Neural cell on computer screen

Molecular level research on health

Doctoral Programme in Molecular Medicine

Molecular medicine studies the causes and mechanisms of origin of diseases on a molecular level and strives to find methods to treat and prevent these diseases.

The Doctoral Programme in Molecular Medicine (DPMM) is an interdisciplinary doctoral training program with the purpose of training researchers as international experts in modern biomedicine.

Doctoral training is organized by A.I. Virtanen Institute for Molecular Sciences and School of Medicine in the Faculty of Health Sciences in the University of Eastern Finland.

150

doctoral researchers

16

Doctoral degrees per year

Research areas in the doctoral programme

Research fields in the program range from basic laboratory sciences and diagnostics to applied clinical research. Doctoral reseachers are actively working in research groups belonging to DPMM research areas.

The research areas in DPMM are:

  • Cardiovascular diseases
  • Neurosciences
  • Type 2 diabetes and obesity
  • Stem cell research
  • Inflammatory diseases
  • Cancer
Man working in a laboratory.

Research areas and supervisors

Program in cardiovascular diseases focuses on the pathogenesis of atherosclerosis at gene and protein levels both in vitro and in vivo with special emphasis on studies of the growth factors playing a major role in the disease progress. The program also includes projects on development of novel therapies based on gene therapy and therapeutic angiogenesis.

Supervisors

  • Vittorio Fortino (research group: Biomedical Informatics). Use of large-scale biomedical data, such as genetics, genomics, transcriptomics and biological knowledge bases, and data mining algorithms to build applications for biomedical research and precision medicine (e.g. biomarker and drug target discovery).
  • Merja Heinäniemi (research group: Systems Genomics). Systems biology of cell-cell interactions in cardiovascular disease.
  • Johanna Laakkonen (research group: Vascular biology). To define causal effects and cell-cell interactions in vascular malformations and ascending aortic aneurysm. To characterize Hippo signalling pathway in vascular diseases.
  • Nihay Laham Karam. Developing regulating and targeted vectors for gene therapy. In particular, we are either using or targeting the non-coding genome to achieve this. One example is our development of lentiviral vectors using elements from super-enhancers to achieve endothelial targeted vectors to mediate angiogenesis for the treatment of ischemic diseases.
  • Anna-Liisa Levonen (research group: Redox signaling). Role of Nrf2 in cancer and cardiometabolic diseases, in order to find new targets for the prevention and treatment of these diseases. Analysis of metabolic control by Nrf2 in cancer cell metabolic reprogramming, endothelial cell biology and inflammatory processes by advanced genomics, proteomics and metabolomics techniques.
  • Minna Kaikkonen-Määttä (research group: Cardiovascular Genomics). Gene regulatory mechanisms underlying coronary artery disease and atherosclerosis; Genetics of cardiovascular and metabolic diseases; Analysis of gene regulation using advanced genomics techniques; Single cell sequencing
  • Pasi Tavi (research group: Molecular physiology). Cellular and molecular physiology of the heart muscle cells; energy metabolism.
  • Seppo Ylä-Herttuala (research group: Molecular Medicine). Pathogenesis of atherosclerosis at gene and protein level both in vitro and in vivo; development of novel therapies based on gene therapy and therapeutic angiogenesis; Virus-mediated gene delivery; Gene therapy of cardiovascular diseases

The molecular mechanisms, treatment and prevention of neurodegenerative diseases such as Alzheimer's disease, ALS, and Parkinson's disease as well as epilepsy and circulatory disorders of brain are under intensive research in this program. The research projects include projects from basic research to clinics: The risk factors, genetics and novel imaging methods of Alzheimer's disease; neuropathology of dementias; mechanisms of memory; molecular biology of the aging nervous system; the role of inflammatory factors and mitochondria in neurodegeneration; stem cell research and; the basic mechanisms and novel therapies of epilepsy.

