A5023011244- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- RNA and protein synthesis mechanisms
- Reproductive System and Pregnancy
- vaccines and immunoinformatics approaches
- Pregnancy and Medication Impact
- Immune Cell Function and Interaction
- Epigenetics and DNA Methylation
- Plant Stress Responses and Tolerance
- Wheat and Barley Genetics and Pathology
- Cancer Mechanisms and Therapy
- Acute Lymphoblastic Leukemia research
- Pancreatic function and diabetes
- Microbial Metabolic Engineering and Bioproduction
- Bioenergy crop production and management
- T-cell and Retrovirus Studies
- Acute Myeloid Leukemia Research
- Single-cell and spatial transcriptomics
- Cytokine Signaling Pathways and Interactions
- Endometriosis Research and Treatment
- Genomics and Chromatin Dynamics
- Blood properties and coagulation
- Erythrocyte Function and Pathophysiology
- Gene expression and cancer classification
University of Turku
2023
Turku Centre for Computer Science
2023
Åbo Akademi University
2023
Linköping University
2016-2022
Linköping University Hospital
2021
Hamline University
1978
Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and typified by widespread alterations DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development targeted therapies prevent relapse key improving prognosis. Whereas mutations demethylating enzyme TET2 are frequent adult malignancies, rare. Here, we analyzed RNA-sequencing data 321 primary T-ALLs, 20 cell lines, 25...
The changes in progesterone (P4) levels during and after pregnancy coincide with the temporary improvement worsening of several autoimmune diseases like multiple sclerosis (MS) rheumatoid arthritis (RA). Most likely immune-endocrine interactions play a major role these pregnancy-induced effects. In this study, we used next generation sequencing to investigate direct effects P4 on CD4 + T cell activation, key event disease. We report profound dampening altering gene protein expression profile...
The serine/threonine-specific Moloney murine leukemia virus (PIM) kinase family (i.e., PIM1, PIM2, and PIM3) has been extensively studied in tumorigenesis. PIM kinases are downstream of several cytokine signaling pathways that drive immune-mediated diseases. Uncontrolled T helper 17 (Th17) cell activation associated with the pathogenesis autoimmunity. However, detailed molecular function PIMs human Th17 regulation yet to be studied. In present study, we comprehensively investigated how three...
T H 1-mediated diseases such as multiple sclerosis (MS) and rheumatoid arthritis (RA) improve during pregnancy, coinciding with increasing levels of the pregnancy hormone progesterone (P4), highlighting P4 a potential mediator this immunomodulation. Here, we performed detailed characterization how affects chromatin transcriptomic landscape early human 1 differentiation, utilizing both ATAC-seq RNA-seq. Time series analysis earlier events (0.5-24 hrs) differentiation revealed that...
In this article we use high-throughput epigenomics, transcriptomics, and proteomics data to construct fine-graded models of the "protein-coding units" gathering all transcript isoforms chromatin accessibility peaks associated with more than 4000 genes in humans. Each protein-coding unit has structure a directed acyclic graph (DAG) can be represented as Bayesian network. The factorization joint probability distribution induced by DAGs imposes number conditional independence relationships...
Abstract Background Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between and protein abundance. We hypothesised that these could be improved mathematical models based on measuring splice variants time delay in translation. Methods characterised time-series primary human naïve CD4 + T cells during early T-helper type 1 differentiation with RNA-sequencing mass-spectrometry proteomics. then performed computational analysis...
Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between and protein abundance. We hypothesised that these could be improved mathematical models based on measuring splice variants time delay in translation. characterised time-series primary human naïve CD4+ T cells during early helper type 1 differentiation with RNA-sequencing mass-spectrometry proteomics. performed computational analysis this system two other key murine...
The simultaneous availability of ATAC-seq and RNA-seq experiments allows to obtain a more in-depth knowledge on the regulatory mechanisms occurring in gene networks. In this article, we highlight analyze two novel aspects that leverage possibility pairing data. Namely investigate causality relationships between transcription factors, chromatin target genes internal consistency omics, here measured terms structural balance sample correlations along elementary length-3 cycles.We propose...
Normal mammalian erythrocytes contain very small amounts of Ca2+. When from most species mammal are subjected to ionophore-induced Ca2+ accumulation, extensive morphologic and metabolic damage occurs. This is not true red cells adult sheep; these appear be totally unresponsive sudden increases in intracellular In contrast, new born lambs responsive influx gradually become during maturation the animal. Although precise reasons for lack response sheep accumulation unknown, this system may...
ABSTRACT The changes in progesterone (P4) levels during and after pregnancy coincide with the temporary improvement worsening of several autoimmune diseases like multiple sclerosis (MS) rheumatoid arthritis (RA). Most likely immune-endocrine interactions play a major role these pregnancy-induce effects. In this study, we used next generation sequencing to investigate direct effects P4 on CD4 + T cell activation, central importance disease. We found that had profound dampening effect altering...
Abstract Background Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between and protein abundance. We hypothesized that these could be improved mathematical models based on measuring splice variants time delay in translation. Methods characterized time-series primary human naïve CD4+ T cells during early T-helper type 1 differentiation with RNA-sequencing mass-spectrometry proteomics. then performed computational analysis...