We participated in Cancer Research Day at our faculty, where we heard a variety of cutting-edge talks on topics related to cancer research, ranging from single-cell data analysis to clinical studies. We also contributed to the event with talks and posters. Zhesi Zhang presented miREA, a tool for microRNA (miRNA) enrichment analysis, and Liang Zhang presented RingNet, a tool for visualising multiomics data in networks.

Dr. Xin Lai attended the second Bonn Conference on Mathematical Life Sciences. He presented the latest research on the HallmarkGraph, a AI tool for classifying hierarchical tumor subtypes, in a 30-minute talk. The conference hosted approximately 300 participants from around the world and covered topics ranging from modeling methodology to single-cell analysis. Our journal, NPJ Systems Biology and Applications, also sponsored four poster awards for the conference.
Many thanks to the local organizers, inlcuding Dr. Jan Hansenauer, Dr. Kevin Thurley, and Dr. Elena Reckzeh, for hosing this great event.

scRGCL is a deep learning framework designed to enhance the clustering of single-cell RNA sequencing data. To overcome common computational challenges such as high sparsity and technical noise, the model uses neighbor-aware graph contrastive learning to more accurately identify distinct cell types. It operates by integrating local neighborhood structures with global cluster information to ensure that similar cells remain grouped together and distinct populations are clearly separated.

The video is created using google's NotebookLM.

It has been two and a half years since Dr. Xin Lai left the University Hospital of Erlangen to establish his laboratory at Tampere University. During this trip to Erlangen, he visited Dr. Julio Vera's laboratory, talked to the collaborators, delivered a seminar talk to the department, and enjoyed reconnecting with former colleagues while meeting new ones.

miREA is a computational tool for miRNA enrichment analysis that identifies biological pathways regulated by miRNAs. Unlike conventional methods that treat genes and miRNAs as independent nodes, miREA explicitly incorporates miRNA–gene interactions as quantitative network edges, capturing the regulatory interdependencies between miRNAs and their target genes. miREA implements five edge-based enrichment methods spanning over-representation, scoring-based, topology-aware, and network propagation approaches. 

The video is created using google's NotebookLM.

Tampere University and Business Tampere hosted a joint seminar and networking day for P4 Medicine at Kauppi campus.

At the event, Dr. Xin Lai presented the collaborative research project with Dr. Teemu Murtola regarding the identification of functional microRNA-gene interactions that regulate atorvastatin treatment in prostate cancer.

This week, Dr. Xin Lai together with other colleagues participated in a leadership program in Brussels, led by Dr. Pauli Kuosmanen. The group attended events organized by the ERC, EERIN, ECIU, and Tampere Region EU Office, aiming to deepen their understanding of EU policy and build contacts with local Brussels authorities. The trip successfully strengthened ties with Tampere's Brussels representatives and opened new pathways for influencing EU policy through research. The team also enjoyed Brussels' renowned cuisine and chocolates.

RingNet is an web-based platform designed to visualize multi-modal data within a unified network structure. By utilizing a specialized concentric ring glyph, the tool allows users to map multiple datasets—such as genomics, transcriptomics, and clinical records—onto individual nodes. The system integrates an R-based backend for intensive data processing with a D3.js frontend to provide an interactive and customizable user experience. 

See the Preprint for details and try it out by yourself at RingNet's website. Report any bugs or send your feedback at the Github Repository. The video is created using google's NotebookLM.

I was saddened to learn of Dr. Amos Bairoch's passing from the ISCB newsletter. Although I only heard him speak once, at ISBM/ECCB2025 in Liverpool, his presentation about Swiss-Prot was so real and unforgettable. His story also taught us that even if you do excellent work and contribute to the scientific community, you may still face a lack of funding due to political reasons. In his case, his initial proposal to expand and maintain the curated protein sequence database was rejected because the funder believed that one of the most widely used databases did not benefit enough Swiss people and should not be funded. Although it can be disheartening when science is involved in politics, this should not prevent us from making good science by building on the work of these lost giants. Salute to Dr. Bairoch.

During the holiday season, we celebrated by making and decorating gingerbread and cookies together. This seemingly simple activity taught us how to properly use sugars. In addition, we enjoyed the so-called best pizza from Pizzeria Napoli Tampere. It was delicious, though not as fabulous as we expected. We wish everyone a peaceful Christmas holiday, and afterwards, we will regain our energy to continue doing and enjoying research.

