Notes

Bioinformatics / Mathematical Modelling Platform

Altuna Akalin

Profile

The application of bioinformatics tools, statistics, and machine-learning methods is a prerequisite for today’s data-driven biomedical research. Computational analyses of large data sets from high-throughput experiments may help to unravel complex diseases.

High-throughput technologies in molecular medicine, such as next-generation genome sequencing, produce vast amounts of data that may help to characterize complex diseases. However, powerful bioinformatics tools for data analysis and interpretation are necessary to understand these high-volume data sets. The application of statistics and machine-learning methods to experimental results on a broad scale has thus become an essential part of biomedical research.

The Bioinformatics Platform is a research group within the Berlin Institute of Medical Systems Biology (BIMSB) at the Max Delbrück Center (MDC). The platform creates and maintains bioinformatics tools and databases, and studies molecular mechanisms using externally available and/or in-house computational techniques. In addition, the platform provides collaboration opportunities and support for MDC scientists.

Unraveling complex disease

As a general principle, we aim at gaining an understanding of the genetic and epigenetic control mechanisms of cellular differentiation and of complex diseases such as cancer by performing computational analyses of high-throughput data sets. These data are derived, for instance, from microarrays and next-generation sequencing experiments.

Ultimately, we aim to uncover genomic and epigenomic anomalies and the interactions between them that lead to disease. In doing so, we strive to maintain state-of-the-art expertise in computational biology and data analysis, and to develop bioinformatics tools and techniques that are relevant, reproducible, and well documented.

    Further information

    Team

    Our tools

    Studying biological mechanisms with computational tools

    We supply infrastructure and expertise for the bioinformatics and scientific IT needs of researchers, providing hardware and software for research-oriented tasks. We have various web-based interactive tools at our disposal, e.g. a local copy of the UCSC (University of California, Santa Cruz) Genome Browser, Shiny Server for interactive analysis, and an internal Galaxy server. We also have access to bioinformatics software solutions such as methylKit, genomation, RCAS, netSmooth, and a GNU Guix bioinformatics software repository.

    We provide additional specialized IT services geared towards bioinformatics end users as well as a mobile teaching system for scientists. In addition, we offer courses and consultation sessions on bioinformatics, IT skills, and programming.

    We provide additional specialized IT services geared towards bioinformatics end- users as well as a mobile teaching system for scientists. In addition, we offer courses and consultation sessions on bioinformatics, IT skills, and programming.

    Databases & web apps

    Software

    Other IT services

    • Reproducible bioinformatics software deployed at workstations and within the cluster via GNU Guix
    • Virtual machines that can deploy publication-related web apps and databases such as DoRiNA and circBase

    Publications

    News

    Dr. Altuna Akalin
    Dr. Altuna Akalin