Doç. Dr. Tunahan ÇAKIR
Biyomühendislik

Tunahan ÇAKIR
Telefon
(262) 605 33 20
E-Posta
tcakirgtu.edu.tr
Web sayfası
http://www.systemsbiology.info.tr
Ofis
, 146
Çalışma alanları
Biyoinformatik, Hesaplamalı Sistem Biyolojisi, Veri Analizi Teknikleri, Patojen-Konak etkileşimleri, Sistem Tıbbı
Detaylı özgeçmiş
DetaylıCV-2019.pdf

  1. Constraint-based modeling of metabolic interactions in and between astrocytes and neurons, Tunahan Çakır, Computational Glioscience, Springer Series in Computational Neuroscience, Editors: M. De Pitta, H. Berry, 393-420, Springer International Publishing, 2019.
  2. A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris, Emrah Özcan, S.Selvin Selvi, Emrah Nikerel, Bas Teusink, Ebru Toksoy Öner, Tunahan Çakır, Applied Microbiology and Biotechnology, 103:3153-3165, 2019.
  3. Next-generation genome-scale models incorporating multilevel ‘omics data: From yeast to human, Tunahan Çakır, Emel Kökrek, Gülben Avşar, Ecehan Abdik, Pınar PirYeast Systems Biology: Methods and Protocols, Editors: S.G. Oliver, J.I. Castrillo, 347-363, Springer International Publishing, 2019.
  4. Genome-scale brain metabolic networks as scaffolds for the systems biology of neurodegenerative diseases: mapping metabolic alterations, Emrah Özcan, Tunahan Çakır, Systems Neuroscience, Advances in Neurobiology: 21, Editors: A.C. Yu, L. Li, 195-217, Springer International Publishing, 2018.
  5. JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data, M. Jafar Khatibipour, Furkan Kurtoğlu, Tunahan Çakır, PeerJ, 6:e6034, 2018.
  6. Computational system biology for metabolism in infection, Muberra Fatma Cesur, Unzile Guven Gulhan, Ecehan Abdik, Saliha Durmuş Tunahan Çakır, Metabolic Interaction in Infection, Experientia Supplementum 109, Editors: R. Silvestre, E. Torrado, 235-282, Springer International Publishing, 2018.
  7. Reconstructed metabolic network models predict flux-level metabolic reprogramming of glioblastoma, Emrah Özcan, Tunahan Çakır, Frontiers in Neuroscience, 10:156, 2016.
  8. Data-based reconstruction of gene regulatory networks of fungal pathogens, Reinhard Guthke, Silvia Gerber, Theresia Conrad, Sebastian Vlaic, Saliha Durmuş, Tunahan Çakır, Erdoğan Sevilgen, Ekaterina Shelest, Joerg Linde ,Frontiers in Microbiology, 7:570, 2016.
  9. Editorial: Computational Systems Biology of Pathogen-Host Interactions, Saliha Durmuş, Tunahan Çakır, Reinhard Guthke, Frontiers in Microbiology, 5, 14563, 2016.
  10. Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach, Tunahan Çakır ,Scientific Reports, 5, 14563, 2015.
  11. A Review on Computational Systems Biology of Pathogen-Host Interactions, Saliha Durmuş, Tunahan Çakır, Arzucan Özgür, Reinhard Guthke, Frontiers in Microbiology , 6, 235, 2015. Atıf: 34
  12. Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation, Tunahan Çakır, M. Jafar Khatibipour, Frontiers in Bioengineering and Biotechnology , 2, 62, 2014.
  13. Biyolojik Ağların Modellenmesi, Tunahan Çakır, Emrah Nikerel Biyomedikal Mühendisliğinin Temelleri , Nobel Kitap, 2014.
  14. The role of flexibility and optimality in the prediction of Intracellular Fluxes of microbial cell metabolism, Fatih Tarlak, Hasan Sadıkoğlu, Tunahan Çakır, Molecular Biosystems , 10, 2459-2465, 2014.
  15. Systematic Analysis of Transcription-Level Effects of Neurodegenerative Diseases on Human Brain Metabolism by a Newly Reconstructed Brain-Specific Metabolic Network, Mustafa Sertbaş, Kutlu Ö. Ülgen, Tunahan Çakır, FEBS Open Bio, 4, 542-553, 2014. Atıf: 18
  16. Sparsity as Cellular Objective to Infer Directed Metabolic Networks from Steady-State Metabolome Data: A Theoretical Analysis, Melik Öksüz, Hasan Sadıkoğlu, Tunahan Çakır, PLoS ONE, 8(12), e84505, 2013.
  17. PHISTO: pathogen–host interaction search tool, Saliha Durmuş Tekir, Tunahan Çakır, Emre Ardıç, Ali Semih Sayılırbaş, Gökhan Konuk, Mithat Konuk, Hasret Sarıyer, Azat Uğurlu, İlknur Karadeniz, Arzucan Özgür, Fatih Erdoğan Sevilgen, Kutlu Ülgen, Bioinformatics, 29, 1357-1358, 2013. Atıf: 44
  18. Infection Strategies of Bacterial and Viral Pathogens through Pathogen–Human Protein–Protein Interactions, Saliha Durmuş Tekir, Tunahan Çakır, Kutlu Ülgen, Frontiers in Microbiology, 3, 46, 2012. Atıf: 41
  19. Metabolic network discovery through reverse engineering of metabolome data, Tunahan Çakır, Margriet Hendriks, Johan Westerhuis, Age Smilde, Metabolomics, 5, 318-329, 2009. Atıf: 34
  20. Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae, Tunahan Çakır, Z.İlsen Önsan, Betül Kırdar, Kutlu Ülgen, Jens Nielsen, BMC Systems Biology, 1:18, 2007. Atıf:31
  21. Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains, Tunahan Çakır, Çağrı Efe, Duygu Dikicioğlu, Amable Hortaçsu, Betül Kırdar, Stephen G. Oliver, Biotechnology Progress, 23, 320-326, 2007. Atıf: 19
  22. Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia, Tunahan Çakır, Selma Alsan, Hale Saybaşılı, Ata Akın, Kutlu Ülgen, Theoretical Biology and Medical Modelling, 4:48, 2007. Atıf: 39
  23. Integration of metabolome data with metabolic networks reveals reporter reactions, Tunahan Çakır, Kiran R. Patil, Z. İlsen Önsan, Kutlu Ülgen, Betül Kırdar, Jens Nielsen, Molecular Systems Biology, 2:50, 2006, Atıf: 102
  24. Analysis of enzymopathies in the human red blood cells by constraint based stoichiometric modeling approaches, Saliha Durmuş, Tunahan Çakır, Kutlu Ülgen, Computational Biology and Chemistry, 30, 327-338, 2006.
  25. Modelling of calcium dynamics in brain energy metabolism and Alzheimer's disease, Senem Tiveci, Tunahan Çakır, Ata Akın, Hale Saybaşılı, Kutlu Ülgen, Computational Biology and Chemistry, 29, 151-162, 2005.
  26. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks, Tunahan Çakır, Betül Kırdar, Kutlu Ülgen, Biotechnology and Bioengineering, 86, 251-260, 2004. Atıf: 46
  27. Metabolic pathway analysis of enzyme-deficient human red blood cells, Tunahan Çakır, Serhan Tacer, Kutlu Ülgen, Biosystems, 78, 49-67, 2004. Atıf: 27
  28. Flux analysis of the recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimum ethanol production, Tunahan Çakır, Kazım Yalçın Arga, M. Mete Altıntaş, Kutlu Ülgen, Process Biochemistry, 39, 2097-2108, 2004. Atıf:15
  29. Transfer function approach in structured modeling of recombinant yeast utilizing starch, K. Yalçın Arga, Tunahan Çakır, Pınar Pir, Nevra Özer, M. Mete Altıntaş, Kutlu Ülgen, Process Biochemistry, 39, 1237-1248, 2004.