Together with Miina Vulli, we organized the first Bioevening, a regular event hosted by the Finnish Society for Bioinformatics, in Tampere, as well as in Turku and Helsinki. There, we enjoyed delicious food and played 80s‘ video games and pinball. It was a lot of fun and brought back many childhood memories. Thank you all for making it happen! We hope to see you and more people at our next Bioevening.

The annual MET Research Day attracts over 300 participants from research institutes and industry, focusing on advancing multidisciplinary research and collaboration. The dedicated Industrial Pre-event spotlights Health AI, Digital Twins & Chip Twins, aiming to bridge AI-driven simulations with organ-on-chip models. This connects AI developers, pharma companies, clinicians, and researchers in a focused effort to accelerate drug discovery and translational relevance.

We contribute several poster presentations covering our published and ongoing research projects. RingNet: an interactive platform for multi-modal data visualization in complex networks (Liang Zhang). miREA: a network-based tool for cancer-specific miRNA-oriented enrichment analysis (Zhesi Zhang). PCaKG: a prostate cancer knowledge graph (Tuulikki Suomela). HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes (Xin Lai).

The 14th National Conference on Bioinformatics and Systems Biology recently took place in Nanning, China. This year's theme covered the foundational and complex areas of biological data analysis and holistic biological systems. It emphasized how the rapid evolution of AI is reshaping the future of scientific research in these critical fields. The event emphasized AI's role in advancing new research methodologies and discoveries in life sciences and medicine. 

My co-supervising doctoral students, Qingsong Zhang (MSc) and Junming Fan (MSc) from Dr. Fei Liu's lab, participated in the event by presenting their latest research. Qingsong gave a talk on our latest publication, HallmarkGraph, a graph neural network that classifies tumor subtypes. Junming presented his poster on contrastive learning for single-cell clustering.

I was shocked to learn of the passing of Dr. Béla Novák at Oxford University in February 2025. His collaboration with Dr. John Tyson on using mathematical models to study the cell cycle of eukaryotes produced must-read papers during my Ph.D. studies. His work laid the foundation for understanding the dynamics of network motifs based on mathematical models. Although I never met Dr. Novák in person, I could tell he was a man of great character who pursued excellence in science from this obituary. I hope he rested in peace, and that the Systems Biology Community continues to grow based on his work.

It was a great tour to learn about the ongoing activities and education at Tampere Centre for Skills Training and Simulation and Tampere Surgical Education Centre. They are operating at full capacity, with over 90% of their time dedicated to training medical professionals and surgeons in #Finland. Though some patient care manikins are over 20 years old, they are still functional and in use. In addition, I have a lot of respect for their attitude towards cadavers! Many thanks to Nina Hutri and Reita Nyberg.

Photo taken by Leena Ukkonen.

The 2nd China-Germany-Finland Life Sciences Forum successfully concluded at Tampere University's Faculty of Medicine and Health Technology from August 6-8, 2025, uniting 60 participants in advancing collaborative health data science research. The three-day symposium focused on computational advances including AI applications in biomedical research, integrating expertise from 13 research institutes and 6 companies with government representatives from China and Finland. This gathering demonstrated international collaboration's transformative potential in addressing global health challenges. See the news article at TAU for more information.

In collaboration with Dr. Jing Tang, we successfully organized the 21st International Symposium on Bioinformatics Research and Applications (ISBRA2025) in Helsinki, Finland, from August 3–5, 2025. The symposium attracted exceptional scholarly engagement, receiving 167 original research submissions spanning the full spectrum of bioinformatics and computational biology. Following rigorous peer review, the Program Committee selected 66 high-quality papers for full publication in the conference proceedings, published in the Lecture Notes in Bioinformatics (LNBI) series. 

The comprehensive scientific program showcased four distinguished keynote presentations delivered by internationally renowned speakers:Dr. Walter Kolch from University College Dublin; Dr. Ritambhara Singh from Brown University; Dr. Kwang-Hyun Cho from the Korea Advanced Institute of Science and Technology; Dr. Serghei Mangul from the University of Southern California. In addition, more than 25 posters were presented at our conference.

