Doctoral Education Pilot in Precision Cancer Medicine

Lauri Aaltonen - Bioinformatic and wet lab analyses of cancer

• We are the leading group in the Academy of Finland's Centre of Excellence in Tumor Genetics Research, and focus on predisposition to and genesis of neoplasia. We use versatile bioinformatic and wetlab tools to understand why cancer arises and how to stop it.

Mikko Airavaara - Novel gene & cell therapy technologies for unmet therapeutic diseases 

• We are interested in novel mechanisms of brain repair. We develop novel cell, nano and gene therapy technologies and and machine learning based disease models (virtual animals/cells) to improve drug development technologies and to develop new therapies. 

Tero Aittokallio - Precision Medicine 

• Our group has expertise in integrating multi-omics profiling and clinical information from cancer patients using mathematical and statistical approaches such as machine learning and network modeling to optimize treatment outcomes for individual patients. 

Ahmed Al-Samadi  - Social services 

• We study the resistance mechanisms to immunotherapy in head and neck (HNC).  We aim to establish a personalized treatment testing assay for immunotherapy in HNC. We investigate the possibility of using IL-17F as the first cytokine therapy for HNC patients. 

Pia Alhopuro - Tissue-specific oncogenic programmes 

• Our research explores the molecular mechanisms of cancer development. We combine experimental work in cancer models with clinical data. The long-term goal is to make discoveries that can be translated into new diagnostic tools and targeted cancer treatment. 

Kari Alitalo - Cancer stem cells and angiogenesis in tumorigenesis

• We study transcription factor and endothelial growth factor mechanisms in normal tissues vs tumor models.

Leonardo Almeida-Souza - Endocytosis, cellular adhesions 

• We study the endocytosis and how this molecular machinery affects various cellular processes. We use cell biology, biochemistry and structural biology techniques. 

Janne Backman - Clinical Pharmacology and Pharmacotherapy 

• The group studies interindividual variability in pharmacokinetics, and uses translational methods and clinical trials. Focus areas are drug interaction mechanisms, and personalized approaches and drug-drug interactions of anti-infective and anticancer agents. 

Matjaz Barboric - Gene regulation in disease 

• We study gene transcription by RNA Pol II and its deregulation in disease. Based on our recent work, we use systems biology, biochemical and functional assays to identify combinatorial approaches of targeting transcriptional cyclin-dependent kinases in cancer.

Oscar Brück - Hematology, cancer, machine learning, data analysis, image analysis, software

• World's largest blood cell image collection combined with detailed clinical data. We design algorithms to predict future leukemia, treatment response, mutations and survival using image and clinical data + perform clinical trials.

Alex Bunker - Computational modelling in drug design and delivery: Beyond the active site interaction

• Large scale molecular dynamics simulation for mechanistic insight relevant to drug design and delivery; in particular 1) the role of the membrane in substrate, thus drug, selection for weakly membrane associated proteins and 2) polymers in drug delivery.

Olli Carpen - Translational ovarian cancer research 

• We study chemoresistance in ovarian cancer and develop predictive tissue-based biomarkers. Combining digital pathology with spatial transcriptomics has revealed new biological features, such as targetable signaling pathways, associated with treatment outcome. 

Eero Castren - Growth factors in cellular growth and plasticity

• My lab investigates the regulation of neuronal growth factors by drugs. We have  identified psychedelic compounds as powerful activators of the receptor tyrosine kinase NTRK2. We are investigating NTRK2 activation on cellular growth malignancy in brain tumors.

Vincenzo Cerullo - Precision Cancer Immunotherapy and Vaccines 

• IVTLab is focused on the development of personalized (or cancer specific) cancer vaccines utilizing viruses and bacteria as delivery platforms for specific cancer antigens.

Ping Chen - Computational biology of human diseases

• My group focuses on RNA biology and its role in human diseases. We use multi-modal data from human subjects to pioneer data-driven approaches aimed at improving disease diagnostics and decoding the  molecular mechanisms underlying disease development. 

Robin Cristofari - Epigenetics of ageing in the King penguin 

• We study the epigenetic process under nutrient forcing in wild and zoo King penguins. Our goal is to understand how the growth/maintenance regulation pathways are modulated by nutrient intake in this naturally fasting bird. 

Nicolas Di-Poi - Vertebrate Evolution, Development and Regeneration

• Our multidisciplinary lab studies the developmental genetic basis responsible for development, evolution and regeneration of craniofacial tissues in emerging reptile models. Our goals include providing an evolutionary context for key developmental pathways.

Filip Ekholm - Biomolecular chemistry

• Our expertise resides in the synthesis,structural elucidation and profiling of all classes of biomolecules. We are an application-oriented group focused on solving challenges at the interface of chemistry, medicine and biology.

Johanna Englund - Extracellular matrix and early breast cancer

• We investigate how the composition and dynamics of ECM are regulated during tissue development and how they are altered especially in breast cancer initiation. For this we use organotypic models of human and mouse mammary epithelium, imaging and proteomics.

Andrew Erickson - Spatial Biology, Prostate Cancer, Clinical Translation 

• I aim to revolutionize the early detection and treatment of cancers with a focus on prostate cancer. My lab develops cutting edge spatial and single-cell wetlab biotechnologies (Erickson et al., Nature, 2022). 

