Research

  • BioDWH2 is an open-source, automated, and graph-based data warehouse and mapping tool. Centered around a workspace concept and with an expansive number of data source modules, creating a knowledge graph (KG) is easier than ever before. Using the web-based configurator, KG creation can be done by everyone without computer-science background. BioDWH2 is available here.
  • NAR db status is a database meta-registry for NAR published databases. Annotations for publications, URLs, cross-references, availability, updates, and more are manually curated. Curation is transparent and all annotations are available for download. NAR db status is available here.
  • miRNAverse is a database meta-registry for miRNA databases. Annotations for publications, URLs, cross-references, availability, updates, and more are manually curated. Curation is transparent and all annotations are available for download. miRNAverse is available here.
  • Trials Annotator is a meta-registry for terminated clinical trials from ClinicalTrials.gov. The trials are manually annotated for their termination reason, such as side effects, supply issues, futility, and failed recruitment. These annotations help produce a gold standard for futile drug clinical trials usable for drug repurposing. Trials Annotator is available here.
  • PIMBase. PIMBase is available here.

2025

  • A. F. F. Hansel-Frose, C. Brinkrolf, M. Friedrichs, B. Dallagiovanna, L. Spangenberg. Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes. Journal of Integrative Bioinformatics, 2025.
    doi
  • M. Friedrichs. Automated Graph-Based Data Integration and Information Fusion: An Open-Source Ecosystem of Tools With a Focus on Maintainability and Usability. Bielefeld: Universität Bielefeld, 2025.
    doi
  • M. Friedrichs, C. Königs. NAR db status Version 2 and miRNAverse: Over Two Years of Manual Meta-Registry Curation and Updates. arXiv, 2025.
    doi

2024

  • C. Türker, C. Panse, B. Sommer, M. Friedrichs, R. Hofestädt. International symposium on integrative bioinformatics 2024 – editorial. Journal of Integrative Bioinformatics, 2024.
    doi
  • A. F. F. Hansel-Frose, M. Friedrichs, J. Allmer. MicroRNA Databases. in L. M. Vaschetto (eds): miRNAs, Human Health and Diseases, Springer Nature Switzerland, 2024.
    doi
  • A. F. F. Hansel-Frose, J. Allmer, M. Friedrichs, H. Geremias dos Santos, B. Dallagiovanna, L. Spangenberg. Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs. Front. Mol. Biosci. 11, 2024.
    doi

2023

  • M. Friedrichs, C. Königs. A web-based platform for the annotation and analysis of NAR-published databases. PLoS ONE 18(10), 2023.
    doi
  • M. Friedrichs. A web-based annotation tool for clinical trial failure reasons. GMS Med Inform Biom Epidemiol 2023.
    doi

2022

  • C. Königs, M. Friedrichs, T. Dietrich. The heterogeneous pharmacological medical biochemical network PharMeBINet. Sci Data 2022.
    doi
  • M. Friedrichs. Automation in Graph-Based Data Integration and Mapping. in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
    doi
  • M. Friedrichs. Data Integration Applications in Medical Information Systems. in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
    doi

2021

  • M. Friedrichs. BioDWH2: an automated graph-based data warehouse and mapping tool. Journal of Integrative Bioinformatics, 2021.
    doi
  • M Edich, M. Friedrichs. EvoDock: Optimization of protein-ligand binding interfaces. Acta Crystallographica Section A: Foundations and Advances, 2021.
    doi

2019

  • M. Friedrichs, A. Shoshi, P.J. Chmura, J. Ison, V. Schwämmle, F. Schreiber, R. Hofestädt, B. Sommer. JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools. Journal of Integrative Bioinformatics 16(4), 2019.
    doi
  • M. Friedrichs, A. Shoshi. History and Future of KALIS: Towards Computer-assisted Decision Making in Prescriptive Medicine. Journal of Integrative Bioinformatics 16(3), 2019.
    doi

2018

  • A. Shoshi, R. Hofestädt, O. Zolotareva, M. Friedrichs, A. Maier, V. A. Ivanisenko, V. E. Dosenko, E. Yu. Bragina. GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. Journal of Integrative Bioinformatics 15(4), 2018.
    doi
  • M. Friedrichs, A. Shoshi, M. Kleine. Data-Driven Assessment of Potentially Inappropriate Medication in the Elderly. IOS Press in the Studies in Health Technologies and Informatics series 253:125-129, 2018.
    doi

Industry Work

Voxel tentacle dancing
AniVoxel is the first tool for grid-constrained skeletal voxel animations, allowing users to easily rig and animate voxel models. Traditionally, voxel models are animated by manually adjusting a model frame by frame, or by breaking the voxel alignment. AniVoxel uses the simplicity of skeletal animation systems while retaining the voxel alignment. Additional features such as voxel interpolation, smear frames, per-frame visibility, and many more provide users with a powerful and expressive animation tool.
[Website, itch.io]
Working at Hacon, i was part of the HAFAS.mobile Android app development team. Among other things, Hacon develops mobility apps for public transport and other mobility options, serving a large volume of route suggestions each day, all across the world. Aside from several core features and app upgrades (Mobiliteit.lu), my main project was the development of the multimodal SBB Reiseplaner app.
Working at exDream and later on for DeltaEngine as a freelancer, i was primarily part of the team developing the DeltaEngine game engine. Developed from the ground up in .NET, a sophisticated build system allowed the deployment of games to all major platforms, including mobile and console. I worked on the build system, platform support, multimedia playback, input, OpenGL/DirectX graphics, and much more. Multiple titles have been successfully released using DeltaEngine during my time: Zombie Party (iPad), SoulCraft, Heroes of SoulCraft, and Arena Wars II.

Other Projects

blender_magicavoxel is an open-source Blender addon for importing MagicaVoxel .vox files. It is the only up-to-date and actively maintained addon with 10k+ downloads across all sites and also published in the offical Blender 4.2+ extensions registry. Features include multiple meshing modes, ability to join models, colors, materials, texture atlas generation, and more.
[Blender extensions, GitHub, itch.io]
blender_magicavoxel
  • IJMIMT was a plugin for the popular ImageJ image editor. It was able to use multiple microscopy images in different spectra as input to detect points of interest (POI), let the user choose multiple points, and then automatically generate a cropped montage with sub-image labels for publication.
    IJMIMT example image
  • FastMol was a small experiment for a web-based molecular 3D-structure viewer using the (at the time) new WebGL API.
    FastMol example image