## 29.08.2024 There are lots of news to share, but probably the largest one is that Marek will move back to Copenhagen, to start a new group at PLEN. Our SBS group will still keep running, but will be supervised remotely by Marek. 1) We have published 13 papers since March 2023. These include: From our lab: 1\) TIPS review on [Large language models in plant biology](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:V3AGJWp-ZtQC) #bioinformatics 2\) [PEO: Plant Expression Omnibus–a comparative transcriptomic database for 103 Archaeplastida](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:LPZeul_q3PIC) to facilitate comparative kingdom-wide gene expression analysis published in the Plant Journal (by Eugene, William, Irene and Erielle) #bioinformatics #evolution 3\) Ken and Ruoxi’s transcriptome assembly pipeline for eukaryotic species without genomes: [LSTrAP‐_denovo_: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:vRqMK49ujn8C) #bioinformatics 4\) Congrats also to Wee Han and Syahirah on their [Transcriptomic and metabolomic characterization of antibacterial activity of _Melastoma dodecandrum_](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:sSrBHYA8nusC) paper about the antibacterial properties of a medicinal plant which was published in Frontiers of Plant Science. #specialized_metabolism #bioinformatics ![[Picture1.png]] Collaborative: 5-6) Two papers on *Camellia sinensis* transcriptomics by Xinghai in collaboration with Yuefei Wang (Zhejiang University): [A method for mining condition-specific co-expressed genes in _Camellia sinensis_ based on k-means clustering](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:PELIpwtuRlgC) [Comparative transcriptome database for _Camellia sinensis_ reveals genes related to the cold sensitivity and albino mechanism of ‘Anji Baicha’](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:WqliGbK-hY8C) 7-9) Three papers on root decay by fungi (collaboration with Hong Yan from SBS): i)  [Locally Isolated _Trichoderma harzianum_ Species Have Broad Spectrum Biocontrol Activities against the Wood Rot Fungal Species through Both Volatile Inhibition and Mycoparasitism.](https://pubmed.ncbi.nlm.nih.gov/37367611/) ii) [A metagenomic survey of wood decay fungi in the urban trees of Singapore](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:B3FOqHPlNUQC) iii) [Volatile-Based Diagnosis for Pathogenic Wood-Rot Fungus _Fulvifomes siamensis_ by Electronic Nose (E-Nose) and Solid-Phase Microextraction/Gas …](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:geHnlv5EZngC) 10\) Jan de Vries' and collaborators brilliant [Genomes of multicellular algal sisters to land plants illuminate signaling network evolution](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:tkaPQYYpVKoC) 11\) A small detour into malaria with Peter Preiser: [Comparative spatial proteomics of Plasmodium-infected erythrocytes](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:q3oQSFYPqjQC) 12\) Jose Estevez is an early adopter of the PlantConnectome, which was used in [New molecular components that regulate the transcriptional hub in root hairs: coupling environmental signals with endogenous hormones to coordinate growth](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:BrmTIyaxlBUC) 13\) Another gem from Jan: [Environmental gradients reveal stress hubs pre-dating plant terrestrialization](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=1WY1xDwAAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=1WY1xDwAAAAJ:Tiz5es2fbqcC) 2) We got another Singaporean Ministry of Education Tier 2 Grant “Predicting the stress resilience mechanisms in the plant kingdom” where we will build machine learning models to understand how monocots respond to combined drought and heat stress. 3) We are joined by: 1) [[Dr. Eugene Koh]] joined us in the Tier 3 project 'From tough pollen to soft matter' 2) [[Jooa Moon]] (Tier 3 grant), who will work on identifying genes important for pollen development 3) [[Shan Chun Lim]] (NTU scholarship), who will work on knowledge graphs and large language models 4) [[Manoj Itharajula]] (NTU scholarship), who will work on building knowledge graph-based chatbots 5) We were also joined by [[Rohan Shawn Sunil]], who first started as Project Officer but transitioned this month to a PhD student (NTU scholarship). Rohan will study knowledge graphs with embedding models to predict gene function 6) [[Paula Tan]] (Tier 2) as PO working on the abiotic stress project. 4) Who left? 1\) Zahin successfully completed the fern project and went abroad to start his PhD in Prof Jan de Vrie’s lab at the University of Goettingen, Germany. His epic work is now in review and available at: https://www.biorxiv.org/content/10.1101/2024.08.27.609851v1 2\) After a very productive year, Xinghai returned to the Tea Institute at Zhejiang University. 3-4) Our visiting professors Yanlin Li and Jiayi Cao went back to their respective universities in China. Good luck and hope to see you again! ## 23.03.2023 It has been a while, and we should probably be better at updating this page. We will try to do better next time! Here are some updates: ​1) We published 9 papers since the last update. 1) I am super happy to see Qiao Wen's study on how Marchantia responds to combined stresses in Nature Communications:  [Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.](https://pubmed.ncbi.nlm.nih.gov/36813788/) 2) My BS1009 Computational Thinking undergrads published two papers: [Protist.guru: A Comparative Transcriptomics Database for Protists.](https://pubmed.ncbi.nlm.nih.gov/35389344/) 3) and [Bacteria.guru: Comparative Transcriptomics and Co-Expression Database for Bacterial Pathogens.](https://pubmed.ncbi.nlm.nih.gov/34838806/). It's great to see that even year one undergraduates can be involved in publishable research, both published in Journal of Molecular Biology. 