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1. barberislab/Forkhead-mediated_regulation barberislab/Forkhead-mediated_regulation Public

   A summarizing analysis of Fkh1,2 target genes as indicated by 6 ChIP binding studies and an overexpression and deletion study | https://doi.org/10.1016/j.csbj.2022.03.033

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2. barberislab/ChIP-exo_Fkh1_Fkh2 barberislab/ChIP-exo_Fkh1_Fkh2 Public

   ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast | T.D.G.A. Mondeel, P. Holland, J. Nielsen and M. Barberis | 2019 | htt…

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3. barberislab/Autonomous_minimal_cell_cycle_oscillator barberislab/Autonomous_minimal_cell_cycle_oscillator Public

   Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs | Thierry D.G.A. Mondeel, Oleksandr Ivanov, Hans V. Westerhoff, Wolfram…

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4. barberislab/GEMMER barberislab/GEMMER Public

   GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae | Mondeel TDGA, Crémazy F, Barberis M. | Bioinformatics | 2018 | http://doi.org/10.1093/bio…

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5. HCC_flux_balance_analysis HCC_flux_balance_analysis Public

   Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines | Ewelina Węglarz-Tomczak, Thierry D.G.A. Mondeel, Diewertje…

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6. Systems_Biology_FBA_tutorial Systems_Biology_FBA_tutorial Public

   Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam

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