Supervisors

  • Vittorio Fortino (research group: Biomedical Informatics). Use of large-scale biomedical data, such as genetics, genomics, transcriptomics and biological knowledge bases, and data mining algorithms to build applications for biomedical research and precision medicine (e.g. biomarker and drug target discovery).
  • Rashid Giniatullin. Molecular pain research, experimental migraine
  • Olli Gröhn (research group: Biomedical MRI). Our goal is to address fundamental neurobiological questions using modern MRI technology in combination with disease models. We use the latest existing MRI methodologies as well as develop novel (f)MRI techniques in order to understand how the brain functions and to find surrogate markers for processes associated with neurodegenerative diseases. The recent interest area has been a combination of novel fMRI techniques with brain stimulation and electrical recording in anesthetized and awake animals. Furthermore we use advanced simultaneous PET-MRI combination imaging. The search for clinically relevant, non-invasive surrogate markers for neurodegenerative processes is of ultimate importance, both for clinical patient management and for the development of specific drugs for treating these processes.
  • Annakaisa Haapasalo (research group: Molecular neurodegeneration).
    Our research focus lies in the genetic background and molecular mechanisms underpinning neurodegenerative diseases, especially frontotemporal dementia (FTD). To this end, we utilize a variety of in vitro and in vivo model systems and patient-derived cells, clinical samples and data. We are especially interested in the function and dysfunction of neuronal synapses, cell metabolism, cellular degradation mechanisms, such as autophagy and proteasomes, as well as glial cells that mediate neuroinflammation.
  • Mikko Hiltunen (research group: Molecular Genetics of Alzheimer's Disease). Molecular and functional genetics of Alzheimer's disease: Research Goals: To identify novel risk gene variants associated with AD and to elucidate their effects on processes relevant for pathogenesis of AD. Risk variant correlations with established biomarker levels in the brain, plasma, and cerebrospinal fluid samples of AD patients are applied; To characterize the functional role of AD-related risk genes, pathways, and co-morbidities in AD pathogenesis using in vitro and in vivo disease models. The focus in these models is set to the factors that affect early synaptic dysfunction, function of glial cells as well as ß-amyloid and tau pathology.
  • Katja Kanninen (research group: Neurobiology of disease). Neurobiology of disease; cellular and molecular mechanisms of Alzheimer's disease; effects of environmental exposures on brain health.
  • Sarka Lehtonen (research group: Human Brain Disease Modelling). Cellular and molecular mechanism of neurological diseases with focus on Parkinson`s disease, schizophrenia and psychopathy.
  • Tarja Malm (research group: Neuroinflammation). The Neuroinflammation research group aims to form a functional fingerpring of microglia-neuron crosstalk in health and disease. We identify novel treatment strategies to modulate neuroinflammation for disease benefit. We develop novel human -based models and investigate cellular responses using various omic approaches, electrophysiology and microscopy  techniques. In addition, we take advantage of in vivo models with long-term functional outcome measures.
  • Riikka Martikainen (research group: Stem cells and mitochondria). Molecular mechanisms underlying mitochondrial disease; mtDNA maintenance and defects; stem cell based models for human disease.
  • Asla Pitkänen (research group: Epilepsy Research). Our goal is to (a) understand the molecular and cellular mechanisms of epileptogenesis after traumatic brain injury, (b) to develop interventions to  prevent epileptogenesis or  alleviate the disease severity.
  • Juha Savinainen (research group: Endocannabinoid system as a drug target). We aim at deeper molecular level understanding on the key players orchestrating lipid signaling in health and disease, especially focusing on the endocannabinoid system. We utilize activity-based protein profiling and metabolomics in exploring serine hydrolase activity in different in vitro and in vivo models. Our current efforts focus specifically on the mechanisms of migraine and other pain conditions.
  • Alejandra Sierra Lopez (research group: Multiscale imaging). The multiscale imaging group is a multidisciplinary team interested in the application, combination and development of imaging modalities focused in brain at several scales. Our greatest interest is the study of the structure of the healthy and diseased brain from the macro- and microscale with non-invasive techniques to the nanoscale with microscopy techniques in combination with image processing, data analyses and tissue modelling.
  • Heikki Tanila (research group: Neurobiology of Memory). Neurobiological mechanisms of memory and memory disorders.
  • Jussi Tohka research group: Biomedical Image Analysis). Biomedical image analysis; Machine learning; Neuroinformatics

Program focuses on the genetic background and interaction of genetic and dietary factors in etiology of type 2 diabetes, metabolic syndrome and obesity. The influence of nutrition factors on the gene expression in adipose tissue and white blood cells is studied in order to find out the regulation of type 2 diabetes, obesity and cholesterol metabolism.

Supervisors

Stem cell research program includes projects studying the differentiation of human embryonic stem cells to brain cells and cardiac muscle cells, differentiation of mouse embryonic brain stem cells to neurons, and the differentiation and transfer of both human and mouse hematopoietic stem cells in disease models of neurodegenerative and cardiovascular diseases. Modification of stem cells with gene transfers, use of stem cells as tools of gene therapy, studies on combining gene and cell therapy with conventional pharmacotherapy, and imaging of the stem cells are among the most important parts of the program.

