A5081215602- DNA and Biological Computing
- semigroups and automata theory
- Advanced biosensing and bioanalysis techniques
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Modular Robots and Swarm Intelligence
- Computational Drug Discovery Methods
- Cellular Automata and Applications
- Logic, Reasoning, and Knowledge
- Logic, programming, and type systems
- DNA and Nucleic Acid Chemistry
- Microbial Metabolic Engineering and Bioproduction
- Chemical Synthesis and Analysis
- Bacteriophages and microbial interactions
- Protein Structure and Dynamics
- Molecular Junctions and Nanostructures
- RNA Interference and Gene Delivery
- Algorithms and Data Compression
- Protein Degradation and Inhibitors
- Heat shock proteins research
- Computability, Logic, AI Algorithms
- Cholinesterase and Neurodegenerative Diseases
- COVID-19 Clinical Research Studies
- Pesticide and Herbicide Environmental Studies
- Machine Learning in Healthcare
University of Helsinki
2011-2024
National Institute of Research and Development for Biological Sciences
2017-2024
Åbo Akademi University
2009-2022
Turku Centre for Computer Science
2004-2020
Aalto University
2011-2015
Helsinki Institute for Information Technology
2011-2013
Western University
2008-2011
University of Turku
2003-2008
Control theory is a well-established approach in network science, with applications bio-medicine and cancer research. We build on recent results for structural controllability of directed networks, which identifies set driver nodes able to control an a-priori defined part the network. develop novel efficient (targeted) networks demonstrate it analysis breast, pancreatic, ovarian cancer. each case protein-protein interaction focus survivability-essential proteins specific type. show that...
Importance Magnetic Resonance Imaging (MRI) coupled with Prostate Imaging-Reporting and Data System (PI-RADS) provides a standardized scoring system for assessing clinical significance of prostate cancer (PCa). However, the association between PI-RADS scores key end-points remains underexplored due to limited follow-up data. Objective To evaluate cancer-specific mortality (PCSM), overall survival (OS), metastasis-free (MFS), biochemical recurrence (BCR) across multiple cohorts. Design,...
Computational analysis of the structure intra-cellular molecular interaction networks can suggest novel therapeutic approaches for systemic diseases like cancer. Recent research in area network science has shown that control theory be a powerful tool understanding and manipulation such bio-medical networks. In 2011, Liu et al. developed polynomial time algorithm computing size minimal set nodes controlling linear network. 2014, Gao generalized problem target control, minimizing within The...
To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein-protein interaction (PPI) networks integrating top-ranked factors, target proteins and PPI data. to identify targets combinations thereof that offer efficient factors. validated our findings against clinical studies data bioinformatics studies. Our method offers a new insight into molecular...
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a coloured tiles that, starting from bordering seed structure, self-assembles given rectangular colour pattern. task finding minimum-size tile sets known be NP-hard. We explore several complete and incomplete search techniques for minimal, or at least small, also assess reliability solutions obtained according kinetic Assembly Model.
The use of MRI-targeted biopsies has led to lower detection Gleason Grade Group 1 (GG1) prostate cancer and increased GG2 disease. Although this finding is generally attributed improved sensitivity specificity MRI for aggressive cancers, it might also be explained by grade inflation. Our objective was determine the likelihood definitive treatment risk post-treatment recurrence patients with diagnosed using targeted relative men GG1 systematic biopsies.
Network controllability focuses on discovering combinations of external interventions that can drive a biological system to desired configuration. In practice, this approach translates into finding combined multi-drug therapy in order induce response from cell; lead developments novel therapeutic approaches for systemic diseases like cancer.We develop bioinformatics data analysis pipeline called NetControl4BioMed based the concept target structural control linear networks. Our generates...
Control theory has seen recently impactful applications in network science, especially connections with medicine. A key topic of research is that finding minimal external interventions offer control over the dynamics a given network, problem known as controllability. We propose this article new solution for based on genetic algorithms. tailor our computational drug repurposing, seeking to maximize its use FDA-approved targets disease-specific protein-protein interaction network. demonstrate...
The heat shock response is a well-conserved defence mechanism against the accumulation of misfolded proteins due to prolonged elevated heat. cell responds by raising levels (hsp), which are responsible for chaperoning protein refolding. synthesis hsp highly regulated at transcription level specific (transcription) factors (hsf). One regulation mechanisms phosphorylation hsf's. Experimental evidence shows connection between hyper-phosphorylation hsfs and transactivation hsp-encoding genes. In...