Susanna Fagerholm - Integrins in immunity 

• We study the roles of integrins in immune cell trafficking, activation and anti-tumor immunity, using mouse models, cell biology, and multiomics methods. Our recent discoveries show that integrins regulate dendritic cell programming and anti-tumor responses.

Mikko Frilander - Pre-mRNA processing defects in human diseases

• We investigate the regulation of pre-mRNA processing in and its dysregulation in human diseases. Our methods include RNAseq, proteomics and RNA biology methods. Our recent discovery (EMBO J, 40: e106536) links splicing to chromosome segregation.

Anniina Färkkilä - SIngle-cell and spatial tumor microenvironment and precision oncology 

• Our goal is to understand the dynamics of the tumor microenvironment using systems oncology approaches. Our research focuses on developing prognostic and predictive biomarkers and new therapeutic approaches to improve the treatment and survival of cancer.

Carl Gahmberg - Leukocyte adhesion and cancer 

• Our group studies how cancer cells survive in the low oxygen environment present in tissues where tumors develop. We focus on the integrin adhesion proteins and their regulation, and how tumors acquire nutrients. 

Andrea Ganna - Health data science and genetic epidemiology 

• Our team aims to improve people’s health by developing and applying computational methods to decode large-scale biological and electronic health records. We leverage world-leading data resources such as FinRegistry and FinnGen. 

Adrian Goldman - Membrane protein structural biology 

• We study the structure and function of membrane protein complexes in disease and in health. Our primary techniques are x-ray crystallography and cryoEM. We have recently shown how mutations in PtchD1 and RET lead to diseases including carcinomas and ASD. 

Karita Haapasalo - Inflammation and Infections

• We study chronic inflammatory diseases such as atherosclerosis and Alzheimers disease and the role of infections in triggering inflammation in these diseases.

Heidi Haikala - Lung cancer, cancer therapies, immunotherapies 

• Our mission is to uncover underlying mechanisms of drug resistance and to improve treatment outcomes for lung cancer patients. We use innovative non-animal methods to discover novel treatment combinations that could prolong therapy responses. 

Sampsa Hautaniemi - Cancer research and bioinformatics 

• Our goal is to understand and overcome chemotherapy resistance together our cross-disciplinary research network. We use computational methods to translate patient-derived multi-modal data into testable predictions and further benefits in cancer patient care. 

Caroline Heckman - Precision medicine for high-risk hematological malignancies 

• We apply different high throughput omic methods to profile samples from patients with high-risk haematological malignancies to understand disease progression and drug resistance mechanisms, and identify new treatment options and indicators of drug response. 

Markku Heikinheimo - Tumor biology; pediatriv oncology 

• Our studies focus on developmental disorders and pediatric tumors. Our studies utilize modern molecular/cell biology techniques, cell and animal models, patient-derived-xenoxrafts and human material. Research training in an essential part of our lab. 

Akseli Hemminki - Cancer Immunotherapy

• We use gene therapy and oncolytic viruses to improve the treatment of cancers lacking currently available effective modalities, alone and in combination with other treatments, like T-cell therapies.

Jussi Hepojoki - Virus cross species transmission and pathogenesis mechanisms

• We study the molecular biology and disease associations of zoonotic (or cross species transmitting viruses) using cell culture and animal models.

Liisa Holm - bioinformatics 

• We develop bioinformatics methods for structural, evolutionary and functional classification of proteins. Techniques used include advanced statistics and AI language models. 

Annette Horstmann - Neuroscience of eating behaviour

• We study the brain's role in eating behaviour and in the development of conditions such as obesity in humans. Obesity is a risk factor for several cancers. We use cognitive neuroscience methods, including neuroimaging, to answer our research questions

Juha Huiskonen - Structural Biology of Macromolecules and Interactions

• We aim to understand the structure and function of biological macromolecules and their complexes, such as those involved in cell-cell contacts. We use different structural biology methods, including cryo-EM. The work is informing rational design of therapies.

Minna Huotilainen - Learning neuroscience

• We use neuroscientific and other quantitative methods to study learning, special education, use of music and other arts, language learning.

Ilkka Ilonen - Translational thoracic oncological research 

• We study thoracic malignancies using novel translational approaches, aiming to facilitate a better treatment response metering, ex-vivo immunotherapy drug sensitivity testing and aiming to coordinate efficient treatment to right patients. 

Harri Itkonen - Transcriptional rewiring in cancer 

• My research group utilizes tools of computational biology to understand how cancer cells rewire their transcriptome to promote rapid proliferation and evade the immune system. We aim to produce concise reports, which increases the number of publications. 

Christopher Jackson - Mitochondrial quality control and cellular homeostasis

• We employ genome-wide screening strategies and novel reporter systems to identify pathways increasing cell fitness as therapeutic avenues for mitochondrial dysfunction-associated diseases.

Mohieddin Jafari - Systems Pharmacology 

• Our group pioneers a systems pharmacology approach for cancer combinatorial therapy. Our research spans dry-lab and wet-lab experiments, addressing key aspects such as prioritizing drug combinations using target deconvolution and functional omics. 

Michael Jeltsch - Sustainable protein drugs 

• We develop biological drugs for vascular diseases and sustainable protein production systems. We identify drug targets based on our molecular vascular biology research. Our most recent success is the drug sozinibercept, which is in phase 3 clinical trials. 

