Merja Heinäniemi

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Professor at University of Eastern Finland

University of Eastern Finland
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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

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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)

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Merja Heinäniemi

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University of Eastern Finland

Postdoctoral Researcher in Bioinformatics and Single Cell Multiomics

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 .

7 months ago

Articles (20)

Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

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.

Year:

2024

Collaborators (36)

Kim Theilgaard-Mönch

Københavns Universitet

DENMARK

Fatima Crispi

Associate Professor

University of Barcelona

SPAIN

Stephen White

Reader in Cardiovascular Biology

Newcastle University

UNITED KINGDOM

Sofia Aakko

University of Helsinki

FINLAND

Piia Karisola

University of Helsinki

FINLAND

Laura Oksa

University of Tampere

FINLAND

Kimmo Porkka

University of Helsinki

FINLAND

Lesley Cheng

La Trobe University

AUSTRALIA

Shady Adnan Awad

University of Oxford

UNITED KINGDOM

Ursula Schwab

Professor

University of Eastern Finland

FINLAND

Markus Vähä-Koskela

Coordinator of the FIMM professional postdoctoral career development programme

University of Helsinki

FINLAND

Samuli Eldfors

University of Helsinki

FINLAND

Robert Mikulik

Professor

Masaryk University

CZECH REPUBLIC

Veronica Rendo

Uppsala University

SWEDEN

Arja Harila-Saari

Professor of paediatrics

Uppsala University

SWEDEN

Christine Klement

Technical University of Munich

GERMANY

Mika Kontro

University of Helsinki

FINLAND

Henrik Lilljebjörn

Lund University

SWEDEN

Reeta Rintamäki

Kuopio University Hospital

FINLAND

Arndt Borkhardt

Prof.

Heinrich Heine University Düsseldorf

GERMANY

Sampsa Hautaniemi

University of Helsinki

FINLAND

Anna-Liisa Levonen

University of Eastern Finland

FINLAND

Satu Mustjoki

University of Helsinki

FINLAND

Atte Nikkilä

University of Tampere

FINLAND

Jetty Chung-Yung Lee

Research Assistant Professor

Korea University

SOUTH KOREA

Krister Wennerberg

Københavns Universitet

DENMARK

Hanna-Riikka Teppo

University of Oulu

FINLAND

Olli Lohi

-

FINLAND

Jessica Nordlund

Associate Professor & Research Group Leader at Uppsala University

Uppsala University

SWEDEN

Tanja Ruokoranta

University of Helsinki

FINLAND

Komal Kumar Javarappa

University of Helsinki

FINLAND

Juho Miettinen

University of Helsinki

FINLAND

Elitsa Dimova

University of Oulu

FINLAND

Heikki Kuusanmäki

University of Copenhagen Biotech Research and Innovation Centre

DENMARK

Peter Maccallum

Chief Technical Officer

ELRIG

UNITED KINGDOM

Sadiksha Adhikari

University of Helsinki

FINLAND
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