We are pleased to announce that our latest research, HallmarkGraph, has been accepted for publication in Bioinformatics. This novel graph convolutional network leverages established cancer hallmarks to accurately classify hierarchical tumor subtypes across 405 distinct categories spanning 26 primary cancer types. The model demonstrates prominent performance in multi-label classification tasks. By integrating biological knowledge with advanced machine learning techniques, HallmarkGraph offers both superior accuracy and interpretable insights, demonstrating its potential in clinical applications. HallmarkGraph represents a significant advancement in cancer classification methodology.

See the publication for details. Report any bugs or send your feedback at the Github Repository. The video is created using google's NotebookLM.

We are pleased to annouced a new publication for decoding the role of SOX10 and miRNAs in melanoam using a systems biology apporach. This research examines how miRNAs control SOX10, a key protein involved in melanoma cancer development. The study shows that miRNAs can regulate cancer cell growth, spread, and resistance to treatment by controlling SOX10 and related proteins. The publication is highlighted in German eMed media.

Summer is approaching, and we're celebrating by visiting FlowPark for adventures. This sport requires not only good fitness but also a sharp mind to navigate the challenges. We had a wonderful day and even enjoyed the satisfying muscle soreness the next day. 

The BIO (Bioscience led by Prof. Vesa Hytönen) and MEDI  (Biomedicine led by Prof. Matti Nykter) units successfully conduct their first collaborative research symposium, showcasing cutting-edge scientific developments. Drawing over 100 attendees, the event feature 16 presentations across four key research domains: cancer, cell and molecular biology, epigenetics, and infection. Among the highlighted research, we present a novel biologically informed AI model for hierarchical tumor subtype classification. The event also establishes a platform for cross-disciplinary exchange between the previously separate research units, fostering potential collaborations.

Following the visit by Dr. Leory Hood in 2024, our faculty organizes a seminar on P4 medicine referring to Predictive, Preventive, Personalized, and Participatory Medicine and focusing on individual-tailored approaches to wellness and treatment. The seminar brings 100+ industrial and academic professionals to attend talks and a poster session aiming at fostering collaboration between academic institutions, Pirha, and Business Tampere. The event highlights ongoing research and partnership opportunities in the Tampere region. 

We presented our melanoma network-driven AI model at the 9th Disease Network Conference hosted at KU Leuven, Belgium. The conference brings together researchers advancing standards such as SBGN and SBML for mechanistic disease map development and also fostering applying disease maps to biomedical challenges, including Inflammation and COVID-19. During the conference, we joined the collaborative community effort supporting the Immune Digital Twin project, further extending our contribution to this important field.

We have a fun group event at the Taverna where we play board games for three hours. We use our creativity and skills not only for research but also for entertainment. It is really a wonderful evening, thank you all for participating.
Taverna is a highly recommended place to play board games with a friendly, relaxed atmosphere. The bar has 700 different board and card games as well as an affordable price.
The news image is produced using ChatGTP.

This our second time to participate the annual Cancer Research Day organized by Tays Cancer Center. In addition to presenting our work, we audited various talks from Finnish, German, and Italian institutes, and had fruitful discussion with colleagues about our research. Many thanks for the organizers (Annika Auranen, Teemu Murtola, and Toni Seppälä), speakers, and the participants for making this wonderful event happen. Liang Zhang gave a talk on the AI framework for analyzing cancer genomics data. Zhesi Zhang gave a pith talk on the method for analyzing miRNA-gene interactions at the pathway level. Tuulikki Suomela presented her poster on the pipeline to analyze miRNA function in chronic lymphocytic leukemia.

We are delighted to announce the conclusion of our Special Issue in NPJ Systems Biology & Applications! The response is extraordinary – we received an collection of 54 submissions from prestigious institutes spanning the globe, with 13 outstanding papers published and 10 still under processing. This Special Issue showcases cutting-edge developments in systems biology research methodology and its groundbreaking applications in both basic and transnational research.
Many thanks for the collaboration of the co-editor Dr. Jing Tang and the editor in chief Dr. Mohit Jolly. 

We together with Julio Vera's lab publish a new tool ENQUIRE in PLoS Computational Biology. The tool automates biomedical literature analysis from PubMed. It builds networks of gene and concept co-occurrences from user-selected publications, expands research through new article discovery, and identifies relevant interactions, including novel ones. 

