Assist. Prof.
Pınar PİR
Bioengineering
- Phone
- +90 (262) NA
- pinarpir@gtu.edu.tr
- Web page
- https://pirismlab.org/
- Office
- , Biyomuhendislik Binasi Ofis 109
- Areas of interest
- Systems Biology, Mathematical Modelling, Bioinformatics, Metabolism, Gene Expression, Epigenetics
- Detailed CV
- ppir-CV-kasım24.pdf
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elżbieta Purta, Małgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avşar, Antonia Romitelli, Pınar Pir, Erik Dassi, Silvestro G Conticello, Francesca Aguilo, Janusz M Bujnicki, MODOMICS: a database of RNA modification pathways. 2021 update,&#160;</span>Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D231–D235,&#160;</span>https://doi.org/10.1093/nar/gkab1083</span>
Ak, E., and Pir, P. (2020). Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells. BioRxiv ;https://doi.org/10.1101/2020.06.20.163006
Karakurt, H. U., and Pir, P. (2020). Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks.Turkish Journal of Biology,;44(3), 168.
Çakır, B, M. Prete, N. Huang, S. van&amp;amp;amp;amp;amp;amp;amp;amp;#160;Dongen, P. Pir, V.Y. Kiselev, (2020) Comparison of visualization tools for single-cell RNAseq data;NAR Genomics and Bioinformatics, Vol. 2, Issue 3, qaa052 ;https://doi.org/10.1093/nargab/lqaa052
Çakır, T., Kökrek, E., Avşar, G., Abdik, E.,&amp;amp;amp;amp;amp;amp;amp;#160; Pir, P. (2019) “Next-Generation Genome-Scale Models Incorporating Multilevel ‘Omics Data: From Yeast to Human”,&amp;amp;amp;amp;amp;amp;amp;#160;Yeast Systems Biology,;&amp;#160;pp. 347-363). Humana, New York, NY.
Jantsch, M.F., Quattrone, A., O'Connell, M., Helm M., Frye M., Pir, P., Macias-Gonzales, M., Ohman M., et al. ,2018, "Positioning Europe for the EPITRANSCRIPTOMICS challenge.";RNA biology 1-3.
Malek, M., Kielkowska, A., Chessa, T.,Anderson, K.E., Barneda, D., Pir, P., Nakanishi, H., Eguchi, S., Koizumi, A., Sasaki, J. and Juvin, V., Kiselev, V.Y., Niewczas, I, Gray, A., Valayer, A., Spensberger, D., Imbert, M., Felisbino, S., Habuchi, T., Beinke, S., Cosulich, S., Le Novère, L., Sasaki, T., Clark, J, Hawkins, P.T., Stephens, L.R., 2017. “PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K”,&amp;amp;amp;amp;amp;amp;amp;amp;amp;#160;Molecular Cell, 68(3), 566-580.
Waltemath, D. J.R. Karr, F.T. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C.J. Myers, P. Pir, B. Alaybeyoglu, N.K. Aranganathan, K. Baghalian, A.T. Bittig, P.E. Pinto Burke, M. Cantarelli, Y.H. Chew, R.S. Costa, J. Cursons, T. Czauderna, A.P. Goldberg, H.F. Gomez, J. Hahn, T. Hameri, D.F.H. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knupfer, M. Konig, D. Lee, A. Lloret-Villas, N. Mandrik, J.K. Medley, B. Moreau, H. Naderi-Meshkin, S.K. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N.J. Stanford, J-H. Song, T. Theile, M. Tokic, N. Tomar, V. Tour´e, J. Uhlendorf, T.M. Varusai, L.H. Watanabe, F. Wendland, M. Wolfien, J.T. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, and F. Schreibery, 2016, "Toward community standards and software for whole-cell modeling." IEEE Transactions on Biomedical Engineering 63.10: 2007-2014.
Pir, P. and N. Le Novère, “Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine,” in Systems Medicine: Methods and Protocols, 331-350, Springer
Kell, D.B., N. Swanston, P. Pir, S.G. Oliver, 2015, “Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis”, Trends in Biotechnology, 33, 237-246.
