Project Officer/Research Associate to work on this project.
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9) We have two Postdoc positions, and one Project Officer position open. Check out the Openings section.
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Selaginella expression atlas and analysis of  transcriptional programs behind vasculature, cell wall, secondary metabolism and roots is out.

1/2/2020

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After a very constructive peer review, the manuscript is out in Plant Cell. Thanks to all people involved!
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Jonathan and Qiao Wen complete their qualifying exams

1/2/2020

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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!
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End of 2019!

6/12/2019

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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​. 
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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.
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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. ​
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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. 
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5) Devendra, Irene and Marek attended a bryophyte workshop in Melbourne in December. It was good to catch up on Marchantia research and hang out with Prof. Dr. Staffan Persson! 
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February update

8/2/2019

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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. 
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We have two postdoc positions opened! Check out the "Openings" section for more details

15/1/2019

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The homepage is online.

31/10/2017

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    Contact

    Asst. Prof. Marek Mutwil
    School of Biological Sciences
    Nanyang Technological University
    60 Nanyang Drive, 02s-88h
    ​Singapore 637551
    ​Email: mutwil[at]ntu.edu.sg

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