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Merja Heinäniemi
Has grant
Professor at University of Eastern Finland
Research Interests
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About
Merja Heinäniemi is a Professor at the University of Eastern Finland, specializing in the fields of cancer research and immunology. Her recent articles address critical aspects of acute lymphoblastic leukemia, including single-cell analysis techniques and combination therapies for treatment. With an emphasis on both genetic and non-genetic factors influencing leukemia and related disorders, she contributes to advancing understanding in the area of molecular subtypes and therapeutic strategies.
Recent Grants
Grant: Close
Genomics-based tools for personalized treatment of cancer
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Genomics-based tools for personalized treatment to reduce chemotherapy burden in pediatric cancer
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Translating genomics into clinical tools for pediatric leukemia
Open Date: 2019-01-01
Close Date: 2024-01-01
Grant: Close
Capturing the cell state space from genomics data into models of treatment resistance in childhood leukemia
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Semi-supervised autoencoder models for scRNA-seq
Open Date: 2018-01-01
Close Date: 2019-01-01
Positions (1)
Merja Heinäniemi
University of Eastern Finland
9 months ago
The University of Eastern Finland invites applications for a Postdoctoral Researcher position in Bioinformatics and Single Cell Multiomics, based at the School of Medicine, Faculty of Health Sciences, Kuopio Campus. This 3-year, full-time position is embedded in the research group led by Professor Merja Heinäniemi and focuses on modelling leukemia and immune cell dynamics to advance personalised medicine approaches. The successful candidate will integrate and model patient transcriptome, metabolome, and proteome data at single cell resolution, aiming to connect these profiles with intra- and intercellular regulatory networks and to capture immune system and disease states in multi-omics models. The role offers extensive collaboration with an international, interdisciplinary team of experts in leukemia biology, immunology, gene regulation, computational biology, and clinical research. Main responsibilities include planning and conducting data-driven studies in leukemia biology and immunology, benchmarking and developing statistical, AI, and systems biology methodologies for multiomics data, producing high-quality scientific publications, and contributing to research proposals. The postdoctoral researcher will also co-supervise PhD students and may participate in undergraduate teaching within their area of expertise. Applicants must have a doctoral degree in a relevant field (bioinformatics, systems biology, computational biology, or related), completed within the last five years (excluding parental leave, military service, etc.), and demonstrate excellent or good English proficiency. Required skills include a formal background in bioinformatics or related fields, practical experience with omics data analysis in a biomedical context, solid knowledge of single cell omics technologies and data analysis, and a strong research record. Additional advantages are experience in leukemia or immunology research, bioinformatics method development, time series modelling, international research cooperation, and student supervision. The position is funded according to the Finnish university salary system, with a job requirement component of 3,293.89 euros/month (level 5) and a personal performance component of 6–50%, resulting in a starting salary of approximately 3,620–4,020 €/month. The university offers comprehensive staff benefits, including professional development, occupational health care, staff training, discounted campus lunches, and affordable sports services. To apply, submit your application via the university's electronic application form by 16 February 2026. Required documents include a CV, list of publications, copies of academic degree and language proficiency certificates, and a motivation letter (max 2 pages). Applications must be in English. For further information, contact Professor Merja Heinäniemi at [email protected]. Join a vibrant, international academic community in Finland, renowned for its high quality of life, modern technology, and excellent education system. For more information about the university and working in Finland, visit www.uef.fi/en .
9 months ago
Articles (20)
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2025
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2025
Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.
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2024
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2024
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2024
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2024
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2024
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2024
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2023
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2023
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2021
Collaborators (38)
Kim Theilgaard-Mönch
Københavns Universitet
Fatima Crispi
Associate Professor
University of Barcelona
Stephen White
Reader in Cardiovascular Biology
Newcastle University
Sofia Aakko
University of Helsinki
Piia Karisola
University of Helsinki
Laura Oksa
University of Tampere
Kimmo Porkka
University of Helsinki
Lesley Cheng
La Trobe University
Michael Bassik
Associate Professor
Stanford University
Shady Adnan Awad
University of Oxford
Ursula Schwab
Professor
University of Eastern Finland
Markus Vähä-Koskela
Coordinator of the FIMM professional postdoctoral career development programme
University of Helsinki
Roman Sankowski
Medical Doctor
Albert-Ludwigs-Universität Freiburg Medizinische Fakultät
Samuli Eldfors
University of Helsinki
Robert Mikulik
Professor
Masaryk University
Veronica Rendo
Uppsala University
Arja Harila-Saari
Professor of paediatrics
Uppsala University
Christine Klement
Technical University of Munich
Mika Kontro
University of Helsinki
Henrik Lilljebjörn
Lund University
Reeta Rintamäki
Kuopio University Hospital
Arndt Borkhardt
Prof.
Heinrich Heine University Düsseldorf
Sampsa Hautaniemi
University of Helsinki
Anna-Liisa Levonen
University of Eastern Finland
Satu Mustjoki
University of Helsinki
Atte Nikkilä
University of Tampere
Jetty Chung-Yung Lee
Research Assistant Professor
Korea University
Krister Wennerberg
Københavns Universitet
Hanna-Riikka Teppo
University of Oulu
Olli Lohi
-
Jessica Nordlund
Associate Professor & Research Group Leader at Uppsala University
Uppsala University
Tanja Ruokoranta
University of Helsinki
Komal Kumar Javarappa
University of Helsinki
Juho Miettinen
University of Helsinki
Elitsa Dimova
University of Oulu
Heikki Kuusanmäki
University of Copenhagen Biotech Research and Innovation Centre
Peter Maccallum
Chief Technical Officer
ELRIG
Sadiksha Adhikari
University of Helsinki
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