Vadim Le Joncour - Neuroplasticity of brain tumors

• We study the similarities between plasticity during neurodevelopment and brain tumor progression, single cell omics, optogenetics and ligand affinity techniques. On this topic we recently published PMID 37280397 and 33986188.

Tommi Kajander - Structural and biochemical studies of protein complexes 

• We study the molecular mechanisms of neurotrophic factors and Hsp70 and IRE1 and PERK in ER homeostasis and unfolded protein response by structural biology and biochemical and biophysical methods, these targets are also implicated in several diseases.

Jukka Kallijärvi - Neonatal mitochondrial diseases

• Disease mechanism and interventions in models of neonatal mitochondial disease, particularly GRACILE syndrome, recently shown by us to be a progeria with cancer-like aspects including Warburg metabolism, mitogenic stimulation and massive c-MYC induction.

Ravi Kant - emerging infections

• We are currently seeking candidates for a project focused on “Next-generation sequencing and integrative multi-omics approaches to study the mechanism of carcinogenesis in urogenital schistosomiasis." The ideal candidate should possess a strong background in scripting, bioinformatics, and genomic sequence analysis. If you have expertise in these areas and are interested in contributing to cutting-edge research in the field of urogenital schistosomiasis, we encourage you to apply.

Peeter Karihtala - Predicting morbidity and toxicity of lung cancer patients during active treatmen 

• With a Finnish start-up-company Evexia, we are developing a mobile phone application, with capability to collect information on daily steps, quality of life and symptoms. The main goal is to improve the accuracy of physician-performed performance status. 

Pekka Katajisto - Stem Cells and Aging 

• We use ex vivo and in vivo approaches to understand tissue regeneration and development of cancer.

Liisa Kauppi - DNA damage and repair 

• We study how cells maintain integrity of their genomes in the face of internal and external damage, arising e.g. from DNA replication or chemotherapy. See Pikkusaari et al. (PMID: 36805632) for our recent discovery on this topic in ovarian cancer. 

Eliisa Kekäläinen - The human thymus, function and pathologies 

• We aim to unravel how hematopoietic stem cell transplantation damages the human thymus, develop diagnostic tools to measure thymopoiesis, and to find the pathological triggers in the thymus that lead to autoimmune diseases with single-cell and spatial methods. 

Ayman Khattab - The complement system in microbial and cancer pathogenesis

• My research focuses on understanding the intricate ways in which pathogens and cancer cells manipulate and make use of the complement system to initiate infections and promote tumorigenesis.

Heidi Kidron - Interindividual variability in drug exposure 

• We study what causes interindividual variability in drug pharmacokinetics, ie. factors that affect absorption, distribution, metabolism and elimination of drugs. We have focused on drug transporters, but are also investigating metabolising enzymes. 

Helena Kilpinen - Stem cell -derived neurons as disease models 

• My group uses human stem cells to model brain-related disorders in the dish. We use single cell technologies to phenotype individual neurons and to identify disease-associated cellular phenotypes. We apply both experimental and computational methods. 

Outi Kilpivaara - hematology, genomics, cancer 

• Our research stems from the intriguing curiosity towards mechanisms of hematopoiesis and leukemogenesis, and furthermore, how the identified mutations or genetic variation may contribute to blood formation on a molecular level. 

Riikka Kivelä - Novel treatment targets for rhabdomyosarcoma 

• We study the molecular mechanisms regulating the development and growth of rhabdomyosarcoma, an aggressive pediatric tumor, to identify and test novel treatment targets. 

Juha Klefström - Targeting MYC-dependence pathways for new cancer therapies 

• We study different possibilities to exploit synthetic lethal interactions in drug discovery and recently, we have focused on MYC-dependent metabolic vulnerabilities found in the mitochndria. 

Hannu Koistinen - Cancer biology and biomarkers 

• We study novel prostate cancer markers and protease drug targets. This involves cancer biology and protein glycosylation studies, development of novel patient-derived tissue and cell models, drug development and a wide international collaborative network. 

Erkki Koivunen - Mechanisms of tumor cell adaptation to hypoxi 

• We study the ability of tumor cells to survive in deep hypoxia, we use several novel cell culture and biomedical technologies and our most recent finding was a novel integrin accounting for cell-surface localization of hypoxia-induced hemoglobin polymer. 

Artturi Koivuniemi - Therapeutic nanodiscs

• Our group aims to engineer therapeutic HDL-mimetic nanodiscs for dyslipidemias and targeted drug delivery through the comprehensive understanding of how peptide-based nanodiscs interact with the key enzymes and transporters in lipoprotein metabolism.

Mika Kontro - Individualized therapies for acute leukemia 

• Our research group focuses on forecasting the treatment responses in acute myeloid leukemia - the most common leukemia in adults. These methods are developed in on-going prospective clinical trials to simultaneously validate their full clinical significance. 

Jukka Koskela - Complex disease genetics to clinical use 

• I study multiple complex diseases in order to identify clinically relevant disease trajectories. A diagnosis of these conditions does not determine the future of a patient - the prognosis is determined by the interplay of intervention and indicidual patient. 

Sangita Kulathinal - Survival and event history analysis 

• We specialize in study design and methods needed for life event histories under various observation schemes. Applications include evaluation of intervention programs, personalised medicine, public health and epidemiology. 

Anil Kumar - Drug development to target cancer persister cells 

• We develop machine-learning algorithm to study persister cancer cell.

