Heterologous Protein Expression
Explore the design of typical DNA sequences for foreign organisms.
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).
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 |
Explore the design of typical DNA sequences for foreign organisms.
Development and examination of algorithms for the prediction of stable Single-α-Helices
Optimization of Lanthanide positions based on PCS and RDC data.
In the last years as a member of the TCS working group, I was involved for the following courses:
Conference | Title | Download |
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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) |
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 |