Algorithmic Bioinformatics

Projects (former)

Algorithm Engineering for Genome Comparison

Knut Reinert

    DFG SPP 1307 There are two main research goals in the proposed project: (1) To design, analyze, implement, and experimentally validate efficient and versatile genome comparison algorithms based upon suitable computation models and (2) to integrate all required algorithmic components in the SeqAn library for biological sequence analysis for the purpose of disseminating the core algorithms and data structures to the bioinformatics and algorithm engineering community. The software ...

Algorithm Engineering for High Throughput Sequencing Data

Knut Reinert

During the last five years modern sequencing technologies have brought a super-exponential growth of sequencing capacities. With the current sequencing technologies it is possible to sequence up to 30 billion nucleotides per day. The tremendous growth threatens to swamp the available data archives of sequencing centers. Furthermore, the costs of sequencing dramatically decreased due to the technically matured sequence instruments making these technologies available for the broad scientific ...

BioStore

Knut Reinert, David Weese

    The VIP BioStore project addresses the current bottleneck in NGS based data analysis. It is meant to be a catalyst for bringing state-of-the-art algorithmic research to a broader community of developers and at the same time enable researchers in the biomedical sciences to have easy access to such tools via a distribution and execution platform.

Predict IV

Knut Reinert

      Predict IV (Collab. large-scale integrating project) The goal of Predict IV is the profiling of the toxicity of new drugs: A non animal-based approach integrating toxico-dynamics and biokinetics. Our group, as a partner, develops algorithms for iTRAQ labeled MS measurements.

BlueIon

Knut Reinert

  BlueIon Ziel ist die Entwicklung eines neuartigen Detektors BlueION für die Hochleistungsflüssigkeitschromatographie (HPLC) bzw. die schnelle Ultra-HPLC (UHPLC). HPLC und UHPLC werden in der Routineanalytik zum Nachweis von sehr geringen Substanzmengen in komplexen flüssigen Mischungen angewandt. Herausragende Eigenschaften des Detektors sind hohe Messgeschwindigkeiten, hohe Empfindlichkeit, vergleichsweise höhere Identifizierung bei geringeren Kosten, Eignung für die multidimensionale ...

MARINA

Knut Reinert

        MARINA (Managing Risks of Nanomaterials) is a large-scale integrating collaborative project concerned with health and safety issues related to ENM. Understanding and mitigating the risks of nanomaterials to human health and the environment is a global challenge, and the European platform MARINA aims at playing a key role in this important arena.Our part in the MARINA project is the implementation of methods for toxicological profiling, using toxicogenomics, proteomics, and ...