Satu Kuure - organogenesis, stem cells, congenital disease modeling 

• We study normal and abnormal fetal development and organogenesis with the focus on renal progenitors. Our research aims to identify mechanisms that transform normal renal stem cells into cancerous and by this way initiate the tumorigenic growth in utero.

Pirjo Laakkonen - Effect of the tumor microenvironment on brain tumor growth and invasion

• My research focuses on molecular pathways underlying the invasive growth of malignant brain tumours. We aim to identify vulnerabilities and actionable drug targets by understanding interactions between tumour cells and the unique brain tumour microenvironment.

Timo Laaksonen - Nanoparticles and Light

• We work on controlled drug release and delivery. We are studying bio- and nanomaterials such as liposomes and cellulose nanofibers, the use light to control drug delivery systems, and tailored materials for pharmaceutical applications. 

Pekka Juhani Lappalainen - Actin-based molecular machines 

• The actin cytoskeleton is critical for cellular processes, including migration and morphogenesis. Defects in the actin cytoskeleton are also typical in many disorders, such as cancer. We study how the actin cytoskeleton is regulated in normal and cancer cells. 

Sari Lauri - Plasticity of neural networks

• We study how signaling via ionotropic glutamate receptors influences normal and pathological development and plasticity of neural networks, underlying behavior.

Sanna Lehtonen - insulin resistance, type 2 diabetes

• Insulin resistance is associated with the development of type 2 diabetes and breast cancer. We aim to identify novel drug targets and design new drug leads for treating insulin resistance, aiding the design of new treatment strategies for these diseases.

Jette Lengefeld - StemCellSize 

• We discovered that cellular enlargement contributes to the functional decline of stem cells during aging. Our aim is to reveal how size affects stem cell function using mice and patient samples and to evaluate whether this mechanism is evolutionarily conserved.

Sirpa Leppä - Lymphomas 

• Our disease model is lymphoma. We perform epidemiological, clinical and translational studies with the aim to establish a roadmap for better clinical and molecular understanding, classification, prognostication and treatment outcome of lymphomas. 

Tuomas Lilius - Translational Neuropharmacology 

• An active international and translational group focusing on the brain's glymphatic system as a new route for delivering drugs to the brain. We use modern methods to modulate and track cerebrospinal fluid flow and aim at high-quality publications.

Nina Linder - Digital diagnostics

• Our research aim is to develop and study digital diagnostic methods and artificial intelligence (AI) for medical purposes. The goal is to make new discoveries, create solutions that perform beyond human expert capability and to improve access to diagnostics.

Robert Luxenhofer - Novel materials for gene therapies

• We are a leading group at the interface of polymer chemistry and nanomedicine and develop new solutions for drug, protein and gene delivery using innovative chemistry. We explore structure property relationships with the goal to understand underlying molecular mechanism and factors that influence safety and efficacy of next generation therapeutics.

Helike Lõhelaid - Stroke 

• To discover new drug targets we study the recovery from stroke and the role of neurotrophic factors, microglia phagocytosis and unfolded protein response in this process. For research we use gene editing, cell culture and animal models. 

Inkeri Lokki - Immunogenetics in atherosclerosis and complex diseases 

• I study atherosclerosis and preeclampsia combining translational research methods including AI-assisted histological analysis, patient registries and immunogenetic predisposition to complex diseases in several patient cohorts collected from HUS. 

Anastasia Ludwig - Ectopic expression of neuronal-specificific K-Cl co-transporter KCC2 in epitheliain

• Some tumor cells of glia origin upregulate neuronal-specific K-Cl co-transporter KCC2. The project aims to address the role of this ectopic expression in glioma progression. We will use bioinformatics and a combination of in vitro and in vivo techniques.

Johan Lundin - Digital diagnostics for precision medicine 

• Our research aim is to develop and study digital diagnostic methods and artificial intelligence (AI) for medical purposes. The goal is to make new discoveries, create solutions that perform beyond human expert capability and to improve access to diagnostics. 

Panu Luukkonen - Mitochondrial metabolism in hepatocellular carcinoma, cirrhosis and liver failur 

• We study the metabolic mechanisms underlying advanced steatotic liver disease, including hepatocellular carcinoma, cirrhosis and liver failure. We utilise stable isotope tracers, metabolomics and genetics at a population, individual and cellular level. 

Tomi Mäkelä - Tumor suppression and tumor microenvironment  

• We explore mechanisms how tumors and normal tissue interact and how specific tumor mutations and normal tissue including immune system characteristics impact these interactions to identify novel therapeutic targets. We leverage the iCAN Flagship Project pan-cancer  dataset and various genetic models and use cutting-edge genomic and data science approaches. 

Veli Mäkinen - Algorithmic bioinformatics 

• We develop algorithms and data structures for the analysis of genome-scale data. We are especially interested in applying our skills in compressed data structures to the analysis of highly abundant high-throughput sequencing datasets. 

Taija Mäkinen - Lymphatic vasculature in development and disease 

• We study the regulation and role of the lymphatic vasculature in health and diseases, including cancer, using genetic mouse models and molecular biology techniques. Our recent work underscores the important role of lymphatic vessels in immune regulation. 

Antti Mäkitie - Head and Neck Cancer Research 

• We focus on predictive and prognostic markers of Head and Neck cancer. 

Nina Mars - Germline influences on disease risk and prognosis in cancer and autoimmune disea 

• The group uses large-scale biobank studies with detailed longitudinal and omics data to understand disease risk and prognosis. The focus is on cancer and autoimmune diseases, with the aim to focus on research questions that aim to address clinical challenges.

