People
Group members of Ville Paavilainen Laboratory
Ville Paavilainen, PhD, Docent, Group Leader

I am the head of the chemical biology and proteostasis research group that continues to identify new inhibitors of protein secretion and uses these small molecules as chemical probes for studying protein homeostasis regulation in eukaryotic cells. The long-term goal of the laboratory is to identify new targets and chemical lead compounds for therapeutic development in areas where protein homeostasis and protein misfolding contribute to disease progression.

I studied the regulation of actin dynamics in the lab of Prof. Pekka Lappalainen at the University of Helsinki. As a postdoc with Prof Jack Taunton at the University of California -San Francisco, I worked on the structure-guided design of covalent-reversible kinase inhibitors and natural product-inspired small molecule inhibitors of protein secretion. In my free time, I am passionate about rock climbing, cycling and spending time with my family.

ville.paavilainen@helsinki.fi
Ville on Twitter
Ville´s ORCiD
Ville on Research Gate

 

Maryna Green, PhD, Research technician

Protein production and purification are my main strengths. I have a broad expertise area in protein expression in bacteria, insect and mammalian cells; protein purification using different chromatography methods and characterization by SAXS, CD, and SLS techniques. 

Currently, I am involved in commercialization project in the Paavilainen lab and I am learning a lot about the business aspects of starting the new biotech company. I completed my PhD degree at the University of Oulu in the group of Petri Kursula. Since then I have been working at the University of Helsinki as a postdoctoral researcher focused on the structural biology of membrane proteins, being also responsible person for the protein crystallization infrastructure headed by Tommi Kajander. While working in Juha Huiskonen’s group, my main role was the production and purification of virus-like particles for structure determination by cryo-EM.  In my free time, I do belly dancing and art photography modeling. Also, I am the founder of the first Russian-speaking women club in Porvoo.

maryna.green@helsinki.fi
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Matti Javanainen, PhD

In the Paavilainen group, I apply my know-how on molecular dynamics simulations to make the static cryo-EM pictures dance on the computer screen and reveal the secrets of the dynamic Sec61-mediated protein translocation process. I am excited about the possibility to learn about structural biology, but also looking forward to promoting the use of simulations in the experimental community.

I have a background in computational biophysics. I obtained my doctorate from the Tampere University of Technology with Prof. Ilpo Vattulainen, and my Thesis considered the dynamics of proteins and lipids in crowded membrane environments. I then moved on to study the interactions of charged peptides and ions with lipid membranes as a postdoc in the group of Prof. Pavel Jungwirth at IOCB Prague. In my free time, I enjoy experimenting in the kitchen, which I try to balance out by long-distance running.

matti.javanainen@helsinki.fi
Matti´s ORCiD 
Matti on ResearchGate

Sudeep Karki, PhD

I joined the Paavilainen group in 2021 to learn new techniques in structural biology and drug discovery. My current research focuses on the structural (crystallography and Cryo-EM) and functional study of the eukaryotic Sec61 channel and its associated protein complexes that facilitate membrane integration or translocation of newly synthesized polypeptides.

I obtained my Master´s degree in microbiology from the University of Bergen, Norway, and worked with Prof. Nils-Kåre Birkeland. Afterward, I joined Dr. Tommi Kajander for my PhD work and learned about protein expression and purification, X-ray crystallography, biophysical studies of purified proteins, small-molecule screening, protein interaction studies, and cell-based binding studies in his group. My PhD study highlighted the structure of leucine-rich repeat proteins, and their complexes present in the synapse, their implication in diseases and disorders, and in identifying effector molecules with potential drug targets.  I received my PhD in January 2021. In my free time, I enjoy traveling and reading or watching movies.

sudeep.karki@helsinki.fi
Sudeep on Twitter

Sarah O´Keefe, PhD

I joined the Paavilainen group as a postdoctoral researcher in 2022. My research aims to advance our understanding of how proteins are synthesised in parasites that infect and cause disease in humans. To this end, I use biochemical, chemical and structural biology approaches to identify and characterise small molecules that inhibit the mechanisms of protein synthesis and secretion in these pathogenic parasites. Ultimately, these molecules are useful tools for discovery biology and will provide new chemical and structural leads for the future development of drugs for the treatment of parasitic diseases, such as leishmaniasis and malaria. 

