A5017066581- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
- Circadian rhythm and melatonin
- Bioinformatics and Genomic Networks
- Nutrition, Genetics, and Disease
- Plant Genetic and Mutation Studies
- Occupational Health and Safety Research
- Digestive system and related health
- Immunodeficiency and Autoimmune Disorders
- TGF-β signaling in diseases
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Colorectal Cancer Treatments and Studies
- Microtubule and mitosis dynamics
- T-cell and B-cell Immunology
- Cytokine Signaling Pathways and Interactions
- Genomic variations and chromosomal abnormalities
- Cancer Immunotherapy and Biomarkers
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Genomics and Chromatin Dynamics
- Healthcare Systems and Public Health
- dental development and anomalies
- Lymphoma Diagnosis and Treatment
- Polar Research and Ecology
- RNA modifications and cancer
University of Helsinki
2008-2023
Aalto University
2016-2019
Institute for Molecular Medicine Finland
2010
Helsinki University Hospital
2010
Aarhus University Hospital
2010
Coordinated efforts to collect large-scale data sets provide a basis for systems level understanding of complex diseases. In order translate these fragmented and heterogeneous into knowledge medical benefits, advanced computational methods analysis, integration visualization are needed.We introduce novel framework, Anduril, translating testable predictions. The Anduril framework allows rapid with state-of-the-art existing in bio-databases. automatically generates thorough summary reports...
Defects in the mismatch repair system lead to microsatellite instability (MSI), a feature observed ∼ 15% of all colorectal cancers (CRCs). Microsatellite mutations that drive tumourigenesis, typically inactivation tumour suppressors, are selected for and frequently detected MSI cancers. Here, we evaluated somatic repeats 790 genes chosen based on reduced expression CRC existence coding mononucleotide repeat 6-10 bp length. All were initially sequenced 30 primary samples whenever frameshift...
The circadian clock regulates daily variations in physiologic processes. CLOCK acts as a regulator the apparatus controlling expression of other genes, including PER1. Clock genes have been implicated cancer-related functions; this work, we investigated possible target somatic mutations microsatellite unstable colorectal cancers. Combining microarray gene data and public sequence information, identified 1 790 putative novel instability (MSI) genes. A total 101 MSI carcinomas (CRC) were...
Abstract A common single nucleotide polymorphism (SNP), rs6983267, at 8q24.21 has recently been shown to associate with colorectal cancer (CRC). Three independent SNP association studies showed that rs6983267 contributes CRC odds ratios (OR) of 1.17 1.22. Here, we genotyped a population-based series 1,042 patients and 1,012 healthy controls for determined the contribution in Finland, using germ line DNA, as well respective DNA heterozygous patients. The comprehensive clinical data available...
Abstract Background Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily growth factors. They known for their roles in regulation osteogenesis and developmental processes and, recent years, evidence has accumulated crucial functions tumor biology. BMP4 BMP7, particular, have been implicated breast cancer. However, little is about BMP target genes context tumor. We explored effects BMP7 treatment on global gene transcription seven cancer cell lines during a 6-point time...
Despite the continuous development of occupational safety, prevalence work-related head injuries is excessive. To promote prevention, we conducted a study evaluating risks and pathways that precede in different economic activity sectors.In Finland, more than 90% employees are covered by inclusive statutory workers' compensation. We obtained data on 2010-2017 from an insurance company database. The European Statistics Accidents at Work (ESAW) variables represented characteristics accidents...
The transcriptional network and protein regulators that govern T helper 17 (Th17) cell differentiation have been studied extensively using advanced genomic approaches. For a better understanding of these biological processes, we moved step forward, from gene- to protein-level characterization Th17 cells. Mass spectrometry-based label-free quantitative (LFQ) proteomics analysis were made in vitro differentiated murine induced regulatory (iTreg) More than 4,000 proteins, covering almost all...