Thomas McWilliams - Autophagy and mitochondrial signaling in tissue development, disease and repair

• We unravel autophagy mechanisms in health and disease and harness these for therapeutic development. We use groundbreaking optical biosensors combined with cutting-edge microscopy, advanced molecular/cellular and multi-OMICS methods in animal & patient systems.

Tuomo Meretoja - Breast Cancer 

• We study germline and tumor genomics in relation to breast cancer treatment outcomes. We have shown that polygenic risk plays a major role in breast cancer susceptibility and are looking at it’s role in tumor genomics and treatmemt outcomes. 

Seppo Meri - Immune escape by microbes, autoimmunity 

• Diseases related to disturbances in complement regulation, role of complement in vascular disease and autoimmunity and microbial escape of innate immunity, complement resistance of tumors.

Tuomas Mirtti - Clinically Relevant Prostate Cancer

• Our main objectives are: 1. tissue biomarkers of prognosis and treatment resistance in urological cancers. 2. combine markers with registry data, imaging, tissue phenotype (histomics) and image analysis (ML/DL augmented), 3. Improve diagnostics and treatment.

Outi Monni - Cancer genomics 

• Our aim is to utilize molecular profiling data to find genetic alterations of diagnostic, therapeutic or prognostic value for rare cancers. We will also perform drug screening to find novel therapeutic options and drug-response related cellular mechanisms.

Alexander Mühleip - Structural biology of mitochondria

• We study how mitochondrial protein complexes generate and maintain a functional organelle. We use structural techniques (cryo-EM, tomography) to understand how protein architecture and lipid composition determine the organisation of the bioenergetic membrane.

Satu Mustjoki - Personalised cancer medicine and cancer immunotherapy 

• We aim to discover how cancer immune therapies can be improved in individualized manner and to understand how somatic mutations impact the function of immune cells. We utilise patient samples, cell line models, wet lab techniques and bioinformatic analysis. 

Mikko Myllymäki - Clonal hematopoiesis 

• The goal of our research group is to understand how somatic genetic alterations in hematopoietic stem cells influence human disease pathophysiology. We leverage population-level and disease-specific cohorts as well as gene editing approaches in cell lines.

Timo Myöhänen - Novel drug therapies for unmet medical needs

• Our focus is to find novel drug therapies for diseases with high unmet medical need, such as neurodegenerative diseases. We work in close collaboration with pharmaceutical chemistry, and use various methods from proteins to animal models. 

Arafath Kaja Najumudeen - INTESTINAL STEM CELL METABOLISM IN HEALTH AND CANCER 

• We study mechanisms employed by intestinal cells to secure vital nutrients and metabolic resources essential for preserving intestinal stem cell fate and function. And how these mechanisms can be exploited or disrupted in diseases such as cancer and inflammation.

Takashi Namba - The dark side of human evolution: Glioblastoma driven by human-specific genes 

• We study the mechanisms of human brain evolution and their relevance in glioblastoma growth by focusing on cell metabolism and human-specific genes. To this end, we will combine evolutionary genomics, multi-omics and patient-derived glioblastoma cells. 

Mikko Niemi - pharmacogenetics 

• We investigate roles of genetic variability in drug pharmacokinetics, efficacy and safety, as well as drug-drug interactions, interindividual variability cholesterol-lowering drug response and adverse drug reactions, and search for pharmacokinetic biomarkers. 

Taina Nieminen - Searching for predisposing gene variants for familial cancers 

• Our aim is to search predisposing gene variants for familial colorectal cancer type X (FCCX) families and non-medullary thyroid cancer families by using whole exome and whole genome (as well as long read) sequencing methods. 

Mikael Niku - Microbial modulation of fetal development

• We study how the maternal microbiota modulates the fetal development of the intestinal immune system and the central nervous system.

Päivi Ojala - Basic and translational cancer biology 

• By cell co-culture and organotypic models, animal tumor models and state-of-the-art imaging and genomic techniques we focus to make fundamental contributions to the fields of virus-host cell interactions, tumor microenvironment and cell therapies for cancer. 

Miina Ollikainen - Epigenomics on complex traits

• We study the role of genome and environment in complex traits using multi-omics datasets of a large Finnish twin cohort. Our recent finding suggests that DNA methylation serves as a valuable biomarker for environmental risk factors for breast cancer.

Saara Eliisa Ollila - Molecular gastroenterology 

• We study stromal cell heterogeneity and interactions with gastrointestinal epithelium in homeostasis, regeneration and tumorigenesis. we use in silico tools together with primary cell and organoid models and in vivo models as well as patient derived materials. 

Ville Paavilainen - Chemical biology of proteostasis 

• We study mechanisms by which our cells maintain healthy proteomes, especially protein biogenesis in the secretory pathway. Mainly using chemical and structural biology (e.g. cryo-EM) and research is often linked to drug discovery with corporate collaborations. 

Lassi Paavolainen - Bioimage profiling 

• We study and develop novel deep learning solutions, such as self-supervised representation learning and image analysis methods, for bioimage profiling. We apply these methods and models to improve knowledge on cancer cells and tumor microenvironment. 