Supervisors

  • Sarka Lehtonen (research group: Human Brain Disease Modelling). Stem cell based models for neurological diseases and drug discoveries (2D, 3D and organoids), Blood-brain barrier on chip .
  • Riikka Martikainen (research group: Stem cells and mitochondria). Stem cell based models for human disease.
  • Pasi Tavi (research group: Molecular physiology). Stem cell based cell and tissue models; Bioengineering.
  • Seppo Ylä-Herttuala (research group: Molecular Medicine). Pathogenesis of atherosclerosis; Development of novel therapies based on gene therapy and therapeutic angiogenesis using stem cells

Acute pancreatitis: Deficiency of polyamines due to increased polyamine catabolism is related to the pathogenesis of severe acute pancreatitis in transgenic mice and rats. The program focuses on clarifying the molecular mechanisms of the early phases of pancreatitis, and also on the use of polyamine analogues in regeneration of lethal lesions of the pancreas and some other organs.

Regulation of the immune system: Special interests include the CD40-mediated influences on the cells of the immune system, and CD40-regulated inflammation reaction mediated by endothelial cells.

Nuclear receptors and transcriptional control of gene expression: The main focus is on steroid hormone regulated gene activity in cancer and inflammatory cells.

Supervisors

  • Carsten Carlberg (research group: Epigenomics of vitamin D). Epigenomics of vitamin D: transcriptomic (RNA-seq) and epigenomic (ATAC-seq and ChPmentation) studies in human monocytic leukemia cells (THP-1) and PBMCs isolated from healthy human donors as well from vitamin D intervention studies
  • Tuure Kinnunen (research group: Immunology of type 1 diabetes). Immunology of type 1 diabetes.
  • Sarka Lehtonen (research group: Human Brain Disease Modelling). Pathological crosstalk between microglia and astrocytes in Parkinson`s disease
  • Einari Niskanen (research group: Regulatory mechanisms of steroid receptors). We aim to understand mechanisms of transcription regulation and transcription factor crosstalk. Our main model systems are glucocorticoid receptor, which we study in context of inflammatory signaling, and androgen receptor, which we study in context of prostate cancer. We use genome-wide techniques (ChIP-seq, RNA-seq, GRO-seq, PRO-seq), latest proteomics tools (ChIP-SICAP, BioID) and various bioinformatics approaches to understand mechanisms of transcription regulation in mammalian cells.
  • Ville Paakinaho (research group: Pioneer factor and steroid receptor biology in disease). Principals of glucocorticoid receptor biology; genomics (ChIP-seq, ATAC-seq), transcriptomics (RNA-seq), oligomerization

Translational cancer research program includes projects on molecular mechanisms, genomics and quantitative imaging features of cancer. A special emphasis is on understanding development of cancer as well as formation of cancer drug resistance. The program also includes projects to develop novel cancer drugs and diagnostic tools. Close collaboration between University of Eastern Finland and Kuopio University Hospital catchment area joins forces of clinical and basic researchers to fight cancer, bringing clinical understanding of the diagnostics and treatment, with the goal to bring personalized medicine to the clinic.

Supervisors

  • Vittorio Fortino (research group: Biomedical Informatics). Use of large-scale biomedical data, such as genetics, genomics, transcriptomics and biological knowledge bases, and data mining algorithms to build applications for biomedical research and precision medicine (e.g. biomarker and drug target discovery).
  • Merja Heinäniemi (research group: Systems Genomics). Our goal is to elucidate disease mechanisms that are related to aberrant regulation of cell states. We develop computational models based on systems biology and data analysis tools with bioinformatics and machine learning methods suitable for integrating different types of genomics data or combining datasets across studies. We apply them in our own research that utilizes large omics datasets and collect new genomics data from cell models and human studies to unravel the complexity of hematological and lymphoid malignancies.
  • Tiina Jääskeläinen. Steroid receptor-coregulator hubs regulating chromatin protein and gene networks in treatment resistant cancer cells: Mechanisms of resistance to hormonal therapies in prostate cancer and leukemia cell models using integrated genome- and proteome-wide approaches.
  • Kirsi Ketola (research group: Cancer Cell Plasticity). Cancer cell plasticity, treatment resistance and neuroendocrine differentiation in prostate cancer.
  • Leena Latonen (research group: Cancer stress biology). Molecular and tissue biology of prostate cancer; role of cellular stress response pathways in cancer drug resistance
  • Anna-Liisa Levonen (research group: Redox signaling). Role of Nrf2 in cancer and cardiometabolic diseases, in order to find new targets for the prevention and treatment of these diseases. Analysis of metabolic control by Nrf2 in cancer cell metabolic reprogramming, endothelial cell biology and inflammatory processes by advanced genomics, proteomics and metabolomics techniques.
  • Einari Niskanen (research group: Regulatory mechanisms of steroid receptors). We aim to understand mechanisms of transcription regulation and transcription factor crosstalk. Our main model systems are glucocorticoid receptor, which we study in context of inflammatory signaling, and androgen receptor, which we study in context of prostate cancer. We use genome-wide techniques (ChIP-seq, RNA-seq, GRO-seq, PRO-seq), latest proteomics tools (ChIP-SICAP, BioID) and various bioinformatics approaches to understand mechanisms of transcription regulation in mammalian cells.
  • Ville Paakinaho (research group: Pioneer factor and steroid receptor biology in disease). Steroid receptor and pioneer factor signaling in cancer cells; genomics (ChIP-seq, ATAC-seq), transcriptomics (RNA-seq, GRO-seq), single-cell genomics, single-molecule imaging.
  • Jorma Palvimo (research group: Steroid Receptors and SUMO Modifications in the Regulation of Gene Networks and Cellular Plasticity). Steroid receptor-coregulator hubs regulating chromatin protein and gene networks in treatment resistant cancer cells: Mechanisms of resistance to hormonal therapies in prostate cancer and leukemia cell models using integrated genome- and proteome-wide approaches.
  • Sanna Pasonen-Seppänen (research group: Tumor-stroma interaction). The molecular mechanisms of tumor-stroma interaction in melanoma. We are studying the interaction of tumor and immune cells and the molecular mechanisms of pro-tumor inflammation, and how extracellular matrix molecule hyaluronan is involved in these.
  • Kirsi Rilla (research group: Rilla group). Extracellular vesicles as systemic messengers

