Modelling of calcium dynamics in brain energy metabolism and Alzheimer's disease. - S. Tiveci; Ata Akin; Tunahan Çakir; H. Saybasili; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2005)

Integrative investigation of metabolic and transcriptomic data. - Pinar Pir; Betül Kirdar; Andrew Hayes; Z. Ilsen Önsan; Kutlu Ö. Ülgen; Stephen G. Oliver (BMC Bioinform., 2006)

Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches. - Saliha Durmus Tekir; Tunahan Çakir; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2006)

Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae. - Tunahan Çakir; Betül Kirdar; Z. Ilsen Önsan; Kutlu Ö. Ülgen; Jens Nielsen (BMC Syst. Biol., 2007)

Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network. - Saliha Durmus Tekir; Kazim Yalçin Arga; Kutlu Ö. Ülgen (J. Biomed. Informatics, 2009)

Drug target identification in sphingolipid metabolism by computational systems biology tools: Metabolic control analysis and metabolic pathway analysis. - Fatma Betül Kavun Özbayraktar; Kutlu Ö. Ülgen (J. Biomed. Informatics, 2010)

Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation. - Fatma Betül Kavun Özbayraktar; Kutlu Ö. Ülgen (Biosyst., 2011)

Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster. - Aysun Eren Toku; Saliha Durmus Tekir; Fatma Betül Kavun Özbayraktar; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2011)

PHISTO: pathogen-host interaction search tool. - Saliha Durmus Tekir; Tunahan Çakir; Emre Ardiç; Ali Semih Sayilirbas; Gökhan Konuk; Mithat Konuk; Hasret Sariyer; Azat Ugurlu; Ilknur Karadeniz; Arzucan Özgür; Fatih Erdogan Sevilgen; Kutlu Ö. Ülgen (Bioinform., 2013)

Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening. - Oya Gursoy Yilmaz; Elif Özkirimli Ölmez; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2014)

Identification of potential Tpx inhibitors against pathogen-host interactions. - Utku Deniz; Kutlu Ö. Ülgen; Elif Özkirimli Ölmez (Comput. Biol. Chem., 2015)

Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site. - Ozge Bayraktar; Elif Özkirimli Ölmez; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2017)

Preliminary Studies on Flow Assisted Propagation of Fluorescent Microbeads in Microfluidic Channels for Molecular Communication Systems. - Merve Gorkem Durmaz; Abdurrahman Dilmac; Berk Camli; Elif Gencturk; Zeliha Cansu Canbek Ozdil; Ali Emre Pusane; Arda Deniz Yalcinkaya; Kutlu Ö. Ülgen; Tuna Tugcu (BICT, 2020)

Exploiting pretrained biochemical language models for targeted drug design. - Gökçe Uludogan; Elif Özkirimli 001; Kutlu Ö. Ülgen; Nilgün Karali; Arzucan Özgür (Bioinform., 2022)

Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets. - Enes Fahri Tezcan; Yigit Demirtas; Zeynep Petek Cakar; Kutlu Ö. Ülgen (Frontiers Bioinform., 2023)