A5020878971- Immunodeficiency and Autoimmune Disorders
- Genomics and Rare Diseases
- Chronic Lymphocytic Leukemia Research
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Protein Structure and Dynamics
- Immune Cell Function and Interaction
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- Glycosylation and Glycoproteins Research
- Blood disorders and treatments
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Cancer Genomics and Diagnostics
- Genetics, Bioinformatics, and Biomedical Research
- Genetic Associations and Epidemiology
- Genomic variations and chromosomal abnormalities
- Enzyme Production and Characterization
- Advanced Proteomics Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Genetic factors in colorectal cancer
- Nutrition, Genetics, and Disease
- Gene Regulatory Network Analysis
Lund University
2016-2025
Tampere University
2007-2019
Tampere University of Applied Sciences
2006-2019
Tampere University Hospital
2005-2015
The University of Melbourne
2015
FIT Biotech (Finland)
2011-2014
Genomics (United Kingdom)
2014
Fimlab (Finland)
2012
Pirkanmaa Hospital District
2011
University of Turku
1988-2008
Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans. The number SNPs identified human genome is growing rapidly, but attaining experimental knowledge about possible disease association variants laborious and time-consuming. Several computational methods have been developed for classification according to their predicted pathogenicity. In this study, we evaluated performance nine widely used pathogenicity prediction available on Internet. were...
Stability is a fundamental property affecting function, activity, and regulation of biomolecules. changes are often found for mutated proteins involved in diseases. predictors computationally predict protein–stability caused by mutations. We performed systematic analysis 11 online stability predictors' performances. These CUPSAT, Dmutant, FoldX, I-Mutant2.0, two versions I-Mutant3.0 (sequence structure versions), MultiMutate, MUpro, SCide, Scpred, SRide. As input, 1,784 single mutations 80...
Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers the most common applications. They usually based on machine learning approaches. For end user it is often problematic evaluate true performance applicability of computational tools as some knowledge about computer science statistics would be needed.Instructions given how interpret compare method evaluation results. systematic analysis needed established...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack community-wide, consensus-based, human- machine-interpretable language for describing phenotypes genomic environmental contexts is perhaps most pressing scientific bottleneck integration across many key fields in biology, including genomics, systems development, medicine, evolution, ecology, systematics. Here we survey phenomics...
More reliable and faster prediction methods are needed to interpret enormous amounts of data generated by sequencing genome projects. We have developed a new computational tool, PON-P2, for classification amino acid substitutions in human proteins. The method is machine learning-based classifier groups the variants into pathogenic, neutral unknown classes, on basis random forest probability score. PON-P2 trained using pathogenic obtained from VariBench, database benchmark variation datasets....
Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique applied primarily to epitope search. New prediction parameters were derived 92 refined protein structures in an unbiased selection of the Data Bank by developing further method Karplus Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy four techniques was studied comparing atomic temperature factors known...
Thermostability of proteins arises from the simultaneous effect several forces, which in fact lead to decreased flexibility polypeptide chain. This is verified by indices, are derived normalized B -values individual amino acids refined three-dimensional structures. Flexibility indices show that overall reduced when thermostability increased. Protein molecules require both and rigidity function, but higher temperature optimum stability more rigid structure needed compensate for increased...
The carbonic anhydrase (CA) gene family has been reported to consist of at least 11 enzymatically active members and a few inactive homologous proteins. Recent analyses human mouse databases provided evidence that genomes contain genes for still another novel CA isozyme hereby named XIII. In the present study, we modeled structure This model revealed globular molecule with high structural similarity cytosolic isozymes, I, II, III. Recombinant XIII showed catalytic activity similar those...
Jak tyrosine kinases have a unique domain structure containing kinase (JH1) adjacent to catalytically inactive pseudokinase (JH2). JH2 is crucial for inhibition of basal activity, but the mechanism this regulation has remained elusive. We show that negatively regulated Jak2 in bacterial cells, indicating an intrinsic property Jak2. suppressed activity by lowering V max Jak2, whereas did not affect K m peptide substrate. Three inhibitory regions (IR1–3) within were identified. IR3 (residues...
Several computational methods have been developed for predicting the effects of rapidly expanding variation data. Comparison performance tools has very difficult as trained and tested with different datasets. Until now, unbiased representative benchmark datasets missing. We a database suite, VariBench, to overcome this problem. VariBench contains experimentally verified high-quality data carefully chosen from literature relevant databases. It provides mapping position levels (protein, RNA...
Two major high-penetrance breast cancer genes, BRCA1 and BRCA2, are responsible for approximately 20% of hereditary (HBC) cases in Finland. Additionally, rare mutations several other genes that interact with BRCA2 increase the risk HBC. Still, a majority HBC remain unexplained which is challenging genetic counseling. We aimed to analyze additional HBC-associated define sensitivity our current BRCA1/2 mutation analysis protocol used Eighty-two well-characterized, high-risk and/or ovarian...
Computational tools are widely used for interpreting variants detected in sequencing projects. The choice of these is critical reliable variant impact interpretation precision medicine and should be based on systematic performance assessment. the methods varies different assessments, example due to contents sizes test datasets. To address this issue, we obtained 63,160 common amino acid substitutions (allele frequency ≥1% <25%) from Exome Aggregation Consortium (ExAC) database, which...