Profiles

Esa Pitkänen

FIMM-EMBL Group Leader, Docent in Bioinformatics

Esa Pitkänen, PhD, is a FIMM-EMBL Group Leader at the Institute for Molecular Medicine Finland (FIMM), HiLIFE. He received his PhD in computer science at the University of Helsinki with Prof. Juho Rousu and Prof. Esko Ukkonen, and holds the title of Docent in Bioinformatics. He held two postdoctoral positions, first with Prof. Lauri Aaltonen in Helsinki and then with Dr. Jan Korbel and Dr. Oliver Stegle at EMBL Heidelberg, and was appointed FIMM-EMBL Group Leader in 2019. He is a principal investigator in the Applied Tumor Genomics research program and leads the data science effort in the iCAN Digital Precision Cancer Medicine Flagship, which integrates molecular profiling, clinical and registry data across 10,000 cancer cases. He also heads the HiLIFE Biodata Analytics Meilahti unit at the FIMM Technology Center.

Guangzhao Cheng

Postdoctoral researcher, large models for nanopore data

Guangzhao is finalizing his PhD in computer science at Aalto University. His work sits at the intersection of computational biology, statistical modeling and deep learning, with a focus on nanopore sequencing data. During his doctoral studies he developed methods for nanopore raw signal analysis, including a multi-task benchmark dataset and open-source tools for RNA modification detection and secondary structure prediction. He is now exploring the integration of nanopore sequencing with foundation models, and is interested in multimodal machine learning for genomic and transcriptomic complexity in precision cancer medicine.

Janne Kantola

Doctoral researcher, multimodal histopathology

Janne is a Master's student in the Life Science Technologies program at Aalto University, majoring in complex systems. Through his studies and previous work he developed a deep interest in the intersection of machine learning and medical imaging, which he is now pursuing in a Master's thesis on foundation models in computational pathology.

Daniyar Karabayev

Doctoral researcher, multimodal cell-free DNA data analysis

Daniyar earned his BSc in biology and MSc in molecular medicine from Nazarbayev University, Kazakhstan. He worked as a bioinformatics technician on genome assembly and genetic variation in the Kazakh population. In 2022 he was selected for the FIMM-EMBL rotation program, after which he joined as a doctoral researcher supervised by the Pitkänen and Ganna groups. His research centers on early cancer prediction from genetic and epigenetic patterns in cell-free DNA.

Riku Katainen

Senior researcher, novel software for large-scale genomics data

Riku is a senior researcher in the Tumor Genomics (Aaltonen) and Machine Learning in Biomedicine (Pitkänen) groups. His research focuses on disease genetics from next-generation sequencing data, analyzing inherited and somatically acquired variants of all types, and on software development. He is currently developing BasePlayer 2, an enhanced version of BasePlayer that will natively support multimodal data, including long-read and methylation sequencing. He received his degrees in computer science (BSc), bioinformatics (MSc) and cancer genetics (PhD) at the University of Helsinki.

Yrjö Koski

Doctoral researcher, computational methods for nanopore sequencing data

Yrjö obtained his MSc in bioinformatics and digital health from Aalto University. His research develops analysis methods for nanopore sequencing data, including simulation of nanopore data and detection of DNA adducts, which can shed light on how various cancers begin. He studies adducts in colorectal cancer in collaboration with the Aaltonen group.

Laura Langohr

Postdoctoral researcher, multimodal determinants of cell size

Laura is a postdoctoral researcher in Jette Lengefeld's lab and Esa Pitkänen's group. Her current project examines cell size variability among healthy blood donors in FinnGen and in hematological patients using multi-omics data. Previously she worked in Outi Kilpivaara's and Ulla Wartiovaara-Kautto's Hematological Genetics lab and in this group within an iCAN subproject, on how leukemias arise from premalignant conditions using single-cell sequencing and TP53 variant status of single cells. She received her PhD in computer science at the University of Helsinki, and her MSc and BSc in bioinformatics at Friedrich Schiller University Jena, Germany.

