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Research Team

Functional Bioinformatics

About this team

About this team

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Objectives Background 

Functional Analyses in Bioinformatics, in contrast to the sister bioinformatics disciplines of Structural Analysis and Sequence Analysis, focuses on molecular profile analysis, pattern detection in mega-variate data, biosignature detection, and network analyses. Molecular profiles can be data on various OMICs levels, i.e. transcriptome, metabolome, miRNA profiles, genome-wide SNP-data, and next generation sequencing data (targeted 16S rRNA genes, (meta-)genome-wide, RNAseq, CRISPR results), and combinations of these kinds of data. These profiles are analysed for their correlation and functional relationships regarding the clinical phenome, consisting of clinical traits and modern high-dimensional measurements. Time-resolved data series of the types outlined above are appropriate for true systems biological reverse engineering, which is, especially for high-throughput data, overlapping with functional bioinformatics. Also computational biology is overlapping, when it focuses on different levels of functional modelling of biological function, ranging from detailed differential equation systems to qualitative modelling using Bayesian modelling or action languages.

 

Specific Objectives for Functional Bioinformatics at Örebro University

The group is integrated within Örebro University Research Environments of NGBI (Nutrition-Gut-Brain-Interactions), Cardiovascular Research Centre, and ÖLSC (Örebro Life Science Center), with a special focus of analysing interactions of molecular profiles and microbiota distributions in healthy and diseased patients, both with respect to candidate biosignature mining as well as for investigating causal structures taking a systems biological approach. Our aim is to contribute to the identification of the defining patterns in gut-microbiome space (bridging composition and diverse functional levels), governing adaptability to disease challenges and ability for resilience. Molecular and immune profiling of different tissues related to the gut-brain axis are studied from a systems bioinformatics point of view. Recently, we began to analyse functional brain imaging data, on different functional levels, including differential connectivity analysis, to find interactions with gut status and the status of the gut-brain axis signalling.  

 

 

Special Competences

Analysis of functional molecular high-throuput datasets (OMICs data): transcriptome (microarray gene expression data), proteome, metabolome, miRNA-profiles, SNP-data, microbiome profiles – univariate by regularized approaches, ,ultivariate by unsupervised and supervised statistical learning, geneset enrichment methods, as well as molecular network analyses (both with Ingenuity® IPA, and based on STRING network structure).

Analysis of Next Generation Sequencing (NGS) data: Whole genome sequencing (human and metagenomic), targeted sequencing (16S rRNA genes, exome sequencing etc), RNAseq, CRISPR-results. Large projects are run on the UPPMAX computer cluster.

Application / interpretation / development of multivariate analysis methods from the field of machine learning for biosignature detection and validation

  • supervised applications: biomarker and biosignatures, PLS-methods
  • un-supervised applications: clustering, PCA/ICA, factor analysis
  • interpretation: detection of structures of the regulatory system (genotype-phenoytype-map) with systems biological focus
  • integrative analyses: using different profiling data and/or different clinical trait data at the same time to both get a better classification and improved functional understanding of the discriminative bio-medical processes
  • recent development focusses:
                 - biosignatures from pooled data
                 - using a priori knowledge of functional network structures
  • qualitative modelling
                 - system properties of regulatory modules
                 - integrating different levels of knowledge for modelling of the regulatory system
  • biostatistical/bioinformatics counselling

 

 

 

External cooperation partners

 

  

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Researchers

Research Projects

Research funding bodies

  • The Knowledge Foundation
  • Lantmännen, Swedish agricultural cooperative