I first trained as a Medicinal Chemist during my degree (MChem, University of Manchester, UK) and, after working in the drug discovery department at Evotec (Abingdon, UK), I returned to the University of Manchester between 2015-2022 for my PhD and a postdoctoral position in Stephen High’s lab. During this time, I gained expertise in the use of in vitro and cellular systems to characterise and exploit the inhibitory properties of small molecules to study protein biogenesis in mammalian cells; methodologies that I am now applying to parasitic discovery. Outside of science, I like spending time with friends and family and exploring new places. 

sarah.okeefe@helsinki.fi
Sarah on Twitter
Sarah´s ORCiD
Sarah on ResearchGate

Juho Kellosalo, PhD

My current research interest is studying the role of translocation co-factors in the biogenesis of ER-targeted proteins and on finding ways to commercialize findings of the Paavilainen group related to secretory protein biogenesis. In my PhD work at the University of the Helsinki, I worked on structural and functional characterization of membrane-bound pyrophosphatases. At work, I get inspired by dialectical discussions and creativity requiring efforts. Outside of work I enjoy playing music and contemplating the philosophy of science.

juho.kellosalo@helsinki.fi

Rahul Nanekar, PhD

I joined the Paavilainen group in 2020 and carry out research to improve protein production in mammalian cells. Industry collaborations as well as possibilities to learn novel methods to investigate protein translocation pathways motivate my current research work. I was introduced to protein biochemistry during my MSc thesis at the University of Oulu, where I studied myelin sheath proteins with Prof. Petri Kursula. Later, as part of my PhD studies, I worked on class A G protein-coupled receptors with Dr. Veli-Pekka Jaakola. In my postdoc with Prof. Janne Ihalainen at the University of Jyväskylä, I studied red-light sensing bacterial phytochromes. When not in the lab, I like to go longboarding and hiking.

rahul.nanekar@helsinki.fi

Anja Paatero, PhD

I am interested in uncovering the cellular targets and mechanisms of action of bioactive small molecules that modulate the co-translational membrane translocation of proteins. I use both biochemical and cell biological methods, and I also apply and develop chemical biology methods including photo cross-linking and click chemistry approaches.

For my PhD in the lab of Prof. Dennis Bamford, University of Helsinki, I studied a bacteriophage genome packaging ATPase. After that, I worked with Prof. Peter Prevelige, in Birmingham, Alabama, where I used phage display to identify peptides that inhibit viral assembly. Since returning to Finland, I have also worked on transposons as gene transfer vehicles and neuronal leucine-rich repeat proteins before joining the Paavilainen lab in 2014. In my free time, I enjoy gardening and dancing salsa.

anja.paatero@helsinki.fi

Katja Rosti, PhD

I work as a postdoctoral researcher and as a business development team member in the Paavilainen lab. My interest is to understand better the underlying cellular mechanisms to enhance the production and characterization of demanding target proteins, such as the expression of therapeutic antibodies, or other suitable candidates for future diagnostic purposes. I find my work inspiring, as it enables me to bind together the traditional Academic research with modern commercial flavor. My strengths include time management and multitasking.

I received my PhD from the University of Helsinki, studying the expression and characterization of neuronal membrane receptor proteins. After my doctoral defense, I worked in a commercial role in an international company for several years, covering the Nordic, Baltic and CIS countries.  In my free time, I study for an EMBA degree in strategic leadership and knowledge management. 

katja.rosti@helsinki.fi
Katja on LinkedIn

Dale Tranter, PhD

Examining protein complexes within the context of the native cellular milieu is essential to the study of their natural interactions. In order to probe the complex pathways of protein biogenesis, we capitalize on recent advances in genome editing to install purification handles to genes of interest using CRISPR-Cas mechanisms in order to preserve the cellular interactome. My current aim is to look beyond the translocon and capture the signal peptidase complex while engaged in processing a native signal peptide.

My background in generating stably expressing cell lines was developed during my PhD studies at the University of Essex in Colchester, where I was interested in investigating the roles of interhelical interaction sites in the thermostability of the G-protein coupled receptor, rhodopsin. 

dale.tranter@helsinki.fi
Dale´s ORCiD
 

Vanessa Bensch, PhD Student

I studied Biological Sciences at the University of Cologne in Germany with a specialization in genetics.  After working in multiple research groups in the field of aging and age-related diseases, I grew an increased interest in proteomics. My current interest lies in ER-mediated protein homeostasis using small molecular modulators. Additionally, I study protein translocation into the ER lumen by depleting essential components of the protein translocation pathway. Outside the lab, I like to keep myself busy by playing ultimate frisbee and exploring new places.

vanessa.bensch@helsinki.fi
Vanessa on Twitter

Alexandru Dumitrescu, PhD Student

I am a first-year student in a collaborative PhD between Helsinki Institute of Life Science and Computational Systems Biology, Aalto. My focus is on various computational methods, primarily using machine learning, that can help us better understand various aspects of proteins. I am currently working on determining epitope specificities of T-cell receptors and predicting the presence of signal peptides in mature cells.

