About me

Currently, I am researcher at the Institute of Computer Science of the University of Göttingen. I completed the PhD at the MPI for Biophysical Chemistry in the group "Systems Biology of Motor Proteins" of PD Martin Kollmar followed by the work in the research group "Theoretical Computer Science and Algorithmic Methods" (TCS) under the supervision of Prof. Stephan Waack.

My research revolves around the application of Information theory based methods in the field of Bioinformatics. This focuses on the examination of Markov-Chain models (MC) applied to the design of typical genes for heterologous protein expression and its practical experimental evaluation. Further fields of my research interests are the biological sequence analysis and the prediction of protein structures, especially the study of coiled-coil prediction and the identification of single-alpha-helix domains (SAHs).

Research Positions

May 2015 - Feb. 2022 Ph.D in Bioinformatics
"New approaches and software for sequence function prediction and gene design integrating specific knowledge on protein structure and translation"
GAUSS: "PhD-program of Computer Science" (PCS)
Prof. Dr. Stephan Waack, PD Dr. Martin Kollmar
Dept. Theoretical Computer Science und Algorithmic Methods
Institute of Computer Science - Georg-August-University Göttingen
Jan. 2014 - Apr. 2015 Ph.D in Bioinformatics
"The human mutually exclusive exome in aging and disease"
GGNB PhD-program: "Biomolecules: Structure - Function - Dynamics"
PD Dr. Martin Kollmar, Prof. Dr. Stephan Waack
Research Group "Systems Biology of Motor Proteins"
Dept. NMR-based Structural Biology
Max-Planck Institute for Biophysical Chemistry, Göttingen

Recent Projects

Heterologous Protein Expression

Explore the design of typical DNA sequences for foreign organisms.

Protein Structure Prediction

Development and examination of algorithms for the prediction of stable Single-α-Helices

Structure determination of protein–protein complexes

Optimization of Lanthanide positions based on PCS and RDC data.

Teaching

In the last years as a member of the TCS working group, I was involved for the following courses:

Contact Information

  • Address

    Dr. Dominic Simm
    University of Göttingen
    Institute of Computer Science
    Goldschmidtstr. 7
    37077, Göttingen
    Deutschland

Talks and Poster Sessions

Conference Title Download
Coiled-coil prediction and PCS/RDC-based structure determination
(MPI-NMR: Department Seminar 2015)
(pdf)
ECCB 14 Waggawagga: a Web Service for the Comparative Visualization of Coiled- Coil Predictions and the Detection of Charged Single-Alpha-Helices (CSAHs) (pdf)
GCB 2013 WaggaWagga: a Web Service to Compare and Visualize Coiled-Coil Predictions, and to Assess the Oligomerisation State of Coiled-Coils. (pdf)

Publications

Simm D. (2022), "New approaches and software for sequence function prediction and gene design integrating specific knowledge on protein structure and translation". Thesis at Georg-August-Universität Göttingen.
Simm D., Popova B., Braus G. H., Waack S. and Kollmar M. (2022) Design of typical genes for heterologous gene expression. Scientific Reports. 12(9625).
doi: 10.1038/s41598-022-13089-1
Simm D., Hatje K., Waack S. and Kollmar M. (2021) Critical assessment of coiled-coil predictions based on protein structure data. Scientific Reports. 11(12439).
doi: 10.1038/s41598-021-91886-w
Hatje, K., Mühlhausen, S., Simm, D., Kollmar, M. (2019) The Protein-Coding Human Genome: Annotating High-Hanging Fruits. BioEssays. 41(1900066).
doi: 10.1002/bies.201900066
Kollmar M., Simm D. (2018) Identifying Sequenced Eukaryotic Genomes and Transcriptomes with diArk. In: Kollmar M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY.
doi: 10.1007/978-1-4939-7737-6_1
Simm D. and Kollmar M. (2018) Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes. PLoS ONE 13(2): e0191924.
doi: 10.1371/journal.pone.0191924
Hatje K., Rahman R., Vidal R., Simm D., Hammesfahr B., Bansal V., Rajput A., Mickael M., Sun T., Bonn S. and Kollmar M. (2017) The landscape of human mutually exclusive splicing. Molecular Systems Biology. 13 (12): 959.
doi: 10.15252/msb.20177728
Simm D., Hatje K. and Kollmar M. (2017) Distribution and evolution of stable single alpha-helices (SAH domains) in myosin motor proteins. PLoS ONE 12(4): e0174639.
doi: 10.1371/journal.pone.0174639
Kollmar M., Hammesfahr B., Simm D. (2015) diArk – the database for eukaryotic genome and transcriptome assemblies in 2014. Nucleic Acids Res. 43 (D1): D1107-D1112.
doi: 10.1093/nar/gku990
Simm D., Hatje K. and Kollmar M. (2014) Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains). Bioinformatics. 31 (5): 767-769.
doi: 10.1093/bioinformatics/btu700
Last Update: 01-May-2022