Anne-Maria Pajari - Molecular mechanisms underlying cancer prevention by diet

• We study molecular mechanisms whereby diets/diet-derived compounds prevent colorectal cancer, using human RCTs, animal models, and cell cultures. Our most recent findings relates to the effects of fibre and berries (Kynkäänniemi 2024, Slaba 2023).

Teijo Pellinen - Digital spatial tissue profiling 

• Exploring tumor microenvironment biology, we use our unique multiplex immunofluorescence imaging tech. Key findings reveal specific cancer-associated fibroblasts' role in cancer progression, offering new insights for potential treatment strategies. 

Päivi Peltomäki - Hereditary cancer 

• We study genetic and epigenetic mechanisms causing susceptibility to hereditary colon cancer, we use omics technologies and functional investigations, and our most recent finding was the identification of DHX40 as a novel susceptibility gene. 

Perttu Permi - Structure and function of the 'dark proteome' -intrinsically disordered proteins

• Our lab is interested in molecular basis of host pathogen interactions, neurodegenerative disorders, and cancer. We use biophysical tools e.g., NMR, SAXS, ITC to address questions involving the "dark proteome" targets inaccessible to other technologies.

Vilja Pietiäinen - Functional precision medicine for pediatric solid tumors 

• We study pediatric solid tumors using functional precision medicine approach with clinical impact. Omics data is combined with drug testing of patient derived cancer cells to improve disease diagnosis and unravel patient-specific drug vulnerabilities.

Päivi Pihlajamaa - Metabolic control of cancer growth

• We study the effect of metabolic reprogramming on epigenetic landscape in cancer cells and how the altered regulatory pathways support cancer growth. We use CRISPR-Cas9 genome editing methods and epigenome and transcriptome profiling at single-cell resolution. 

Matti Pirinen - Statistics 

• We develop and apply statistical and computational methods to large-scale data sets in human genomics research. We study high-dimensional models and dimension reduction with applications in a wide variety of complex diseases. 

Esa Pitkänen - Machine Learning in Biomedicine, especially precision cancer medicine 

• We develop novel machine learning and bioinformatics methods for key problems in biology and medicine, e.g. tumor typing and subtyping with NGS data, imaging flow cytometry, digital histopathology and genetic variant analysis. 

Kimmo Porkka - Predictive modeling for precision cancer medicine 

• We implement precision cancer medicine by facilitating global tumor profiling & modeling, and large-scale cancer data networking, integration & automation. Our aim is to establish a robust, globally connected, open-source clinical decision support system (CDS).

Minna Poukkula - Epithelial morphogenesis

• We study epithelial integrity, morphogenesis and collective cell migration and how it is regulated by changes in cytoskeleton and adhesive properties of cells

Antti Rannikko - Urological cancers 

• We focus on prostate cancer from screening to diagnosis, treatment of local and advanced prostate cancer and to cancer follow-up. Methodology include clinical trials, large registry data, translational research and AI for images and large data sets. 

Janne Ravantti - Structural Bioinformatics

• My lab's main focus is on developing computational methods for multiple structural alignments. We also have strong collaboration with Lauri Aaltonen's group focusing on tumor genetics. Naturally, there are other bioinformatics related collaborations.

Risto Renkonen - Glycobiology, systems biology 

• We apply the HUS Date Lake with their EHRs. We develop algorithms to dissect patient outcomes.  Our most recent findings with over one million patients comorbidities is published here; Koskinen M, ... Renkonen R. Sci Rep. 2022 Nov 2;12(1):18492.

Samuli Ripatti - Complex Disease Genetics 

• The Ripatti group studies genetics of common complex diseases from discovery to translation to health care. We utilize Finnish research cohorts and a global network of biobank data with longitudinal health event histories to identify genetic associations and p 

Antti Ripatti - Macroeconomic research 

• We study the aggregate economic outcome of monetary and fiscal policies. In addition, we extend our focus on issues and interaction related to above policies and macroprudential policies. 

Ari Ristimäki - Molecular subtyping of colorectal cancer with impact on treatment 

• Colorectal cancer (CRC) is a heterogenous disease with different treatment response. Molecular alterations stratify CRC into subtypes, which predict response to oncologic therapy. We aim to identify novel diagnostic methods to aid treatment of CRC patients. 

Jani Saarela - Development of data analysis tools for high-throughput screening 

• We perform high-throughput screening with small molecules for academic and commercial users. We also develop data analysis tools for high-throughput screening results. Our most recent published data analysis tool is Breeze2.0 (https://breeze.fimm.fi/v2/). 

Mart Saarma - Cell survival and regeneration in disease

• We study the role of neurotrophic factors in development and disease. We develop neurotrophic factor-like drugs for neurodegeneration and metabolic disorders. We also investigate RNA methylation and its role in neuronal survival, neuroregeneration and cancer.

Juha Oskari Saarikangas - The plasticity of the proteome in health and disease 

• Our research aims to elucidate how dynamic changes in protein folding and assembly states regulate the phenotypic plasticity of cells and organisms. This information is crucial for understanding fundamental biological processes and disease. 

Mart Saarma - Neuroregeneration 

• We investigate the signaling and biological functions of GDNF family ligands and endoplasmic reticulum located CDNF/MANF neurotrophic factor families. We study the therapeutic potential of these proteins and their mimetics in various neurological diseases. 

Pipsa Saharinen - Molecular control of vascular barriers in cancer and inflammation 

• We employ cross-disciplinary methods including in vivo models, 3D protein structures and nanobodies to study vascular leakage and tumor metastasis. We recently unveiled a novel vascular function for a cancer drug target, illuminating its clinical trial failure.

