A5069360583- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Chromatin Remodeling and Cancer
- Acute Myeloid Leukemia Research
- Protein Degradation and Inhibitors
- Genomics and Chromatin Dynamics
- Plant Disease Resistance and Genetics
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Biosimilars and Bioanalytical Methods
- Acute Lymphoblastic Leukemia research
- Glioma Diagnosis and Treatment
- Cancer, Hypoxia, and Metabolism
- Genetic Associations and Epidemiology
- Neuroscience and Neural Engineering
- Ferroptosis and cancer prognosis
- Bone Metabolism and Diseases
- Nursing Diagnosis and Documentation
- CAR-T cell therapy research
- Machine Learning in Healthcare
- Antiplatelet Therapy and Cardiovascular Diseases
- interferon and immune responses
Tampere University
2015-2024
Tampere University Hospital
2016-2024
Prostate Cancer Research
2024
Cancer Research Center
2024
Tieto (Finland)
2023
Tieto (Czechia)
2023
Fimlab (Finland)
2016
Changes in DNA methylation are among the mechanisms contributing to ageing process. We sought identify ageing-associated changes at single-CpG-site resolution blood leukocytes and ensure that observed were not due differences proportions of leukocytes. The association between gene expression levels was also investigated same individuals.We identified 8540 high-confidence CpG sites, 46% which hypermethylated nonagenarians. hypermethylation-associated genes belonged a common category: they...
Laminins are one of the major protein groups in extracellular matrix (ECM) and specific laminin isoforms crucial for neuronal functions central nervous system vivo. In present study, we compared recombinant human (LN211, LN332, LN411, LN511, LN521) isoform fragment (LN511-E8) vitro cultures pluripotent stem cell (hPSC)-derived neurons. We showed that substrates containing α5-chain important attachment, viability network formation, as detected by phase contrast imaging, staining,...
We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence multiple prostate cancer metastases in a single patient (A21). Whole-genome was obtained from nine anatomically separate metastases, targeted DNA sequencing performed cancerous noncancerous foci within primary tumor specimen removed 5 yr before death. Transcriptome revealed increased expression androgen receptor (AR)-regulated genes liver that harbored an AR p.L702H mutation,...
Abstract Our aim was to investigate in a real‐life prospective patient cohort how CYP2C19 loss‐of‐function (LOF) variants and inhibitor omeprazole or esomeprazole influence the incidence of cardiovascular events patients using clopidogrel. Data based simultaneously on these factors are conflicting sparse. A ( n = 1972) with acute coronary syndrome 1302) symptomatic chronic disease 656) followed for 365 days after hospitalization information purchased prescription drugs, hospital discharge,...
Large collections of genome-wide data can facilitate the characterization disease states and subtypes, permitting pan-cancer analysis molecular phenotypes evaluation context for new therapeutic approaches. We analyzed 9,544 transcriptomes from more than 30 hematologic malignancies, normal blood cell types, lines, showed that types could be stratified in a data-driven manner. then identified cluster-specific pathway activity, biomarkers, silico drug target prioritization through interrogation...
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression altered transcription factor binding it is linked to upstream Medulloblastomas, choroid plexus tumors, pluripotent stem cells, fetal were used as references. A part of the genomic regions, which hypermethylated in AT/RTs...
Existing large gene expression data repositories hold enormous potential to elucidate disease mechanisms, characterize changes in cellular pathways, and stratify patients based on molecular profiles. To achieve this goal, integrative resources tools are needed that allow comparison of results across datasets types. We propose an intuitive approach for data-driven stratifications profiles benchmark our methodology using the dimensionality reduction algorithm t-distributed stochastic neighbor...
Abstract Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such are subject to mix-ups, contamination, accumulation of secondary mutations, verification strains samples is not an established part many experimental workflows. With plummeting cost next generation technologies, it conceivable whole genome sequencing (WGS) could be applied routine strain sample future. To demonstrate need for validation by WGS, we...
Bone morphogenetic protein 4 (BMP4) is a remarkably powerful inhibitor of breast cancer cell proliferation, but it also able to induce migration in certain cellular contexts. Previous data demonstrate that BMP4 controls the transcription variety protein‐coding genes, not much known about microRNAs (miRNA) regulated by BMP4. To address this question, miRNA expression profiles following treatment were determined one mammary epithelial and seven lines using microarrays. While analysis revealed...
Rare disease diagnoses are often delayed by years, including multiple doctor visits, and potential imprecise or incorrect before receiving the correct one. Machine learning could solve this problem flagging patients that doctors should examine more closely.Making prediction situation as close possible to real situation, we tested different masking sizes. In phase, data was removed, it applied all points following first rare diagnosis, day when diagnosis received, in addition selected number...
Brain tumors typically arise sporadically and do not affect several family members simultaneously. In the present study, we describe clinical genetic data from two patients, a mother her daughter, with familial brain tumors. Exome sequencing revealed germline missense mutation in TP53 ATRX genes both cases, somatic copy-neutral loss of heterozygosity (LOH) atypical teratoid/rhabdoid tumor (AT/RT) astrocytoma was associated protein expression. case, R132C found known hotspot site isocitrate...
Abstract Importance Many clinically significant health conditions are frequently underreported, underdiagnosed or recorded only in unstructured textual records, yet they contain critical information for patient assessment, care and prognosis. Objective To determine whether deep learning-based natural language processing employed named entity recognition can effectively identify conditions, such as incontinence, falls, mobility limitations loneliness electronic records. The identified were...
Abstract Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such are subject to mix-ups, contamination, accumulation of secondary mutations, verification strains samples is not an established part many experimental workflows. With plummeting cost next generation technologies, it conceivable whole genome sequencing (WGS) could be applied routine strain sample future. To demonstrate need for validation by WGS, we...
Abstract The existing large gene expression data repositories hold enormous potential to elucidate disease mechanisms, characterize changes in cellular pathways, and stratify patients based on their molecular profile. To achieve this goal, integrative resources tools are needed that allow comparison of results across datasets types. We propose an intuitive approach for data-driven stratifications profiles benchmark our methodology using the dimensional reduction algorithm t-SNE with...
Abstract Alternative splicing of pre-messenger RNA is responsible for the diversity transcriptome and proteome, with majority multi exon genes producing multiple transcripts. Aberrations in regulative factors alternative are known to produce transcript isoforms associated cancer progression prognosis. Both mutations proximity spliced regions regulation previously identified factor alter patterns. In this study, we utilized publicly available TCGA data study association patterns between its...
<p>Summary of data</p>
<p>Supplementary Data includes Methods and Figures Legends for Supplementary tables. Fig. S1: Sample-level quality control pre-processing; S2: Two-dimensional representations of sample distances; Fig S3: Known vulnerabilities confirmed by Hemap; S4: Evaluation drug screening results confirmation using hemap data; S5: Candidate immunotherapy targets in pre-B-ALL</p>
<p>User guide for hemap web application.</p>
<p>Annotation table</p>
<p>Summary of data</p>
<p>Supplementary Data includes Methods and Figures Legends for Supplementary tables. Fig. S1: Sample-level quality control pre-processing; S2: Two-dimensional representations of sample distances; Fig S3: Known vulnerabilities confirmed by Hemap; S4: Evaluation drug screening results confirmation using hemap data; S5: Candidate immunotherapy targets in pre-B-ALL</p>
<p>Annotation table</p>