How to apply?

A doctoral study right is granted as a result of an application in which the applicant suggests supervisors and makes a research and funding plan. 

Following post graduate degrees can be taken in the Doctoral programme in Molecular Science:

  • Doctor of Philosophy
  • Doctor of Philosophy (Pharmacy)
  • Doctor of Health Sciences
  • Doctor of Medical Science
  • Doctor of Odontology
  • Licentiate of Philosophy
  • Licentiate of Philosophy (Pharmacy)
  • Licentiate Health Sciences

According to the Universities Act of Finland (558/2009, Chapter 5, Section 37), eligible for studies leading to a doctoral degree shall be:

  • a person who has completed an applicable higher university or polytechnic degree,
  • a person who has completed an applicable education abroad which in the awarding country gives eligibility for corresponding higher education,
  • a person whom the university judges otherwise to have sufficient knowledge and skills for the studies.

Eligible applicants to the Doctoral Programme in Molecular Medicine have a Master's degree in sciences, medicine, dental sciences, pharmacy, health care or other relevant field. Persons who university otherwise finds to possess adequate knowledge and skills for PhD studies, can also be given the post graduate study right.

Applicants should have the necessary background knowledge (scientific basic knowledge obtained during the completion of the basic qualification) and skills (scientific methods and their application learned during the completion of the basic qualification) for carrying out research projects, and they should be competent and motivated to pursue a doctoral degree.

The skills of eligible applicants to any of the doctoral programmes provided by the Faculty of Health Sciences and their commitment to a successful completion of their doctoral studies are assessed according to the following joint criteria, which constitute the admission criteria of the programme:

  • quality of the research plan,
  • innovativeness of the research topic, feasibility, clarity and implementation methods of the research plan as well as its suitability to the research profile and strategy of the department, school or unit where the research project is to be carried out,
  • scientific and practical relevance of the research topic,
  • evidence of any previous research projects carried out by the applicant, such as working as a researcher,
  • funding plan,
  • performance in Master's studies or corresponding studies, and
  • international orientation and language skills required in the studies.

In the selection process, the adequacy of supervision and the special expertise required from the supervisor are also taken into consideration. Applicants' preparedness, motivation and commitment to doctoral studies can also be estimated with interviews.

Study right to doctoral studies in Finland does not include scholarship or funding.

  1. The applicant discusses the possibility to pursue doctoral studies with the potential supervisor. Further information may also be asked from the contact person of the doctoral programme.

  2. The applicant discusses the research topic, doctoral studies and their completion, funding, as well as other supervisors with the main supervisor. The applicant and the supervisors must negotiate and agree on responsibilities and commitment to supervising the student's research project. 

  3. Each applicant must have a minimum of two supervisors. Each supervisor must have at least PhD degree. ll supervisors must have a doctoral degree and the main supervisor must hold, at the minimum, the qualification of a docent or have a corresponding scientific qualification. At least one of the supervisors must be employed by the Faculty of Health Sciences of the University of Eastern Finland.  All supervisors must give their written consent on the research plan.