I finished my Bachelor's degree in Computer System Engineering in 2018 at the Polytechnic University of Bucharest. During my last year of studies there, I have become highly interested in the Data Science field. I decided to pursue these interests and joined the Master of Science program at Aalto with a major in "Machine learning, Data Science, and Artificial Intelligence" finishing my degree in April 2021. During my first year at Aalto, I worked for a startup company that develops Machine Learning solutions for a patent search engine. Having a good background in Machine Learning techniques for natural language, both through academic and industry work experience, I joined the Computational Systems Biology group in Aalto. The idea of joining a research group that deals with computational biology sparked a great deal of enthusiasm for me, realizing that I can apply a wide variety of the techniques I learned to solve very complex biological processes.  In my spare time, climbing and hiking are my favorite activities.

alexandru.dumitrescu@aalto.fi

Tamara Somborac, PhD Student

I work as a PhD student with Dr. Cory Dunn, co-supervised by Dr. Ville Paavilainen, with the focus on targeting tail-anchored proteins to subcellular compartments. I hold a Master's degree in Pharmacy from the University of Novi Sad, Serbia. The topic of my Master's research was the incidence and prevalence of nosocomial infections caused by antibiotics. I obtained my second MSc in Drug Discovery and Development from the University of Turku Finland. I investigated molecular interactions of prenylflavonoids at GABA-A receptor subunits by application of computational modeling methods. In my free time, I enjoy long walks, spending time with friends and colleagues and reading. Now, my favorite hobby is trying to learn and improve my Finnish language.

tamara.somborac@helsinki.fi

 

Paula Collin, Laboratory technician

I joined the Paavilainen laboratory in spring of 2021 and carry out cell culture work and various RNA, DNA, and protein analyses. I have worked in different research groups at the Institute of Biotechnology since 1997: Digital microscopy scanner service, DNA Sequencing and Genomics Laboratory and Saarma Research Group. I have also worked at private companies as a laboratory coordinator. My educational background is as a laboratory technician in chemistry. I have studied chemistry at the University of Helsinki and cell and molecular chemistry at the Metropolia University of Applied Sciences. Outside of work, I enjoy sporty activities like agility with my Australian shepherds, hiking and knitting. 

paula.collin@helsinki.fi

Zane Dekere, MSc, Research assistant

In the Paavilainen group, I contribute to the protein production efforts through the use of my skills in growing and modifying microorganisms. I have my Master's degree in Hydrobiology from the University of Latvia and have been working for eight years in the Institute of Biology, University of Latvia. After arriving in Finland, I graduated as a laboratory technician from the StadinAO, Helsinki Vocational College and Adult Institute. I learned a lot about cloning, protein expression and many laboratory methods while working in the Laboratory of Microbiology and Biotechnology, University of Helsinki. In my free time, I have become a passionate folk dancer and a gardener.

zane.dekere@helsinki.fi

Julia Lindholm, BSc, Research assistant

I am a bachelor’s degree student in biology and currently, I am studying in the genetics and molecular biosciences master’s program at the University of Helsinki. On the side of my studies, I work part-time in the Paavilainen lab as a research assistant. Here I have gained a lot of work experience, especially with cloning. My interest lies in the field of human and cancer genetics. In my spare time, I like to stay active and play golf and other hobbies that bring me closer to nature.

julia.lindholm@helsinki.fi

 

 

Mila Hyytinen, PhD, Project Coordinator

I work as a project coordinator in the Paavilainen Group and some other research groups working with financial, HR, and general matters. I have research experience in clinical nutrition, diabetes, celiac disease, and food hypersensitivities. I have studied clinical nutrition at the University of Eastern Finland and done my PhD at the University Hospital of Oulu in 1999-2005 and worked as a clinical nutritionist during research. I also have work experience in product and service development in companies. I have worked in the University of Helsinki since 2008 coordinating studies at Pediatric Diabetes Research Group, Finnish Centre of Excellence of Sustainable Space, Inverse Modelling and System Biology of Drug Resistance in Cancer Groups. Outside work, I love yoga and seaside walking.

mila.hyytinen@helsinki.fi
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Alumni

Shahid Rehan, PhD, OMass Therapeutics