Katri Maljanen

Doctoral researcher, epigenetic determinants of structural variants

Katri received her Bachelor's in biology and Master's in life science informatics from the University of Helsinki. Her research looks at how genomic and epigenomic features affect cancer mutagenesis, in particular their effect on specific mutation types and on different cancer types. Her broader interest is applying machine learning to DNA sequence data to gain novel biological insight.

Hanna Nebelung

Doctoral researcher, spatial transcriptomics in prostate cancer

Hanna holds a Master's degree in life science informatics from the University of Helsinki, specializing in bioinformatics and systems medicine, after a Bachelor's in bioinformatics at Saarland University. Her doctoral research is on Xenium spatial data analysis in prostate cancer.

Prima Sanjaya

Doctoral researcher, deep learning of somatic mutagenesis

Prima is a doctoral researcher working on artificial intelligence in biomedicine. His research develops explainable deep learning for multimodal genomics and medical image data for clinical use. He received his MSc from Dongseo University, South Korea, working in the Machine Learning Research Lab, and then worked at the Department of Radiology, Seoul National University Hospital, as a medical imaging researcher.

Nora Schreiber

Doctoral researcher, integrative precision cancer medicine

Nora studies genomics- and transcriptomics-based tumor typing and subtyping across cancer types, with the goal of improving personalized treatment choices. She joined the group for her Master's thesis (MSc in bioinformatics, University of Tübingen), investigating clinically feasible tumor type classification. During her BSc in biomedical science at the University of Marburg she developed an interest in tumor and immune biology, which she now combines with machine learning.

Ara Taalas

Doctoral researcher, biomedical machine learning

Ara is a doctoral researcher in biomedical machine learning at FIMM, with an MSc in bioinformation technology from Aalto University. He splits his time between Terveystalo and FIMM to pursue research on predictive diagnostics from complex longitudinal clinical data. He has previous experience in modeling stem cell differentiation and novel drug candidate discovery, and enjoys playing excessively complex board games.

Arina Tagmazian

Doctoral researcher, deep learning for neuroimaging

Arina is a doctoral researcher at the Helsinki Institute of Life Science. She holds a Bachelor's in biology from the Russian State Agrarian University and a Master's in bioinformatics from the Higher School of Economics in Moscow. Her earlier research ranged from bovine leukemia virus resistance in cattle to alternative splicing in Polypedilum vanderplanki. She now works on neuroscience research combining image processing, deep learning and epigenetic analysis. Outside the lab she meditates, plays the ukulele and paints watercolors.

Alireza Tajmirriahi

Doctoral researcher, FIMM-EMBL rotation program

Alireza is a doctoral researcher in the FIMM-EMBL rotation program. He received his MSc in bioinformatics from Aalto University in 2025. His work has explored applications of AI in healthcare from several angles, including multi-omics integration, bacterial genetics, synthetic medical images, medical device innovation, and behavioral data analysis. His current research combines histopathology foundation models with paired spatial transcriptomics data, working toward multimodal AI methods for tumor microenvironment–aware drug-target and biomarker discovery. He is particularly interested in the translation of computational methods, from discovery to clinical and commercial application.

Lei Xia

Postdoctoral researcher, joint Nordic EMBL Partnership appointment with the Sahu group at NCMBM, Oslo

Lei holds a joint Nordic EMBL Partnership postdoctoral appointment, working in both the Pitkänen group at FIMM and the Biswajyoti Sahu group, Precision Cancer Epigenomics, at NCMBM in Oslo. He earned his PhD at the Institute of Hydrobiology, CAS, and held a postdoctoral position at Guangzhou Medical University studying RNA biology in human cell lines. His research uses machine learning to decode the regulatory logic of cancer genes through nanopore sequencing, and investigates how DNA methylation and chromatin accessibility influence DNA adduct formation.