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MF1: Bioinformatics

Head:
Max von Kleist
Deputy:
Oliver Drechsel

Subject

Our work focuses on developing fast and robust bioinformatics procedures for high-throughput experiments, the main aim being to clarify issues related to diagnosing and characterizing pathogens. The scope of our work ranges from formulating the respective question in mathematical terms to developing or adapting algorithms, evaluating biomedical data, and, finally, to implementing and publishing open-source software.

We develop novel bioinformatics algorithms and statistical procedures, but also provide a bioinformatics core service for data analysis. Both areas of our work are closely interlinked. By analyzing data we often identify novel research questions and tools that we developed in bioinformatics research are rapidly transferred to application as part of the core service.

Technological advances in high-throughput processes are allowing previously unimagined insights into biomedical contexts. Today, billions of genetic bases can be sequenced and millions of mass positions can be analyzed for protein identification in a single experiment. The ongoing, rapid growth of technical possibilities can thus generate datasets for single experiments that fill entire computer hard drives. The risk is, however, that the process of data analysis will be unable to keep up with the pace of data acquisition.

The main challenge with high-throughput experiments, therefore, is not so much the actual collection of information as data analysis and the automated extraction of relevant information. In view of the huge amount of data and their structures, we require special algorithms if we are to obtain prompt and reliable results.

Our work focuses on next-generation sequencing data for analyzing DNA and RNA sequences, as well as on mass spectrometry measurements for protein identification and structure predictions. In this context, we are especially interested in the integration of complementary data sources. It is also essential for our bioinformatics procedures and data analysis to consider the statistical effects of high-dimensional data and to determine accurate error rates to avoid potentially misleading interpretations. Another key aspect for us is to ensure the robustness of the algorithms and the integration of experiments.

We develop and adapt machine learning algorithms and analysis methods for these amounts of data and prepare them for practical application in collaboration with experimental groups.

Vacancies

Vacancies are published at Robert Koch Institute vacancies.

We are always looking for dedicated and highly motivated students for projects in the context of internships, or theses, and as research assistants. Please contact the head of unit for these and other questions.

Software

An important objective of our group is to integrate the methods we have developed into freely available software. We have been and are involved in several projects available from https://gitlab.com/rki_bioinformatics/
See also here http://www.disease-control.org

Date: 09.01.2020

Publications

  • Duwal S, Dickinson L, Khoo S, von Kleist M (2019): Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis.
    PLoS Comput. Biol. 15 (1): e1006740. Epub Jan 30. doi: 10.1371/journal.pcbi.1006740. more

  • Duwal S, Dickinson L, Khoo S, von Kleist M (2018): Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes
    PLoS Comput Biol. 14 (6): e1006155. Epub Jun 14. doi: 10.1371/journal.pcbi.1006155. more

  • Smyth RP, Smith MR, Jousset AC, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, Paillart JC, von Kleist M, Marquet R (2018): In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging
    Nucleic Acids Res. 46 (9): e57. doi: 10.1093/nar/gky152. more

  • Smith MR, Smyth RP, Marquet R, von Kleist M (2016): MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments
    Bioinformatics 32 (21): 3369-3370. Epub 2016 Jul 10. more

  • Yousef KP, Meixenberger K, Smith MR, Somogyi S, Gromöller S, Schmidt D, Gunsenheimer-Bartmeyer B, Hamouda O, Kücherer C, von Kleist M (2016): Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses
    J. Acquir. Immune Defic. Syndr. 73 (3): 356-363. Epub Jul 5. doi: 10.1097/QAI.0000000000001122. more

  • Smyth RP, Despons L, Huili G, Bernacchi S, Hijnen M, Mak J, Jossinet F, Weixi L, Paillart JC, von Kleist M, Marquet R (2015): Mutational interference mapping experiment (MIME) for studying RNA structure and function
    Nat Method 12 (9): 866-72. doi: 10.1038/nmeth.3490. Epub 2015 Aug 3. more