Publications from year: 2023

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• Simulated Design-Build-Test-Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Eng. | 2023
  Publication year: 2023

  Authors: Paul van Lent , Joep Schmitz , Thomas Abeel

  Location: Open publication on Pubmed.
• Rolling Horizon Simulation Optimization For A Multi-Objective Biomanufacturing Scheduling | 2023
  Publication year: 2023

  Authors: Esteban Freydell , Kim van den Houten , Mathijs de Weerdt , Alessandro Nati , Eva Christoupoulou , David M.J. Tax

  Location: Open publication.
• Unveiling microbial biomarkers of ruminant methane emission through machine learning | 2023
  Publication year: 2023

  Authors: Ali May , Chengyao Peng , Thomas Abeel

  Location: Open publication on Frontiers.
• ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology | 2023

  The ability to quantify structural changes of the endoplasmic reticulum (ER) is crucial for understanding the structure and function of this organelle. However, the rapid movement and complex topology of ER networks make this challenging. Here, we construct a state-of-the-art semantic segmentation method that we call ERnet for the automatic classification of sheet and tubular ER domains inside individual cells. Data are skeletonized and represented by connectivity graphs, enabling precise and efficient quantification of network connectivity. ERnet generates metrics on topology and integrity of ER structures and quantifies structural change in response to genetic or metabolic manipulation. We validate ERnet using data obtained by various ER-imaging methods from different cell types as well as ground truth images of synthetic ER structures. ERnet can be deployed in an automatic high-throughput and unbiased fashion and identifies subtle changes in ER phenotypes that may inform on disease progression and response to therapy.

  Publication year: 2023

  Authors: Meng Lu , Charles N Christensen , Jana Marie Weber , Tasuku Konno , Nino F Läubli , Katharina M Scherer , Edward Avezov , Pietro Lio , Alexei A Lapkin , Gabriele S Kaminski Schierle , Clemens F Kaminski

  Location: Open publication on Nature Methods.