Research

The mission of our institute is to advance new fundamental understanding of the molecular, cellular and etiological basis of human diseases. We integrate molecular medicine research, Technology Centre and Biobank Infrastructure “under one roof” and thereby promote translational research and adoption of personalised medicine in health care. As part of the Nordic EMBL Partnership for Molecular Medicine, we follow the EMBL operational model and principles. This means aiming at scientific excellence and establishing mechanisms for independent, regular scientific evaluation of the research activities; scientific integrity and good scientific practice, as well as commitment to significant levels of staff turnover.

The research at FIMM focuses on two main areas:

The disease areas of interest for our research groups cover cancer, cardiovascular disease, diabetes, immunological diseases, neurology, neuropsychiatric diseases and viral infections. In 2015, there were altogether eighteen research groups at FIMM. Of these, seven were led by FIMM-EMBL Group Leaders, two by FiDiPro Professors Juni Palmgren and Leif Groop and one by a FiDiPro Fellow, Peter Horvath. FIMM has been very successful in applying FiDiPro - the Finland Distinguished Professor Programme – funding, led and financed by the Academy of Finland and Tekes, which enables distinguished researchers to work and team up with Finnish academic researchers. Professor Jonathan Knowles who held a FiDiPro Professorship in Personalised Medicine at FIMM for a five-year period 2010-2014 now continues as a part-time Research Director. 


Tissue microarray (TMA) of prostate cancer patients with different epithelial and stromal stains.

Analysing and modelling large-scale genetic, drug testing and other molecular profiling data is an essential part of all of FIMM’s research activities. During 2015, the FIMM group leader community was further strengthened by two new bioinformatics experts. Through a joint international group leader call together with the other nodes of the Nordic EMBL Partnership for Molecular Medicine we recruited EMBL Research Scientist, Dr. Simon Anders as our newest FIMM-EMBL Group Leader. He started his research activities at FIMM in September 2015 and is already involved in many of our central research projects, such as developing new bioinformatics methods for single cell analysis. Read more. Dr. Matti Pirinen obtained the status of a FIMM group leader by receiving a highly-competitive Academy of Finland funded 5-year Academy Research Fellow post starting from September 2015. His research focuses on multivariate statistical methods in genetics.

Dr. Simon Anders started as the newest FIMM-EMBL Group Leader in September, 2015.           

Furthermore, FIMM had the privilege of continuing our collaboration with Dr. Mark Daly, Associate Professor at the Massachusetts General Hospital/Harvard Medical School and an Associate Member of the Broad Institute of Harvard and MIT, by offering Visiting Professorship to him. Mark Daly is a global leader and one of the world’s most often cited scientists in human genetics. As in 2014, Dr. Daly spent one summer month of 2015 at FIMM and will be visiting our institute also in 2016.

Also in 2015, Tero Aittokallio was promoted as a Professor of Applied Mathematics and Statistics at the University of Turku. He is now the second FIMM-EMBL group leader having been promoted to a full professorship.

Wind of Change

In March 2015, FIMM staff members and the whole Finnish research community were shaken by the news of our founding Director Professor Olli Kallioniemi being appointed as Director of the Science for Life Laboratory in Sweden. He stepped down as the Director of FIMM in autumn 2015 but continues as a part-time Research Director at FIMM. All his ongoing research activities continue and remain at FIMM. Read more. Furthermore, his new position has opened new possibilities for close collaboration between the two organisations and several collaborative projects have already been established.

After a few months of uncertainty and intense recruitment work, FIMM staff was relieved to hear that Academy Professor Jaakko Kaprio will be appointed as the new interim Director. He started in this position in October 2015. He is an internationally recognized and distinguished researcher who has served as a Professor of Genetic Epidemiology in the Department of Public Health, University of Helsinki and as a Research Professor at the National Institute for Health and Welfare. Kaprio’s own research area is genetic epidemiology and he has had a key role in collecting several Finnish twin cohorts. His central interests are in the study of substance use and addictions, nicotine dependence in particular. In the beginning of 2016, Kaprio’s own research group also joined FIMM. Read more.

In October, FIMM encountered more administrative changes when our Administrative Manager Reetta Niemelä announced her new position at CIMO. Reetta Niemelä has had a major role in the set-up and development of the institute, being actually the first person employed at FIMM, and the hole that her absence created in still evident at FIMM.