Anne Salonen - Human microbiome

• We study human intestinal and female reproductive tract microbiomes in health and disease using HTP sequencing and other omics, integrated with host data e.g. in relation to immunity and cancer development, using advanced bioinformatics and -statistics.

Mari Sandell - Individual differences in sensory perception

• Our research is focused on 1) multisensory perception including senses of smell, taste, sight, touch and hearing, 2) the relationship between individual differences in sensory perception, well-being and food consumption, 3) sensory based food education

Biswajyoti Sahu - Cancer epigenomics

• We study the lineage-specificity of human cancers, how transcription factors control gene regulation through epigenetic cancer genome reprogramming. For this, we employ state-of-the-art next-generation sequencing based assays and their computational analysis.

Kalle Saksela - Basic and translational virology 

• We study cell biology of viruses, and develop new types of biologics and vaccines for preventing viral infections. We also use viruses of bacteria as tools for discovery of proteins for biomedical targeting of other diseases, such as cancer. 

Abdelhakim Salem - Bacterial Role in Head and Neck Cancer

• We study the role of the dynamic interplay between oral bacteria and cancer cells in the pathogenesis of head and neck cancers using multiple ex vivo and in vivo approaches. My group includes 4 young doctoral candidates (2 completed theses, 1 in final stage).

Tuula Salo - Oral cancer 

• We study the ethiological, pathogenesis & treatment of oral cancer (OSCC) using e.g. histological, IHC, and cell culture 3D models with humanized tumor matrices, and zebrafish models. Most recently we have set-up personalized OSCC treatment assays. 

Peter Sarin - Protein synthesis regulation 

• We study the role of tRNA modifications as modulators of translation, broadly exploring their impact on topics such as host-pathogen interaction, cancer formation, tissue differentiation and aging, and as tools for optimization of bioproduction systems. 

Mirkka Sarparanta - Radiopharmaceutical chemistry

• We develop targeted radiolabeled molecular imaging agents for positron emission tomography for cancer and neuroscience applications, as well as new theranostic nanosystems for cancer therapy.

Toni Seppälä - Precision Medicine in Abdominal Cancers 

• We study clinically relevant precision medicine approaches focusing on colorectal cancer, utilizing e.g. circulating tumor DNA and patient-derived organoids. 

Hanna Seppänen - Pancreatic cancer research - towards a chronic disease 

• We study pancreatic cancer in clinical and translational settings. We use patient-derived pancreatic cancer organoids to evaluate the best culturing conditions. We also do drug screening and look for new and targeted therapies for patients with these organoids.

Harri Sihto - Precision medicine for rare cancers 

• I seek new precision medicine targets in sarcomas by using next generation sequencing of tumor materials and drug screening in ex vivo and PDX mouse models and cancer cell lines. Recently we found novel targeted therapy for aggressive round cell liposarcoma. 

Tiina Sikanen - Microfluidics, organ-on-a-chips, drug metabolism

• We develop and validate microfluidic in vitro models, such as organ-on-a-chips and immobilized enzyme reactors, for drug safety and efficacy testing as well as for diagnostic purposes, with focus on human liver metabolism and interindividual variation therein.

Pia R-M Siljander - Extracellular vesicles in health and disease 

• Role of EV heterogeneity in platelet and cancer biology, EVs as biomarkers, and their inherent therapeutic properties. Our endeavors in EV method development and standardization are hallmarked by the founding of world’s first EV core facility in 2016. 

Olli Silvennoinen - Molecular mechanisms of normal and pathogenic JAK signaling

• We study molecular mechanisms of JAK kinase activation in immunological diseases and cancer using techniques from molecular/structural biology to clinical studies and shown mechanism of  pathogenic JAK2 activation and established novel therapeutic concept.

Nelli Sjöblom - Factors influencing the onset, progression and prognosis of PSC

• Our objective is to study NGS on brush cytology samples of patients with primary sclerosing cholangitis (PSC). In the previous studies we have shown that liver biopsy specimens can demostrate prognostic features for patients with PSC.

Clare Strachan - Advancing pharmaceutical spectroscopy and imaging

• We aim to understand and optimise therapeutic performance of pharmaceuticals through innovative spectroscopy and imaging. In pursuing this goal, have a strong focus on advanced vibrational spectroscopy and mass spectrometry imaging solutions.

Tomas Strandin - The pathogenesis of hantavirus and coronavirus infections

• We investigate the pathological mechanisms of Hantavirus- and Coronavirus-associated diseases. We concentrate on the role of the immune response, specifically neutrophils and IgA, in mediating disease progression.

Vassileios Stratoulias - Microglial Engineering as a Novel Therapeutic Strategy for Targeting and Treatin 

• We are pioneers in microglial diversity (Stratoulias Nat. Neurosci. ‘23, EMBO ‘19). We develop innovative approaches and tools to investigate unexplored, naturally existing microglial subsets. We uncover potential therapeutic targets for brain diseases. 

Rubina Tabassum - Genetics of complex disorders

• We study genetics of complex diseases, with particular focus on cardiometabolic disorders and lipid dysregulations. We utilize large-scale omics data (genomics, lipidomics, metabolomics) to identify risk factors and understand disease mechanisms.