YÜRÜTÜLMEKTE OLAN DOKTORA TEZLERİ

  1. Hücre metabolizmasının kinetik modellemesi: yukarıdan-aşağı ve aşağıdan-yukarı sistem biyolojisi yaklaşımlarının bütünleştirilmesi için bir platform. M. Jafar Khatibipour (2014- )

TAMAMLANMIŞ DOKTORA TEZLERİ

  1. Metabolic Network-based Analysis of Cheese Starter Cultures as a Microbial Community. Emrah Özcan (2019) Co-supervisor: Prof. Dr. Ebru Toksoy Öner

TAMAMLANMIŞ YÜKSEK LİSANS TEZLERİ

  1. Integrative Analysis of transcriptome data and genome-scale metabolic networks to identify drug targets and drug candidates for Parkinson’s Disease. Ali Kaynar (2019)
  2. Integrative analysis of bladder cancer transcriptome data and genome-scale metabolic networks to understand dormancy mechanism. Merve Kutay (2019)
  3. Network-based analysis of cognitive impairment and memory deficits from transcriptome data. Elif Emanetci (2019)
  4. Molecular Effects of Plant-Based Drugs on Breast Cancer by Mapping Transcriptome Data on Protein-Protein Interactions. Regan Odongo (2019) Co-supervisor: Asuman Demiroglu-Zergeroglu
  5. Reconstruction of Brain-Specific Genome-scale Metabolic Network Model for Mus musculus for the Investigation of Neurodegenerative Diseases. Ecehan Abdik (2019)
  6. Reconstruction and Constraint-based Analysis of the Genome-scale Metabolic Network for Klebsiella pneumoniae to Identify New Putative Drug Targets. Müberra Fatma Cesur (2018) Co-supervisor: Assist. Prof. Saliha Durmuş
  7. Systems biology approach to investigate the effect of nitrogen and phosphate metabolism on actinorhodin production by Streptomyces coelicolor using genome scale metabolic models. Hamza Umut Karakurt (2016) Co-supervisor: Prof. Sedef Tunca Gedik
  8. Investigation of the Effect Neurological Diseases on Brain Metabolism by using Computational Systems Biology Techniques. Mustafa Sertbaş (2013) Co-supervisor: Prof. Kutlu Ülgen
  9. Investigation of the Biological Objective of the Cell by using Network Inference from Metabolome Data. Melik Öksüz (2012) Co-supervisor: Prof. Hasan Sadıkoğlu
  10. Investigation of the Biological Objective of the Cell by using Metabolic Flux Analysis Techniques. Fatih Tarlak (2012) Co-supervisor: Prof. Hasan Sadıkoğlu
  • Doktora: Boğaziçi Üniversitesi, Kimya Mühendisliği Bölümü, 2006
  • Yüksek lisans: Boğaziçi Üniversitesi, Kimya Mühendisliği Bölümü, 2002
  • Lisans: Boğaziçi Üniversitesi, Kimya Mühendisliği Bölümü, 2001