Tunahan Cakir

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Kutlu O. UlgenProfessor of Chemical Engineering, Bogazici UniversityVerified email at boun.edu.tr
Saliha DurmuşPhiTech BioinformaticsVerified email at phitech.com.tr
Betul KirdarProfessor of Molecular Biology of Genetics,Department of Chemical Engineering, Bogazici UniversityVerified email at boun.edu.tr
Arzucan OzgurDepartment of Computer Engineering, Bogazici UniversityVerified email at boun.edu.tr
Jens NielsenProfessor in Systems Biology, Chalmers University of Technology, SwedenVerified email at chalmers.se
Fatih Erdogan SevilgenGebze Technical UniversityVerified email at gyte.edu.tr
Emrah ÖzcanVrije Universiteit AmsterdamVerified email at vu.nl
Kiran Raosaheb PatilMRC Toxicology Unit, University of CambridgeVerified email at cam.ac.uk
Mahmut AltinbasIstanbul Technical UniversityVerified email at itu.edu.tr
Mehmet Mete AltintasAssociate Professor of Medicine, Rush UniversityVerified email at rush.edu
Kazim Yalcin ArgaProfessor of Bioengineering @ Marmara UniversityVerified email at marmara.edu.tr
Reaz Uddinuniversity of karachiVerified email at iccs.edu
Johan WesterhuisUniversity of AmsterdamVerified email at uva.nl
age smildeprofessor of biosystems data analysisVerified email at uva.nl
Melik ÖKSÜZOndokuz Mayıs ÜniversitesiVerified email at omu.edu.tr
Bas TeusinkProfessor of Systems Biology, VU University AmsterdamVerified email at vu.nl
Ebru Toksoy OnerMarmara University Department of BioengineeringVerified email at marmara.edu.tr
Emrah NikerelYeditepe University, Department of Genetics and BioengineeringVerified email at yeditepe.edu.tr
Ata AkinAcıbadem UniversityVerified email at acibadem.edu.tr
Pinar PirDepartment of Bioengineering, Gebze Technical University, TurkeyVerified email at gtu.edu.tr

Tunahan Cakir

Department of Bioengineering, Gebze Technical University

Verified email at gtu.edu.tr - Homepage

computational systems biology neurodegenerative diseases metabolic networks


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Integration of metabolome data with metabolic networks reveals reporter reactions T Çakır, KR Patil, ZI Önsan, KÖ Ülgen, B Kirdar, J Nielsen Molecular systems biology 2, 50, 2006	166	2006
PHISTO: pathogen–host interaction search tool S Durmuş Tekir, T Çakır, E Ardıç, AS Sayılırbaş, G Konuk, M Konuk, ... Bioinformatics 29 (10), 1357-1358, 2013	125	2013
A review on computational systems biology of pathogen–host interactions S Durmuş, T Çakır, A Özgür, R Guthke Frontiers in Microbiology 6, 235, 2015	113	2015
Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia T Çakιr, S Alsan, H Saybaşιlι, A Akιn, KÖ Ülgen Theoretical Biology and Medical Modelling 4 (1), 48, 2007	108	2007
Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks T Çakır, B Kırdar, KÖ Ülgen Biotechnology and bioengineering 86 (3), 251-260, 2004	82	2004
Infection Strategies of Bacterial and Viral Pathogens through Pathogen–Human Protein–Protein Interactions SD Tekir, T Çakır, KÖ Ülgen Frontiers in Microbiology 3, 46, 2012	77	2012
Metabolic network discovery through reverse engineering of metabolome data T Çakır, MMWB Hendriks, JA Westerhuis, AK Smilde Metabolomics 5 (3), 318-329, 2009	67	2009
Systematic analysis of transcription-level effects of neurodegenerative diseases on human brain metabolism by a newly reconstructed brain-specific metabolic network M Sertbaş, K Ülgen, T Çakır FEBS open bio 4, 542-553, 2014	53	2014
Metabolic pathway analysis of enzyme-deficient human red blood cells T Çakır, CS Tacer, KÖ Ülgen Biosystems 78 (1-3), 49-67, 2004	51	2004
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae T Çakır, B Kırdar, Zİ Önsan, K Ülgen, J Nielsen BMC systems biology 1 (1), 18, 2007	45	2007
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation T Çakır, MJ Khatibipour Frontiers in Bioengineering and Biotechnology 2, 62, 2014	35	2014
Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production T Çakır, KY Arga, MM Altıntaş, KÖ Ülgen Process biochemistry 39 (12), 2097-2108, 2004	34	2004
Flux Balance Analysis of a Genome‐Scale Yeast Model Constrained by Exometabolomic Data Allows Metabolic System Identification of Genetically Different Strains T Çakır, Ç Efe, D Dikicioǧlu, A Hortaçsu, B Kırdar, SG Oliver Biotechnology progress 23 (2), 320-326, 2007	33	2007
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma E Ozcan, T Cakir Frontiers in Neuroscience 10, 156, 2016	26*	2016
Effect of iron and magnesium addition on population dynamics and high value product of microalgae grown in anaerobic liquid digestate H Ermis, U Guven-Gulhan, T Cakir, M Altinbas Scientific reports 10 (1), 1-12, 2020	23	2020
Modelling of calcium dynamics in brain energy metabolism and alzheimer's disease S Tiveci, A Akın, T Çakır, H Saybaşılı, K Ülgen Computational biology and chemistry 29 (2), 151-162, 2005	22	2005
Network-based metabolism-centered screening of potential drug targets in Klebsiella pneumoniae at genome scale MF Cesur, B Siraj, R Uddin, S Durmuş, T Çakır Frontiers in Cellular and Infection Microbiology 9, 447, 2020	19	2020
Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches S Durmuş Tekir, T Çakır, K Ö Ülgen Computational biology and chemistry 30 (5), 327-338, 2006	18	2006
A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris E Özcan, SS Selvi, E Nikerel, B Teusink, E Toksoy Öner, T Çakır Applied Microbiology and Biotechnology 103 (7), 3153-3165, 2019	14	2019
Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach T Çakır Scientific reports 5, 14563, 2015	13	2015

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