  4. The applicant draws up a research plan. Please, see further instructions in ‘Research plan’

  5. The right to pursue doctoral studies is applied at Studyinfo portal. Please note: Partially filled application form cannot be saved. You have to have all the obligatory attachments ready once you start filling the application form.

Following documents must be attached to the application: 

  • Research plan, which consist of a cover page + four pages (including the list of references). The supervisors must give their written consent on the research plan in the cover page. Please, see the instructions.

  • Copy of the basic university degree certificate and a transcript of earlier academic records. In case applicant’s MSc, or equivalent, degree is not completed the applicant should submit a transcript of academic records and a personal study plan for completing the remaining studies in the previous degree as well as state the estimated time of master’s graduation in the application form.

  • CV, including the list of publications if any.

In addition, the following attachments need to be attached:

  • Certificate or proof of English language skills (foreign applicants)

  • Statement by the Main Supervisor on the applicant's ability based on their degree to complete a doctoral degree and the need to undertake any supplementary studies (Word template). N.B.! Save the form to your own computer before filling in any information.

Processing of the application

The faculty requests amendments to the study right application, if needed. The dean decides whether the right to pursue doctoral studies should be granted on the basis of a proposal made by the doctoral programme within approximately three months from submitting the application. When the right to study is granted, the faculty decides on any supplementary studies required, confirms the research topic, appoints the supervisors and approves the research plan. The faculty communicates its decision to the applicant, the supervisors, the Student and Learning Services and the doctoral programme. The applicant must confirm the study right in the Studyinfo portal within seven days from the decision being sent. Similarly, negative decisions and their justifications are communicated to the applicant, the supervisors and the doctoral programme. In addition, the applicant is provided with instructions on how to appeal the decision. 

When applying for doctoral degree studies, a research plan must be enclosed with the application. The student prepares the plan with his/her supervisors, and it must be approved by them. The research plan must cover the entire licentiate thesis or doctoral dissertation. If the research topic and materials change substantially, a new plan must be made. If the changes are significant, approval must be sought from the faculty. The research plan is usually drafted in Finnish or English.


The research plan can include the following information, for example:

  1. Title of the research and the name and contact information of the postgraduate student
  2. Background
    • a short summary of the background to the research with necessary sources (including the theoretical and methodological basis)
    • a description of earlier research related to the topic
    • a description of what remains unknown about the research topic and an explanation of the research’s relevance on a national and/or international scale
  3. Aims
    • the research hypotheses
    • the aims of the research clearly defined and presented
  4. Materials and methods
    • a description of the research methods and materials used, and the grounds for choosing the particular methods
    • a description of how the materials will be handled and used (also after the research has been completed)
    • a working plan, a plan for different stages of the work
  5.  Schedule and funding plans
    • a description and a schedule for the different stages of the work
    • the funding plan and funding sources of the research
  6. The ethical aspects of the research
    • the ethical aspects of the research (e.g. whether the research requires statements from ethics committees or statutory research permits; possible permits should be attached to the research plan)
  7. Publication plan
    • the means and mode of publishing and/or presenting the research results
  8. Applications of research results
    • an estimation of the applications and the social significance of the research results
  9. References
    • a list of the research field’s principal literature used for the research
  10. The names of the persons and units participating in the research project

When applying to the doctoral programmes in the Faculty of Health Sciences the research plan (1+4 pages) consists of a cover page, which includes signatures of all supervisors, and of a research plan which maximum length is four pages. 

Funding plan is a compulsory part of the application. The funding plan is written to the research plan and to the application form. Funding should be planned with the supervisors. Funding for own salary and for research costs should be described in the funding plan. 

Research funding can be applied from various foundations as grants or from the university as paid doctoral research positions. Funding may also be available from established research projects.

More information on different funding options in Kamu.

Application period

Application periods are from Jan 1 to May 31 and Aug 1 to Nov 30. Applying is done at Studyinfo.fi portal. Applications are processed also within the application periods. Decisions of admissions are sent within approximately three months of submitting the application.  

What is Studyinfo.fi?

Studyinfo.fi is the official national admissions portal with all the up-to-date information about study programmes leading to a degree in Finland.

Apply via Studyinfo.fi

Fill in the online application for the programme at the Studyinfo portal.

News and events

Further information on the doctoral program

The director of the doctoral programme is Prof. Jorma Palvimo from School of Medicine (Institute of Biomedicine), vice director is Prof. Katja Kanninen from A.I. Virtanen Institute for Molecular Sciences. The coordinator of the doctoral programme is Dr. Jenni Küblbeck from A.I. Virtanen Institute for Molecular Sciences.