Assessing protein mass spectrometry data using Percolator – how to weed out valuable information from the noise
Mass spectrometry (MS) is currently the most effective way to analyze protein on a large scale, and hence one of the most important tools for answering those questions. There are still however difficult challenges in analysing the wealth of data MS-based experiments produce.
Computational methods to assess and remedy mapping bias in allele-specific expression and genomic cis-element analysis
Assessing allele-specific expression (ASE) and allele-specific cis-element (ASC) binding or modification from massively parallel sequencing read data is a straightforward way to home in on transcriptional and cis-regulatory variation at the level of single individuals.
D1R-Golf signaling modules segregate into compartments
The development of a large signaling model that takes into consideration the existence of at least two D1R-Golf signaling compartments explains the data pattern.
Deep learning in protein structure predictions
Protein structure prediction is fundamental for our understanding of molecular functions in cells. Fundamental for this is the prediction of contact between interacting residues and the evaluation of the quality of protein models. We are developing novel deep learning approaches for both these problems.
Improved model quality assessment using deep neural networks
Protein structure modeling is crucial for a detailed understanding of the biological function at the molecular level (Wallner&Elofsson, 2003; Wang et al, 2009). In 2003 we developed the first single-model quality estimation program…
MCP Brain-IT: ’Embedding’ – Investigate activation of receptor induced cascades in the context of an active neuronal network
MCP Brain-IT: Comparative analysis (data/models) of the dynamics of networks
MCP Brain-IT: Computational modeling of intracellular signaling cascades in the basal ganglia
The striatum is the input layer of basal ganglia, a set of ancient brain nuclei involved in control of movements, action selection, reinforced learning and in pathologies like drug addiction and Parkinson disease. The striatum receives several chemical signals not only through projections from the cortex (glutamate) and midbrain (dopamine) but also from striatal interneurons like TAN (acetylcholine) and nNOS (NO).
MCP Brain-IT: Implementing models in hardware
MCP Brain-IT: Parameter estimation, uncertainty analysis and global sensitivity analysis of intracellular neuronal models
Within this project we develop a workflow combining uncertainty analysis with global sensitivity analysis and apply this on intracellular models of synapses.