Frameshift mutations frequently accumulate in microsatellite-unstable colorectal cancers (MSI CRCs) typically leading to downregulation of the target genes due nonsense-mediated messenger RNA decay. However, frameshift that occur 3′ end coding regions can escape decay, which has largely been ignored previous works. In this study, we characterized decay-escaping MSI CRC an unbiased, genome wide manner. Combining bioinformatic search with expression profiling, identified were predicted decay...
Malignant transformation in ulcerative colitis (UC) is associated with pronounced chromosomal instability, reflected by aneuploidy. Although aneuploidy can precede primary cancer diagnosis UC for more than a decade, little known of its cellular consequences. Whole-genome gene expression analysis was applied to noninflamed colon mucosa, mucosal biopsies patients UC, and UC-associated carcinomas (UCCs). DNA image cytometry used stratify samples into ploidy types. Differentially expressed genes...
Mechanistic models based on ordinary differential equations provide powerful and accurate means to describe the dynamics of molecular machinery which orchestrates gene regulation. When combined with appropriate statistical techniques, mechanistic can be calibrated using experimental data and, in many cases, also model structure inferred from time-course measurements. However, existing are limited sense that they rely assumption static network cannot applied when transient phenomena affect,...
Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because truly are generally unknown and be either reported GWAS studies other proxy their linkage disequilibrium. Hence, a comprehensive pipeline SNP co-localization analysis that utilizes all relevant information about both genotyped proxies needed.We developed an R package...
<p>Supplementary Figures S1-S3 and Supplementary Tables S1-S3.</p>
<p>Supplementary Figures S1-S3 and Supplementary Tables S1-S3.</p>
<div>Abstract<p>The circadian clock regulates daily variations in physiologic processes. <i>CLOCK</i> acts as a regulator the apparatus controlling expression of other genes, including <i>PER1</i>. Clock genes have been implicated cancer-related functions; this work, we investigated possible target somatic mutations microsatellite unstable colorectal cancers. Combining microarray gene data and public sequence information, identified 1 790 putative novel...
<div>Abstract<p>The circadian clock regulates daily variations in physiologic processes. <i>CLOCK</i> acts as a regulator the apparatus controlling expression of other genes, including <i>PER1</i>. Clock genes have been implicated cancer-related functions; this work, we investigated possible target somatic mutations microsatellite unstable colorectal cancers. Combining microarray gene data and public sequence information, identified 1 790 putative novel...
Abstract Genomic instability drives tumorigenesis by allowing the accumulation of genetic alterations that provide cells with growth advantage. Microsatellite-instability (MSI) and underlying mutator phenotype caused a defect in mismatch repair (MMR) functions is hallmark Lynch syndrome, also observed subset all colorectal cancers (CRC). In defective MMR system, spontaneous length changes repetitive microsatellite sequences accumulate over genome at highly increased rates. At coding regions...
Einleitung: Patienten mit Colitis ulcerosa (UC) haben ein erhöhtes Risiko für das Entstehen kolorektaler Karzinome. Trotz Vorsorgekoloskopien werden frühe Läsionen übersehen und Karzinome erst spät detektiert.
Abstract Bone morphogenetic proteins (BMPs) are members of the transforming growth factor beta superfamily factors. They well-known for their key roles in regulation various developmental processes and bone formation, but recent years, evidence has also accumulated crucial contribution tumor biology. In particular, BMP4 BMP7 have been implicated breast cancer pathogenesis. However, little is known about BMP target genes context cells. Here, we used whole-genome microarrays to explore effects...
<h3>Objectives</h3> Despite of continuous development occupational safety, there is still an excess work-related head injuries. Prevention injuries can be promoted by evaluating risks and pathways events preceding <h3>Methods</h3> In Finland, more than 90% employees are insured with inclusive mandatory coverage. Data on in 2010–2017 was obtained from a workers' compensation insurer database. European Statistics Accidents at Work (ESAW) variables represented the conditions accidents...