Group members
Our research team has members working in University of Helsinki and in Nanyang Technological University in Singapore.
Jarkko Salojärvi, Group Leader

I am a machine learning guy who turned into a biologist. After my PhD in computer science, I did two post-docs, one in plant stress signaling and second one in human gut microbiome analysis. Moving on, I started my group on (plant) genomics in 2014, and currently I have two groups, one in Helsinki from my Academy Research Fellow position, and a second one in Nanyang Technological University (NTU) Singapore where I am an Assistant Professor. 

My group uses computational methods to study biological questions related to genome evolution. Over time, the biological scope of the research has widened from studying a single clone (Col-0) to looking at (gut) ecosystem and finally at NTU to the analysis of all plant genomes and (some) populations in an entire patch of rainforest. All this has made me even more intrigued by genome evolution; how it is shaped by the past environmental changes, pathogens and microbial symbionts. Understanding these issues will be crucial for future plant adaptation with the currently ongoing rapid climate change and habitat fragmentation. Genomes contain information from the past, from different climate conditions, and this may help in identifying future “evolutionary winners and losers” and hopefully suggest ways to prevent the impending loss of biodiversity.

Jarkko Salojärvi's contact and research profile in the University of Helsinki People Finder

Jun Ying Lim, Post Doc

I recently joined the lab at Nanyang Technological University in Singapore as a Post-doctoral Fellow. My interests are largely focused on understanding how abiotic and biotic changes in deep time have shaped or are continuing to shape modern ecological communities. My work relies on a huge variety of analytical tools, from big data biodiversity informatics, phylogenetic / genomics, metabarcoding, to geospatial statistics.

Sara Mehrabi, Post Doc

I am Wallenberg-NTU postdoctoral fellow and joined the group in Singapore in December 2019. I am interested in studying plant-microbe interactions from different angels. During my postdoctoral work at Swedish university of agricultural sciences (SLU), I studied the interaction between Fungus Magnaporthe oryzae and finger millet or rice. I completed my PhD at Stockholm University, where I studied the candidate genes for resistance and susceptibility to the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley (Hordeum vulgare L.). Currently I am working on two projects; (1) comparative transcriptomics between symbiotic Parasponia and non-symbiotic Trema , and (2) comparative analysis of symbiotic Alnus and non-symbiotic Betula.

Aleksia Vaattovaara, Post Doc

I am a postdoc in University of Helsinki and working with population genomics of birch and alder. I am interested in the evolutionary biology and especially how genes and genomes evolve.

Aleksia Vaattovaara's contact and research profile in the University of Helsinki People Finder

Cui Wang, Post Doc

I am working in both Helsinki and Singapore sides. I am interested in evolutionary history and population genetics of plants and animals, especially in the reorganization of genome elements in accompany with species divergence. Currently I am employing genomic approaches on a polyploid plant species Phragmites australias as a model, to study the role of whole genome duplication and interspecific hybridization play in the intraspecific divergence of this widespread weed. By comparing the genome structure of different populations, we would be able to infer how modern genomes were formed after multiple whole genome duplication and diploidization events, and to understand whether reorganization of genomic structure helps plants with developing local adaptation and invasiveness to the changing environment.

Cui Wang's contact and research profile in the University of Helsinki People Finder

Nicholas Cho, PhD student

I am studying the population genomics of the Tembusu (Cyrtophyllum fragrans) tree in Singapore in order to elucidate genomic patterns of fragmentation in the Tembusu, and aim to use this information to examinine the state of deforestation in forests in SEA, by using Tembusu as a reference. In addition, I am looking into the genome annotation and comparative genomics of Tembusu to identify genes selected when adapting to nutrient poor soils. Finally, I will be studying the microbiome of Tembusu in the aims of identifying genes which causes Tembusu to associate with symbionts. These genes which are identified could then be used in genome editing in other tree species for reforestation projects.

Position: 2nd Year PhD Student at Nanyang Technological University, Singapore

Topic: The Tembusu Genome as a Reference for Adaptability and Tree Selection

Maja Ilievska, PhD student

I am Maja Ilievska, PhD student in the Doctoral Programme in Plant Sciences (DPPS) at the University of Helsinki. I am in the third year of my doctoral studies, and the topic of my dissertation is "Data integration for network inference and network analysis in Plant Systems Biology”. One of my projects focuses on gene co-expression network analysis and xylan biosynthesis pathway in plants. The other projects are related to method development and data integration for inference of gene regulatory networks. 

Maja Ilievska's contact and research profile in the University of Helsinki People Finder

Thomas Jenner, PhD Student

I am Thomas Jenner, a doctoral student in the Food Chain and Health doctoral programme. My research is focused on Bacterial Functional Genomics and Mammalian Transcriptomics, specifically Host Microbe Interaction in Bovine Mastitis. I am interested in examining how mastitis causing bacteria establish infection in ruminants (i.e. Bovine), and how the host immune system responds to the infection caused by the bacterial pathogens. I anticipate that my research will contribute towards developing novel approaches to mastitis diagnostics and control. In addition to bacterial genomics, I'm working on the annotation of plant genome(s).

Thomas Jenner's contact and research profile in the University of Helsinki People Finder

Sitaram Rajaraman, PhD student

I am currently a Research Associate at Nanyang Technological University, Singapore and a Doctoral student at the University of Helsinki, Finland. I have seven years of experience in the field of Plant Biology and Bioinformatics. My main interests lie in unravelling the evolutionary history of trees. Current key projects include Biodiversity study of the forest of Bukit Timah (Singapore) and Adaptive Landscape of Silver Birch (Finland). I have also collaborated with fellow researchers studying fungal genomes (Taphrina betulina, Protomyces), other non-model plant genomes (Coffea arabica, Alnus glutinosa, Drosera sp., Nepenthes sp., Stenogyne calaminthoides, Syzygium sp., Fagraea sp.,) and dog genomes. Apart from academics, I have a keen interest in the field of music, doing occasional gigs with my fusion band Sitaram and Friends (Finland).

Pezhman Safdari, PhD student

My name is Pezhman Safdari and I am a Ph.D. candidate in Anna-Liisa Laine group and also a member of the BMBG group in University of Helsinki. I am a bioinformatician and I specialize in transcriptome analysis and automatic manual and functional gene/transcript annotations. 

Pezhman Safdari's contact and research profile in the University of Helsinki People Finder

Xiaoxue Ye, PhD student

I joined the lab at Nanyang Technological University in Singapore as an exchange PhD student. I'm focused on understanding the mechanism of salt tolerance in plants through their transcriptomes and non-coding RNA regulation. During my time in Singapore, I am expanding my comparative genomics skill set by looking at genomic signatures involved in the evolutionary transition to aquatic habitats in angiosperms.