Bioinformatics @ SDU


The University of Southern Denmark is known for excellent research in natural sciences. SDU facilitates the collaboration across departments and faculaties and conducts state-of-the-art Bioinformatics reseach. This webpage provides an overview of SDU's ongoing Bioinformatics Research.

More about Bioinformatics @ SDU

Computational BioMedicine Master Program


SDU offers a modern Master programme in Computational biomedicine focusing towards applied computational projects associated with the health sector and the biotech and pharmaceutical industries.

Computer-based methods for modelling, simulation and statistics play a fundamental role in modern science and health research, along with databases and bioinformatics.

Interested? Learn more!

Core Bioinformatics


Richard Röttger

Computer Scientist
Richard Röttger mainly focuses on the development of efficient algorithms for the analysis of biological networks and large-scale biomedical datasets. He particularly focuses on unsupervised machine learning and the integration of heterogeneous datasets. Only the efficient combination of several types of biological datasets allows for a deeper understanding on how organisms manage cell responses, reproduction, and adaption to changing environmental conditions.

Main research Interests:

  • Machine Learning
  • Clustering
  • Genomic Analysis

Webpage: here

Veit Schwaemmle

Veit Schwämmle is an expert in the analysis of mass spectrometry data, bioinformatics and biostatistics with focus on data analysis and algorithm development for the characterization and interpretation of proteins and their post-translational modifications (PTMs). He uses methods adapted from statistics, bioinformatics, and general computer modeling approaches to improve information depth and quality in proteomics experiments. His current research interest focuses on applying PTM research to problems in functional biology and biomedicine, with the aim to provide new algorithms for the analysis of top-down and middle-down mass spectrometry data. His group is currently developing algorithms and smart visualization methods to characterize protein modifications and their crosstalk to provide deep insight into the regulatory programs of the cell.

Webpage: here

Jan Baumbach

Computer Scientist, former member
The Computational Biology research group was established in October 2012 at the Department of Mathematics and Computer Science (IMADA) at the University of Southern Denmark (SDU). It emerged from the Computational Systems Biology group, founded in March 2010 at the Max Planck Institute for Informatics. Jan Baumbach will move to Munich but still supervises PhD students here at SDU.

Active PhD students & PostDocs:

  • Christian Wiwie
  • Philipp Weber
  • Simon Larsen
  • Anders Christiansen
  • Maria Louise Elkjær
  • Tobias Frisch
  • Weilong Li
  • Marisol Salgado Albarrán
  • Alexander Gulliver Bjørnholt Grønning

Webpage: here

Applied Bioinformatics


Qihua Tan

Qihua is Professor of genetic epidemiology at the Dept. of Public Health at SDU. His research focuses on statistical analysis of (epi)genomic data especially on twins and its application to understand diseases, aging and development. Tan's research focuses on genetics and genomics of human aging and aging-related diseases using biostatistics and bioinformatics approaches applied to genomics, transcriptomics, epigenomics and proteomics data. In the recent years, his research on epigenomics includes exciting studies on homocygoteous twins discordant for diseases and other phenotypes, as well as on aging elderly cohorts reporting important findings on genomic variations and biological pathways implicated in human complex diseases and aging phenotypes.

Webpage: here

Torben Kruse

Torben is head of the Centre of Clinical Genomics at Odense University Hospital (OUH) and the Institute for Clinical Research at SDU. He was scientific coordinator of the DBCG Translational Research Centre and is board member in the scientific committee of the Danish National Programme for Personalized Medicine. He developed computational methods for making the massive next-generation sequencing (NGS) data emerging nowadays usable in clinical practice. His main research focus lies on identification of driver mutation profiles, amongst others for the prediction of tumor recurrence after surgery and for the design of optimized cancer treatment profiles.

Webpage: here

Workgroups


Proteomics

Our research focuses on the development and application of sensitive and specific mass spectrometry based methods for biomolecule identification and microcharacterisation. We study proteins, oligonucleotides, lipids and carbohydrates by MALDI and ESI mass spectrometry. We also use a variety of chemical, biochemical and bioinformatics techniques.

Affiliated PIs

Functional Genomics & Metabolism

In the Functional Genomics & Metabolism Research Unit, we use advanced genomic tools to understand the transcriptional plasticity and regulatory networks involved in differentiation, metabolism and disease of mammalian cells.

Affiliated PIs

Center of Excellence

Center for Functional Genomics and Tissue Plasticity

Clinical Genomics

Focus of the research lies in clinical genomics, transcriptomics and epigenomics. Computational methods are developed for making the massive next-generation sequencing (NGS) data emerging nowadays usable in clinical practice. Another research focus is on genetics and genomics of human aging and aging-related diseases using biostatistics and bioinformatics approaches applied to genomics, transcriptomics, epigenomics and proteomics data.

Affiliated PIs

Metabolomics / Lipidomics

The major theme of our research revolves around how metabolism and signalling are coordinated to meet the nutritional needs of cells and organism with emphasis on how lipids are synthesized, transported and metabolized and how they act as signalling molecules. We aim at understanding the relationship between lipid metabolism and lipid mediated signalling in the development of various diseases like obesity, diabetes, neurological disorders and cancers.

Affiliated PIs

Bio Imaging

The research is focused on the use of advanced Bioimaging techniques to answer fundamental questions in biological systems. With the techniques we develop, we can extract more information than was previously available from simple images.

Affiliated PIs

Epidemiology

We study human development and aging and the link between them, using data from large Danish population-based surveys. The Danish health registers and The Danish Twin Registry are valuable resources in the study of gene-environment interactions in human development and aging.

Affiliated PIs

Support Facilities

SDU offers great support for bioinformatics. SDU hosts Scandinavia's largest super computer ABACUS, a state-of-the-art super-cumputer including GPU nodes facilitating deep learning. Furthermore, SDU is part of the ELIXIR network Denmark and hosts the Danish Twin Registry, an unprecedented dataset source for cutting-edge research.

Further Information


For further information reagrding Bioinformatics at SDU visit the corresponding departments:

IMADA

Department of Mathematics and Computer Science

BMB

Department of Biochemistry and Molecular Biology

HEALTH

Faculty of Health Sciences

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