FIMM Dissertations

Here we list all the FIMM Doctoral Researchers who have already defended their thesis.
FIMM Dissertations 2023
Karina Barreiro

Urinary extracellular vesicles in diabetic kidney disease : Assessment of pre-analytical variables and identification of novel candidate markers

2 June 2023

M.Sc. Karina Barreiro's thesis focused on describing best practices for transcriptomic studies of extracellular vesicles found in urine (uEV) and to discovering transcriptomic biomarkers in uEV for early detection of diabetic kidney disease and stratification of individuals with risk of diabetic kidney disease progression.

The results showed that the uEV transcriptome is indeed a source of promising non-invasive kidney disease biomarkers with potential prognostic value. However, rigorous assessment of pre-analytical variables and guidelines on best practices are a must not only for generating reliable and replicable results but also to understand the limitations when comparing uEV studies.

The thesis was supervised by Professor Harry Holthöfer and Dr. Maija Puhka.

FIMM Dissertations 2022
Sanni Ruotsalainen

Novel genetic risk factors in coronary artery disease and related biomarkers

7 October 2022

M.Sc. Sanni Ruotsalainen's thesis focused on improving understanding of the genetic background of coronary artery disease (CAD) and its risk factors as well as improving the risk estimation for CAD 1) by developing statistical methods and tools used in multivariate genetic analysis of biomarkers, 2) by expanding the traditionally used biomarker set for coronary artery disease, 3) by studying an isolated population to identify high-impact variants either very rare or absent in other populations and 4) by identifying individuals in high- risk for CAD using both traditional and genetic risk factors.

The thesis was supervised by Prof. Samuli Ripatti and Dr. Ida Surakka.

Elmo Saarentaus

Using large-scale cohorts to identify genetic backgrounds of complex traits

14 February 2022

LL Elmo Saarentaus's thesis focused on investigating and comparing the contribution of rare and common genetic variance to complex traits. The studies of this thesis highlight distinct features of both rare and common variation and challenge the single gene hypothesis for complex traits.


The thesis was supervised by Aarno Palotie, Olli Pietiläinen and Mitja Kurki.

Jie Bao

Histopathology-selective spatial oncogenic phenotypes in non-small cell lung cancer

February 7, 2022

Image-based tissue phenotyping has been commonly used for histological classification. It also allows the direct visualization of the distribution and expression of functional molecules. In this thesis, Jie Bao developed a spatial image analysis tool package (Spa-RQ) and applied these tools to discover spatial phenotypic features in non-small cell lung cancer histotypes, contributing to understanding the heterogeneous nature of tumorigenesis, cancer progression, and drug sensitivities.

The thesis was supervised by Dr. Emmy Verschuren and Dr. Peter Horvath.

FIMM dissertations 2021

Precision Medicine for Lung Cancer: Models, Functional Assays and Mechanisms

November 29, 2021

Functional profiling of tumor cells collected from cancer patients has the potential to tailor individualized cancer treatments. In this thesis, the translational potential of this strategy for non-small cell lung cancer was examined. Drug sensitivity and resistance testing were conducted using tumor-derived fresh uncultured or cultured cells from mouse models and clinical samples. The results demonstrate the clinical feasibility and utility of tumor-derived fresh uncultured or cultured cells for pharmacological research and for identifying individualized cancer treatments.

The thesis was supervised by Dr. Emmy Verschuren and Professor Krister Wennerberg.

As­so­ci­ations with child­hood ag­gress­ive be­ha­vior us­ing mul­tiple raters : co-oc­cur­rence, an­ti­so­cial per­son­al­ity dis­order pre­dic­tion, and bio­mark­ers

Oc­to­ber 15, 2021

In her thesis, Alice Whipp aimed to improve our understanding of aggressive behavior in childhood and adolescence by looking at the following aspects: co-occurring behaviors/problems, differences between raters, aggression subtypes, adolescent aggression as a predictor of a young adult personality disorder, and biomarkers of aggression.

The findings help to clarify the co-occurrence of aggressive behavior with other behaviors across raters and countries, to show how common the co-occurrence is and that it should be taken into consideration when studying aggressive behavior, including from (epi)genetic or biological perspectives. Her thesis provides refinements to the aggressive behavior phenotype, new avenues for aggression biology investigations, and ideas for where to improve or personalize treatment options.

The thesis was supervised by Docent Tellervo Korhonen and Academy Research Fellow Eero Vuoksimaa.

Tar­get­ing STAT3 and kinases in lymph­oid ma­lig­nan­cies

May 27, 2021

Elina Parri’s thesis focused on a molecule called STAT3. In cancers, activation of the STAT3 is associated with enhanced cellular transformation, increased metastasis and drug resistance. Direct therapeutic targeting of STAT3 has proven to be challenging and only a few direct STAT3 inhibitors have entered early phase clinical trials. The thesis used high-throughput screening applications for identifying novel strategies for indirect STAT3 targeting. The results suggest novel drug combinations for targeting malignant NK-cells.

The thesis was supervised by Professor Krister Wennerberg.