We are excited to announce the second China-Germany-Finland Life Sciences Forum, which will be hosted in August at Tampere University! This year’s forum will focus on cutting-edge bioinformatics and medical informatics in biomedicine, featuring presentations and discussions by leading experts. 

Following the success of the first forum in Chengdu, China (2024), which brought together researchers from around the world and attracted 200,000+ online viewers, this event promises to be another milestone in fostering global collaboration and innovation in life sciences.

We are delighted to announce the publication of the second edition of Computational Biology of Non-coding RNA. This book is a continuation of the first edition whose chapters have so far received 36k accesses and 180+ citations. This new volume features 20 expertly crafted chapters from researchers across global institutions, presenting cutting-edge methodologies in ncRNA research. The collection advances our understanding of novel ncRNA identification, target prediction, functional annotation, and disease associations across diverse biological contexts. We extend our sincere gratitude to all contributors whose expertise and dedication made this valuable scientific resource possible. 

We enjoyed and got into the Christmas spirit by going to an indoor climbing park where we challenged not only our intelligence but also our physical fitness. Hopefully, we will continue to show our courage and determination to face scientific challenges in the coming year.

In addition, we received a surprising Christmas gift: the second edition of our book on the Computational Biology of Non-coding RNA is now officially online. The book contains 20 chapters contributed by experts from institutes around the world. It is a collection of state-of-the-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in various biological contexts.

We are co-organizing the International Symposium on Bioinformatics Research and Applications (ISBRA2025) in August 3-5, Helsinki. The conference is already calling for papers (DL: March 25, 2025). All accepted papers will be published in the conference proceedings by Lecture Notes in Computer Science, and selected papers will be invited for publication in special issues of partner journals.. We look forward to receiving your contribution and meeting you in Helsinki.

The first ISBRA was held in 2005 and is an affiliated conference of the International Society for Computational Biology (ISCB).  The conference has evolved into a globally recognized conference series dedicated to advancements in bioinformatics, computational biology, and related fields. Since its inception, the symposium has provided a platform for researchers worldwide to collaborate, share findings, and discuss innovations in computational methods for biological data analysis. 

We welcome Mr Toivo Parjanen to join our lab to work on his BSc thesis.

His research topic will be modeling and analyzing the effect of genetic mutation on miRNA-mediated gene regulation.

We presented our work at the faculty's annual MET Research Day event, audited various talks at our faculty, and had a great discussion with other colleagues about our research. 

• Liang Zhang presented a poster on an AI framework for analyzing patient omics data and gave a 3-minute Pich talk.

• Zhesi Zhang presented her poster on a method to analyze miRNA-gene interactions.

• Tuulikki Suomela presented her poster on a published paper on miRNA function in chronic lymphocytic leukemia.

Dr. Jan Hansenauer visited our faculty and gave an inspiring keynote talk at MET Research Day. Afterwards, he had discussion with interested researchers and students of their research work. In the evening, we drank glögi together with Biomedicine Unit members at and enjoyed dinner at a Sushi restaurant . 

Hansenauer's lab develops and applies computational methods (e.g., statistical inference for dynamical systems, multi-scale models, metabolic models, statistical analysis, and scientific machine learning) for the analysis of complex biological processes. 

We welcome Mr Aleksi Kauppinen who will be working on his BSc thesis over the next several months.

His research topic will be the analysis of gene regulation by miRNAs in prostate cancer.

At the Finnish Nordic CompBio Week, Dr. Xin Lai gave a presentation on the use of the disease-network informed AI model to characterize melanoma.

The Nordic CompBio Week is a free and open hybrid bioinformatics conference. The conference has a format where participating Nordic regions organize in-person conference programmes and where sessions are live-streamed for virtual attendance for free, according to a hub-and-spoke model. 

Dr. Mohit Jolly from the Centre for BioSystems Science and Engineering (BSSE) recently visited Tampere University to serve as a PhD thesis opponent. After the thesis defending, I met with Dr. Jolly to discuss our ongoing research and exchanged ideas about the research environment in Germany, Finland, and India. 

Jolly’s lab is renowned for its innovative use of systems biology approaches to unravel the complexities of cancer metastasis and therapy resistance. His visit provided valuable insights and fostered collaborative opportunities, enriching our understanding of these critical areas in cancer research.