Publications
2023
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
WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning
Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, and Michael Gertz
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
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
2021
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
