R
Rogier J. P. Van Berlo
Researcher at Delft University of Technology
Publications - 4
Citations - 680
Rogier J. P. Van Berlo is an academic researcher from Delft University of Technology. The author has contributed to research in topics: Flux balance analysis & Metric (mathematics). The author has an hindex of 4, co-authored 4 publications receiving 577 citations.
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Shifts in growth strategies reflect tradeoffs in cellular economics
TL;DR: It is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways, and elucidate how the optimization of growth by natural selection shapes growth strategies.
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Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints
Rogier J. P. Van Berlo,Dick de Ridder,Jean-Marc Daran,Pascale Daran-Lapujade,Bas Teusink,Marcel J. T. Reinders +5 more
TL;DR: This work provides a new algorithm that directly uses regulatory up/down constraints based on gene expression data in FBA optimization (tFBA), and shows that changes in gene expression are predictive for changes in fluxes.
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Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels
Rogier J. P. Van Berlo,Wynand Winterbach,Marco J. L. de Groot,Andreas Bender,Peter J.T. Verheijen,Marcel J. T. Reinders,Dick de Ridder +6 more
TL;DR: A novel algorithm is proposed that significantly reduces computation time for finding large MCSs, compared to a number of state-of-the-art approaches, and is demonstrated in an application predicting the transcriptional response of breast cancer cell lines to different drug-like compounds.
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Protein complex prediction using an integrative bioinformatics approach
TL;DR: A new protocol is proposed for combining the likelihoods of protein interaction and the probabilities of complex association as output by the prediction rule as distances and employs hierarchical clustering to find groups of interacting proteins.