Publications
2024
Hepatic ChREBP orchestrates intrahepatic carbohydrate metabolism to limit hepatic glucose 6-phosphate and glycogen accumulation in a mouse model for acute Glycogen Storage Disease type Ib
K.A. Krishnamurthy, M.G.S. Rutten, J.A. Hoogerland, T.H. van Dijk, T. Bos, M. Koehorst, M.P. de Vries, N.J. Kloosterhuis, H. Havinga, B.V. Schomakers, M. van Weeghel, J.C. Wolters, B.M. Bakker, M.H. Oosterveer
Mol Metab 79 (2024). doi: 10.1016/j.molmet.2023.101838
2023
Development of HILIC-MS/MS method for acyl-CoAs covering short- to long-chain species in a single analytical run
Madhulika Singh, Ligia Akemi Kiyuna, Christoff Odendaal, Barbara M. Bakker, Amy C Harms, Thomas Hankemeier
ChemRxiv (2023). doi: 10.26434/chemrxiv-2023-h0w52
Personalised modelling of clinical heterogeneity between medium-chain acyl-CoA dehydrogenase patients
Christoff Odendaal, Emmalie A. Jager, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Nicolette C. A. Huijkman, Ligia A. Kiyuna, Albert Gerding, Justina C. Wolters, Rebecca Heiner-Fokkema, Karen van Eunen, Terry G. J. Derks & Barbara M. Bakker
BMC Biol 21(1) (2023). doi: 10.1186/s12915-023-01652-9
Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme
Yvan Rousset, Oliver Ebenhöh, Adélaïde Raguin
PLoS Comput Biol 19(5) (2023). doi: 10.1371/journal.pcbi.1010694
Kinetic data for modeling the dynamics of the enzymes involved in animal fatty acid synthesis
Chilperic Armel Foko Kuate, Oliver Ebenhöh, Barbara M. Bakker, Adélaïde Raguin
Biosci Rep 43(7) (2023). doi: 10.1042/bsr20222496
Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators
Hong Yang, Xiangyu Li, Han Jin, Hasan Turkez, Gurkan Ozturk, Hamdi Levent Doganay, Cheng Zhang, Jens Nielsen, Mathias Uhlén, Jan Borén, Adil Mardinoglu
Free Radic Biol Med 204:347-358 (2023). doi: 10.1016/j.freeradbiomed.2023.05.013
Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial
Burak Yulug, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Hong Yang, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacimuftuoglu, Serkan Yildirim, Muhammad Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Borén, Mathias Uhlén & Adil Mardinoglu
Transl Neurodegener 12(1):4 (2023). doi: 10.1186/s40035-023-00336-2
Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia
Martijn G. S. Rutten, Yu Lei, Joanne H. Hoogerland, Vincent W. Bloks, Hong Yang, Trijnie Bos, Kishore A. Krishnamurthy, Aycha Bleeker, Mirjam H. Koster, Rachel E. Thomas, Justina C. Wolters, Hilda van den Bos, Gilles Mithieux, Fabienne Rajas, Adil Mardinoglu, Diana C. J. Spierings, Alain de Bruin, Bart van de Sluis & Maaike H. Oosterveer
Cancer Metab 11(1):5 (2023). doi: 10.1186/s40170-023-00305-3
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII
Leaman R, Islamaj R, Adams V, Alliheedi MA, Almeida JR, Antunes R, Bevan R, Chang Y, Erdengasileng A, Hodgskiss M, Ida R, Kim H, Li K, Mercer RE, Mertová L, Mobasher G, Shin H , Sung M, Tsujimura T, Yeh W, Lu Z
Database (Oxford) (2023). doi: 10.1093/database/baad005
WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning
Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, and Michael Gertz
ACL Anthology (2023) doi: 10.18653/v1/2023.bionlp-1.40
2022
In vitro grafting of hepatic spheroids and organoids on a microfluidic vascular bed
Flavio Bonanini, Dorota Kurek, Sara Previdi, Arnaud Nicolas, Delilah Hendriks, Sander de Ruiter, Marine Meyer, Maria Clapés Cabrer, Roelof Dinkelberg, Silvia Bonilla García, Bart Kramer, Thomas Olivier, Huili Hu, Carmen López-Iglesias, Frederik Schavemaker, Erik Walinga, Devanjali Dutta, Karla Queiroz, Karel Domansky, Bob Ronden, Jos Joore, Henriette L. Lanz, Peter J. Peters, Sebastiaan J. Trietsch, Hans Clevers & Paul Vulto
Angiogenesis 25(4):455-470 (2022). doi: 10.1 007/s10456-022- 09842-9
Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
St. Elmo Wilken, Mathieu Besançon, Miroslav Kratochvíl, Chilperic Armel Foko Kuate, Christophe Trefois, Wei Gu, Oliver Ebenhöh
Metab Eng 74:72-82 (2022). doi: 10.1016/j.ymben.2022.09.002
Combining dictionary- and rule-based approximate entity linking with tuned BioBERT
Ghadeer Mobasher, Lukrécia Mertová, Sucheta Ghosh, Olga Krebs, Bettina Heinlein, Wolfgang Müller
bioRxiv (2022). doi: 10.1101/2021.11.09.467905
Multiomics Analysis Reveals the Impact of Microbiota onHost Metabolism in Hepatic Steatosis
Zeybel M., Altay O., Arif M., Li X., Altay O., Yang H., Shi M., Akyildiz M., Saglam B., Gonenli M.G., Yigit, B., Ulukan B., Ural D., Shoaie, S., Turkez H., Nielsen J., Zang, C., Uhlén M., Borén J., Mardinoglu A.
Adv Sci 9(11) (2022). doi: 10.1002/advs.202104373
2021
Finding new edges: systems approaches to MTOR signaling
Heberle A.M., Rehbein U., Rodríguez Peiris M., Thedieck K.
Biochem Soc Trans 49 (1): 41–54 (2021) . doi: 10.1042/BST20190730
A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease
Yang H., Arif M., Yuan M., Li X., Shong K., Türkez H., Nielsen J., Uhlén M., Borén J., Zhang C., Mardinoglu A.
iScience, 24(11):10322 (2021). doi: 10.1016/j.isci.2021.103222
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients
Zeybel M., Altay O., Arif M., Li X., Yang H., Fredolini C., Akyildiz M., Saglam B., Gonenli M.G., Ural D., Kim W., Schwenk J.M, Zhang C., Shoaie S., Nielsen J., Uhlén M., Borén J., Mardinoglu A.
Mol. Syst Biol. 17(10): e10459 (2021). doi: 10.15252/msb.202110459
Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet
Yang H., Mayneris-Perxachs J., Boqué N., Del Bas J.M., Arola L., Yuan M., Türkez H., Uhlén M., Borén J., Zhang C., Mardinoglu A., Caimari A.
Biomedicines 9(10): 1440 (2021). doi: 10.3390/biomedicines9101440
2020
Thermodynamic limits and optimality of microbial growth
Saadat N.P., Nies T., Rousset Y., Ebenhöh O.
Entropy, 22(3):277 (2020). doi:10.3390/e22030277