Virpi Talman - Molecular disease mechanisms, drug discovery and pharmacology

• We study the molecular mechanisms of cardiac diseases in order to identify new drug targets for heart failure and related conditions such as cancer. We develop and characterize new compounds with potential to treat heart diseases and cancer.

Jing Tang - Medical bioinformatics 

• Mathematical, statistical and informatics tools to tackle biomedical questions that may potentially lead to breakthroughs in drug discovery. We are focusing on network pharmacology modeling, aiming at a systems-level understanding of drug resistance in cancer.

Ziaurrehman Tanoli - Drug discovery, precision medicine, chemoinformatics

• We develop AI based models for drug discovery and repurposing. We also develop computational methods for precision medicine and other Chemoinformatic applications. 

Jaakko Teppo - Mass spectrometry 

• We develop methods for mass spectrometry (MS) based analysis of biomolecules and apply them primarily in the context of drug research. Our research focuses on proteomics, metabolomics, and MS imaging. 

Topi Aulis Tervonen - ONCOGENIC SIGNALING PATHWAYS AS THERAPEUTIC TARGETS IN BREAST CANCER 

• We study MYC oncogene dependencies in breast cancer models to develop better treatments for MYC dependent cancers. 

Joni Turunen - Genetics of eye diseases 

• Inherited eye diseases are complex and numerous group of sight-threatening conditions. The group focuses on a detailed clinical phenotypic characterization of genetic eye diseases, gene discovery, and functional testing of pathogenic variants.

Kari Vaahtomeri - Guidance of cell migration and cell-cell interactions in lymphatic system 

• We use cell culture, explant, and in vivo models to study guidance of cell migration in the context of lymphatics, adaptive immunity, and tumorigenesis. Recently, we identified mechanisms that ensure optimal tissue coverage by dermal lymphatic capillaries.

Markus Vähä-Koskela - Functional precision medicine for solid and hematological cancers 

• We study malignant transformation of the hematopoietic myeloid compartment and the gastrointestinal epithelium. We develop novel primary culture assays for phenotypic multiparameter drug resistance and sensitivity testing and integration with omics data.

Anna Vähärautio - Single cell analysis of treatment resistance in ovarian cancer 

• We use scRNA-seq and tracking techniques to study why certain ovarian cancer cells survive through a treatment that kills other cells. We investigate the roles of genetic changes, microenvironment, and cell states in both pre-existing and induced resistance. 

Pia Vahteristo - Gynecological genomics 

• We focus on genomic alterations in common female diseases. We use multiomics approach and integrate the molecular data with detailed clinical information. Our recent study revealed a novel leiomyoma subgroup with specific molecular and morphological features. 

Sakari Vanharanta - Functional cancer genomics 

• We study the molecular mechanisms that underlie cancer development. Our research combines experimental work in cancer models with with clinical association studies. Our long-term goal is to find new mechanism-based approaches for targeted cancer therapy. 

Markku Varjosalo - Systems Biology/Medicine, cancer, immunological diseases, host-pathogen interact 

• Our longstanding interest lies in comprehensively systems level understanding how cellular signaling molecules like protein kinases, phosphatases, and transcription factors drive signaling, particularly their altered roles in immunology-oncology diseases. 

Maria Kristina Vartiainen - Nuclear organization by actin 

• We study the role of actin in nuclear organization and gene expression in normal and disease contexts, including cancer by using functional genomics and advanced microscopy methods.

Ilpo Vattulainen - Computational Life Science

• We use biosimulations to identify the molecular mechanisms that cause cancer (e.g., Wilmes et al., Science 2020; Abraham et al., Sci Adv 2023). To realize this, we simultaneously develop new simulation methods and ML-based data analytics techniques.

Keni Vidilaseris - Structural biology of polyphosphate processing enzymes

• Our research aims to understand the role of polyphosphate and its processing enzymes in the adaptation of protozoan parasites, cancer cell metabolism, and blood clotting. We employ a combination of biochemical, cellular, and structural biology methods.

Merja Voutilainen - Developing regenerative treatments for incurable neurological diseases

• We study the molecular mechanisms and therapeutic potential of novel drug candidates for amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), and multiple sclerosis (MS).

Erik Wallen - Medicinal Chemistry for Neurodegenerative Disorders 

• Design and synthesis of small molecules that can be used as pharmacological probes or leads in drug discovery. Structure-based drug design is a key starting point. All activities are integrated with the collaborating pharmacological research group. 

Shiqi Wang - Intracellular drug delivery 

• We aim to understand how nanoparticles deliver biological drugs inside cells, and use these understanding to develop new nanomedicine for novel biotherapeutics. Our research topics are at the interfaces of chemistry, biology and pharmaceutical sciences. 

Henri Xhaard - Computational drug discovery

• We use a broad panel of computational methods to study the interactions of ligands with molecular targets; to design ligands; and to predict some of their property. We have experience with database and chemoinformatics predictions.

Jari Yli-Kauhaluoma - Medicinal chemistry 

• We design and synthesize new compounds as probes for studying drug targets or as chemical entities in the search for new therapeutic compounds. We focus on antimicrobial agents, protein kinases, and chemical induction of cellular differentiation. 

Fathiah Zakham - Emerging infectious diseases 

• My research envisages the use of next generation sequencing for the identification of rare infections, characterization of known and novel pathogens in vectors of diseases, outbreak investigations,contact tracing and surveillance of emerging infectious disease.