Our staff collaborates with researchers in the analysis of their data. Within these projects we sometimes extend our in-depth participation to develop complex tailored analyses including integration and visualization of omics data.
Bioinformatics from an Engineering point of view
BCF collaborator(s); Marcela Dávila. In collaboration with Francisco Gomes, Jennifer Horkoff and Alexander Schliep, Chalmers University of Technology
Bioinformaticians execute frequent, complex, manual and semi-scripted workflows to process data. There are many tools to manage and conduct these workflows, but there is no domain-specific way to textually and diagrammatically document them. Besides the characterization of NGS data tools was investigated with a focus on maintainability and process quality.
BMI epidemiology study
BCF contributor(s): Jari Martikainen. In collaboration with Jenny Kindblom (UGoT)
Factors during fetal life and adolescence can contribute to health and disease in adulthood. The knowledge about the consequences of obesity and overweight during adolescence is far from complete. This project uses population-base records from the Swedish health data registers to understand whether a large BMI change during puberty increases the rist of developing COPD or asthma.
Distribution of the RNase MRP
BCF contributor(s): Marcela Dávila. In collaboration with Tore Samuelsson and Magnus Alm Rosenblad (UGoT)
The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups.
Gall bladder cancer profiling
BCF contributor(s): Sanna Abrahamsson and Marcela Dávila. In collaboration with Justo Bermejo (Heidelberg University)
Research on gallbladder cancer (GBC) has been largely neglected and molecular GBC data is underrepresented in public databases. Cancer cell lines constitute a valuable tool to examine the mechanisms of malignant transformation and identify potential therapeutic targets. Here we use RNA sequencing to characterize 23 commercial hepatobiliary cancer cell lines, including ten GBC cell lines, and provide detailed mutation and gene expression data to the research community.
Integration of omic data in Bipolar Disorder
BCF contributor(s): Katarina Truvé. In collaboration with Keiko Funa (UGoT)
Identification of causative genetic variants leading to the development of bipolar disorder (BD) could result in genetic tests that would facilitate diagnosis. A better understanding of affected genes and pathways is also necessary for targeting of genes that may improve treatment strategies. To date several susceptibility genes have been reported from genome-wide association studies (GWAS), but little is known about specific variants that affect disease development. Here, we performed quantitative proteomics and whole-genome sequencing (WGS).
Molecular regulation of homeostasis in human liver
BCF contributor(s): Marcela Dávila. In collaboration with Christina Jern (UGoT)
Worldwide stroke is the most common cause of disability and the second most common cause of death (GBD, 2020). Blood clot formation is a key mechanistic event in ischemic stroke and is regulated by platelets and hemostatic factors, many of which are produced in the liver. Increased levels of circulating coagulation factors can lead to thrombus formation (e.g. ischemic stroke) and reduced levels can lead to bleeding. Understanding the genetic basis underlying hepatic hemostatic gene expression variability may reveal genetic variants that are important for thrombotic and/or bleeding disorders.