4) Jonathan's foray into machine learning was published in FIPS as [Feature importance network reveals novel functional relationships between biological features in _Arabidopsis thaliana_.](https://pubmed.ncbi.nlm.nih.gov/36212273/) 5) Review on transcriptomic databases [Exploiting plant transcriptomic databases: Resources, tools, and approaches.](https://pubmed.ncbi.nlm.nih.gov/35605200/) in Plant Communications 6) Review on kingdom-wide analyses of expression data: [Toward kingdom-wide analyses of gene expression.](https://pubmed.ncbi.nlm.nih.gov/36344371/) in TIPS 7) Review on  [Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data.](https://pubmed.ncbi.nlm.nih.gov/36874159/), our first foray into chemoinformatics in CSBJ 8) One spotlight with Ally Fernie [Ancestral genome reconstruction for studies of the green lineage.](https://pubmed.ncbi.nlm.nih.gov/36871157/)in Molecular Plant 9) Last but not least Irene's and collaborator's tremendous work on [Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites.](https://pubmed.ncbi.nlm.nih.gov/36807520/) in Journal of Integrative Plant Biology.  ​2) Funding-wise, we managed to pull in: 1) Tier 1 (to study biosynthesis of antibacterial metabolites) 2) Tier 2 (to produce and study gene expression and metabolic atlases in the plant kingdom) 3) Tier 3 grant (to design new nanomaterials from pollen). 4) 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) 7) Olivia Agatha (PhD student working on producing sesquiterpene lactones in yeast). 8) 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.** 4\) Who left: 1) I am super happy that Jonathan (now Dr. Ng) graduated and landed a nice job in an AI startup even before graduation 2) After productive two years, Jong Ching Goh (seen below in the brown sweater) received multiple offers and decided to study AI 3) After a productive year, Syahirah (first person, left row) started a Masters degree in bioinformatics 4) Wee Han (last person, left row) started at Lonza to work on bioreactors. Good luck to you all and let's stay in touch!  ## 27.09.2021 Time for another update. We published four papers this year so far: 1. Riccardo's paper on structural landscape of viruses (a singular detour to virus land) was published in BMC Genomics 2. Irene's comparative transcriptomic analysis of land plants was accepted in Nature Plants 3. William's pipeline allowing construction of expression atlases for kingdoms of life landed in Bioinformatics 4. 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). 1. One a comparative study of stress responses in the plant kingdom 2. One to study how local crops modify their metabolism and transcriptome to stresses and different growth conditions 3. And one to identify biosynthetic pathways of specialized metabolites in medicinal plants. Exciting times ahead! 3\) We are joined by: 1. 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, 2. Syahirah Nur (project officer), who will work together with Wee Han 3. Muhammad Zahin Bin Mohd Ali (Zahin Ali, project officer) , who will study gene expression in non-flowering plants 4. Jong Ching ​Goh (project officer), who will work with Rajesh 5. Peng Ken Lim (project officer), who is working on single cell transcriptomics 6. Xinghai Zheng, who is working on omics analysis of heat stress acclimation in Brachypodium. 4\) Who left: 1. Riccardo left the group to pursue his passion on structural biology of viruses, 2. 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](https://bacteria.guru/), while the other group downloaded and processed gene expression data to make [protist.guru](https://protist.guru/). you can find the preprints [here](https://www.biorxiv.org/content/10.1101/2021.08.02.454836v1.abstract) and [here](https://www.biorxiv.org/content/10.1101/2021.08.04.455173v1.abstract), respectively.    9\) Peng Ken Lim received a PhD scholarship and will join us as a PhD student in Jan 2022.  Great job! ## 02.01.2021 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](https://www.plant.tools/publications.html) papers (2 reviews and 4 original research) this year.  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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470450/), and you can read more about our pedagogical adventure here: [Strength in Numbers: Research Amidst a Pandemic](https://blogs.ntu.edu.sg/science/2020/10/09/strength-in-numbers-research-amidst-a-pandemic/). ​  3\) 23 of the BS1009 undergrads did a two month-long internship in our lab to construct an online database [www.fungi.guru](http://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](https://pubmed.ncbi.nlm.nih.gov/33304470/) and our journey is described in this article:  [Approaching New Frontiers in Fungi Research](https://blogs.ntu.edu.sg/science/2020/12/29/approaching-new-frontiers-in-fungi-research/).  4\) Devendra got a lucrative offer from [ACM Biolabs Pte Ltd](https://www.acmbiolabs.com/), working there now as a Scientist since September, while IngTsyr moved to [Yongui Gao](https://www3.ntu.edu.sg/home/ygao/Site/Home.html)’s lab to continue as Project Officer. Well done, both, and see you around the campus! ​ 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](https://twitter.com/LabMutwil/status/1313087572017438722).  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](https://scientistseessquirrel.wordpress.com/2016/06/16/the-opponent-system-my-experience-at-a-swedish-phd-defence/) 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.  ​ 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.  9\) We have two Postdoc positions, and one Project Officer position open. Check out the [Openings](https://www.plant.tools/openings.html) section. ## 01.02.2020 After a very constructive peer review, the manuscript is out in [Plant Cell](http://www.plantcell.org/content/early/2020/01/27/tpc.19.00780.long). Thanks to all people involved!  2. Jonathan and Qiao Wen complete their qualifying exams. 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! ## 06.12.2019 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.  1. 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._  2. 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](https://www.plant.tools/publications.html) out this year and produced two comparative transcriptomic databases: [malaria.tools](https://malaria.sbs.ntu.edu.sg/) allows comparative genomic and transcriptomic analyses for _Plasmodium_ species, while [diurnal.tools](https://diurnal.sbs.ntu.edu.sg/) 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.   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](https://blogs.unimelb.edu.au/persson-lab/people/)! ## **08.02.2019** 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.