Successful utilization of diverse and innovative funding sources

FIMM has always been effective in receiving competitive, external funding and more than half of our total funding arises from these sources each year. In 2015, our researchers succeeded exceptionally well in establishing industrial collaboration projects and in receiving international funding. Professors Jaakko Kaprio, Samuli Ripatti, Aarno Palotie and FIMM-EMBL Group Leader Krister Wennerberg received significant international research funding from the National Institutes of Health (NIH) and Aarno Palotie from The Stanley Center for Psychiatric Research at Broad Institute. Collaborations between pharmaceutical industry and our Grand Challenge Programmes, especially “Finnish Genomes Empowering Personalised and Predictive Health” and “Individualised Systems Medicine in Cancer”, produce several millions of euros worth of industrial funding for FIMM over the next few years. Research Director Johan Lundin received Tekes funding from the funding instrument “New knowledge and business from research ideas”.

In addition, FIMM researchers received funding from more traditional funding sources such as Finnish foundations, the Academy of Finland and EU. Positive Academy of Finland funding decisions were received in Academy Project, pHealth Research Programme, Academy Research Fellow, Scientific Risk-taking and Infrastructure calls. FIMM-EMBL Group Leaders Tero Aittokallio and Krister Wennerberg and Professor Olli Kallioniemi are members of the MedBioinformatics H2020 project that was launched in May and three other FIMM affiliated H2020 projects started in the beginning of 2016. Furthermore, University of Helsinki awarded 3-year research grants to FIMM-EMBL Group Leader Denis Kainov and Dr. Matti Pirinen.

Scientific excellence in all levels of our operations

The Scientific Advisory Board (SAB) of FIMM visited the institute in May 2015. During their visit, the SAB heard presentations about FIMM, FIMM infrastructure facilities and the Helsinki Life Science Center initiative. Several FIMM Group Leaders introduced their work and future plans. The SAB also met with FIMM’s Senior Researchers, Post-Doctoral Researchers and PhD Students.

The SAB of FIMM. From left to right: Professors Edison Liu, Kai Simons, Nadia Rosenthal, Carl-Henrik Heldin, Cornelia van Duijn.

Based on the visit and documentation provided beforehand, the SAB prepared a highly positive evaluation report. Here are some quotes from the report:

“Most importantly, FIMM has become a brand name internationally and thus a flagship for the University of Helsinki. However, brands are fragile entities that demand protection, especially in difficult times.”

“FIMM has built up an amazingly efficient research infrastructure that provides the internal and external user community with state-of-the-art technologies.”

 “Another reflection of success is the capability of FIMM to procure external funding from national and international resources. The success is based both on the organisational skills of the Director, Olli Kallioniemi and the excellent staff and on the quality of the researchers recruited.”

The various roles of the Senior Researchers at FIMM were also introduced to the SAB for the first time. FIMM has several projects that aim to tackle grand challenges in the society, and the institute works together towards these goals. The special environment created by these grand challenges and personalised medicine program requires a new type of multi-talented researchers to carry out implementation. Senior Researchers manage and coordinate projects, work as team leaders, apply for funding and, e.g. ethical approvals for studies, handle budgets and take care of project administration, supervise and teach, create and manage academic and company collaborations and organise scientific events. At the same time, they are highly skilled experts on their own fields. In their report, the SAB stated that:

 “The SAB was immensely impressed by the quality of the Senior Scientists. A number of essential activities depend on this group of experienced scientists within FIMM. --- This feature of having flexible and knowledgeable staff scientists engaged in running institute key functions is completely unique to FIMM. We have never seen such an amazing organisational innovation anywhere else. The SAB is convinced that the Senior Scientists, as now organised, are a substantial contributor to the success of FIMM.”

In the early fall, FIMM researchers exceled in prognostic modeling of prostate cancer in an international crowdsourcing challenge. The team was headed by FIMM-EMBL Group Leader Tero Aittokallio and the clinical part by Tuomas Mirtti. They participated in the Prostate Cancer DREAM Challenge, a crowd-sourcing competition for highly demanding scientific problems by top research teams around the world. Together with their collaborators, the team developed a winning solution for predicting overall survival of patients with metastatic castrate resistant prostate. Read more.

Our publication highlights from 2015 are presented in this part of the annual report. More information about all the FIMM affiliated scientific publications is available on this page.

FIMM’s sixth Annual Scientific Retreat

In June, the whole institute gathered for two days in Korpilampi for our sixth Annual Scientific Retreat. This time, the theme of the retreat was “Keep Calm and Love Science” and the programme contained, among others, a session featuring “person” in personalised medicine using Helsinki Urological Biobank as an example, a session about personalised imaging and two FIMM breaking news sessions. On the first day, Katriina Aalto-Setälä gave an excellent keynote lecture about iPSC technology and its application. On the second day, we were inspired by a keynote lecture from Leo Price, who talked about ultra-high content phenotypic screening in cultured 3D tissues.

Katriina Aalto-Setälä from the University of Tampere presenting at FIMM’s sixth Annual Scientific Retreat.

Research