Func­tional mo­lecu­lar pre­ci­sion medicine for acute my­el­oid leuk­emia

Feb­ru­ary 5, 2021

In Disha Malani's thesis, a real-time precision systems medicine strategy was applied to identify targeted therapeutic options and biomarker associations in 252 samples from 186 acute myeloid leukemia patients. The integration of molecular profiling and drug sensitivity and resistance testing data revealed drug efficacies and underlying mutations and gene expression biomarkers for a subset of patient samples.

The results suggest that functional precision medicine could have clinical utility, although it needs supportive evidence from formal prospective clinical trials. The thesis highlighted novel avenues to define therapeutic opportunities for specific molecular subgroups of adult acute myeloid leukemia. 

The thesis was supervised by Professor Olli Kallioniemi.

Fine-scale ge­netic struc­ture and poly­genic scores in Fin­land

Janu­ary 29, 2021

Sini Kerminen's doctoral thesis examined the fine-scale genetic structure and its role in the geographic distribution of polygenic scores in Finland.

The first part of the thesis expanded the understanding of the genetic structure of Finland by determining the geographic border for the major genetic split between East and West Finland, and by identifying 17 previously unreported genetic fine-scale populations. The second part of the thesis utilized the earlier results by building, based on the fine-scale genetic structure, reference groups to estimate the genetic ancestry profile of an individual within Finland. he third part of the thesis assessed the role of the genetic split between East and West in the geographic distribution of the genetic risk of five complex diseases (coronary artery disease, rheumatoid arthritis, schizophrenia, ulcerative colitis, and Crohn’s disease) and three quantitative traits (height, body mass index, and waist-hip ratio) using polygenic scores.

The thesis was supervised by Dr. Matti Pirinen and Professor Samuli Ripatti.

FIMM dissertations 2020

The DISC1 gene net­work in ma­jor men­tal ill­nesses in Fin­land

17 Decem­ber, 2020

Vishal Sinha's thesis focused on studying the impact of the DISC1 gene network on the aetiology of schizophrenia and other major mental illnesses in Finland.

In his thesis, Vishal performed comprehensive studies of 8 Finnish cohorts and identified functional variants within the PDE4DNDE1, and the DISC1 gene increasing susceptibility to schizophrenia.

The thesis was supervised by Dr. William Hennah.

Poly­genic con­tri­bu­tions to dys­lip­idemias and re­lated car­di­ometa­bolic dis­eases

Septem­ber 17, 2020

Pietari Ripatti's thesis focused on answering fundamental questions about the genetic architecture of common cardiometabolic diseases, and about the impact of genomic risk measurements on disease incidence prediction.

In his thesis, Pietari first showed that the most common familial dyslipidemia traditionally considered monogenic, FHC, is mainly polygenic. Second, he found that polygenic hyperlipidemias considerably increase lipid levels as well as CAD risk. Finally, polygenic risk scores were demonstrated to predict future disease onset better than current clinical risk scores alone.

The thesis was supervised by Professor Samuli Ripatti.

Point-of-care diagnostics with digital mi­cro­scopy and ar­ti­fi­cial in­tel­li­gence

Septem­ber 4, 2020


In his doctoral thesis, Oscar Holmström described, developed, implemented and evaluated novel diagnostic solutions to digitize microscopy samples at the point of care for analysis either visually or with automatized digital algorithms. This topic has enormous global health implications, since the lack of access to diagnostics is an enormous problem which causes underdiagnosis of various common and treatable diseases.

Oscar's thesis was supervised by FIMM Research Director Johan Lundin and Dr. Nina Linder.

In search of peri­natal cor­rel­ates of left-handed­ness

Au­gust 21, 2020


The known bias in human hand usage is fascinating, but the origins of handedness remain largely unknown, with about 10% of people being left-handed. Studies however point to early development in handedness formation. The main aim of  Kauko Heikkilä's thesis work was to study whether perinatal covariates have an association with left-handedness.

The thesis was supervised by late Professor Emeritus Matti IivanainenEero Vuoksimaa, Jari Haukka and Aulikki Saari-Kemppainen.

Computational frame­works to aid phar­ma­co­lo­gical stud­ies: Tools, Data­bases and Pre­dic­tion mod­els

28th Feb­ru­ary 2020 


The accumulation of large-scale drug molecule profiling datasets has paved the way to a new field of science, called chemoinformatics. Developed in silico models can serve as an efficient and cost-effective augmentation to the experimental laboratory screening approaches. The main aim of Balaguru Ravikumar's thesis was to develop novel computational methods, databases and tools for interpreting drug screening data.

The thesis work was supervised by Professor Tero Aittokallio.

Epigenetic Pro­fil­ing of Obesity and Smoking

March 27th, 2020


Sailalitha Bollepalli's thesis work focused on elucidating the role of epigenetic and transcriptomic markers in obesity and smoking. Her main aim was to identify weight-loss and smoking-associated signals by integrating these different types of genome-wide omics datasets by various statistical approaches and bioinformatics tools.

The thesis was supervised by  Dr. Miina Ollikainen and Professor Jaakko Kaprio