Alcasabas, A. A. , P. I. Darley , P. Pir, 2014 , “Novel Yeast Strains”, US patent WO2014102201 A1
Dikicioğlu D., S. Öç, B. M. Rash, W. B. Dunn, P. Pir, D. B. Kell, B. Kırdar, S. G. Oliver, 2014, “Yeast cells with impaired drug resistance accumulate glycerol and glucose”, Molecular BioSystems, 10, 93-102.
Castrillo, J. I., P. Pir, S. G. Oliver, 2013, “Chapter 18 - Yeast Systems Biology: Towards a Systems Understanding of Regulation of Eukaryotic Networks in Complex Diseases and Biotechnology“, in Handbook of Systems Biology: Concepts and Insights, 343-365, Academic Press.
Alcasabas A. A. , M. de Clare , P. Pir, S. G. Oliver, 2013, “Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids”, BMC Genomics, 14, 744.
Smallbone K., H. L. Messiha, K. M. Carroll, C. L. Winder, N. Malys, W. B. Dunn, E. Murabito, N. Swainston, J. O. Dada, F. Khan, P. Pir, E. Simeonidis, I. Spasić, J. Wishart, D. Weichart, N. W. Hayes, D. Jameson, D. S. Broomhead, S. G. Oliver, S. J. Gaskell, J. E. G. McCarthy, N. W. Paton, H. V. Westerhoff, D. B. Kell, P. Mendes, 2013, “A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes“, FEBS Letters, 587, 17, 2832-2841.
Dikicioğlu D., P. Pir, S. G. Oliver, 2013, “Predicting complex phenotype–genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory”, Biotechnology Journal, 8, 9, 1017-1034.
Bilsland E., A. Sparkes, K. Williams, H. J. Moss, M. de Clare, P. Pir, J. Rowland, W. Aubrey, R. Pateman, M. Young, M. Carrington, R. D. King, S.G. Oliver, 2013, “Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds”, Open Biology, 3,2.
Mülleder M., F. Capuano, P. Pir, S. Christen, U. Sauer, S. G. Oliver, M. Ralser, 2012, “A prototrophic deletion mutant collection for yeast metabolomics and systems biology”, Nature Biotechnology, 30, 12, 1176-1178.
Pir P., A. Gutteridge, J. Wu, B. Rash, D.B. Kell, N. Zhang, S.G. Oliver, 2012, “The genetic control of growth rate: A systems biology study in yeast”, BMC Systems Biology, 6,4
Carroll, K. M. , D. M. Simpson, C. E. Eyers, C. G. Knight, P. Brownridge, W. Dunn, C. L. Winder, K. Lanthaler, P. Pir, N. Malys, D. B. Kell, S. G. Oliver, S. J. Gaskell, R. J. Beynon, 2011, “Absolute quantification of a metabolic pathway in yeast: deployment of a complete QconCAT approach”, Molecular and Cellular Proteomics, 10,12.
Lanthaler, K., E. Bilsland, P. D. Dobson, H. J. Moss, P. Pir, D. B. Kell, S. G. Oliver, 2011, “Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast”, BMC Biology, 9, 70.
Bilsland E., P. Pir, A. Gutteridge, A. Johns , R. D. King, S. G. Oliver, 2011, “Functional Expression of Parasite Drug Targets and Their Human Orthologs in Yeast.”, PLoS Neglected Tropical Diseases, 5, 10, e1320.
Dikicioğlu, D., E. Karabekmez, B. Rash, P. Pir, B. Kirdar, S. G. Oliver, 2011, “How yeast re-programmes its transcriptional profile in response to different nutrient impulses”, BMC Systems Biology, 5, 148.
M. de Clare, P. Pir, S. G. Oliver, 2011, “Haploinsufficiency and the sex chromosomes from yeasts to humans”, BMC Biology, 9, 15.
Dobson, P., K. Smallbone, K., D. Jameson, E. Simenodis, K. Lanthaler, P. Pir, C. Lu, N. Swainston, W.B. Dunn, P. Fisher, D. Hull, M. Brown, O. Oshota, N. Stanford, D.B. Kell, R. King, S.G. Oliver, R. Stevens, P. Mendes, 2010, “Further developments towards a genome-scale metabolic model of yeast”, BMC Systems Biology, 4, 1, 145-150
Gutteridge*, A., P. Pir*, J.I. Castrillo, P.D. Charles, K. Lilley, S.G. Oliver, 2010, “Nutrient control of eukaryote cell growth: A systems biology study in yeast”, BMC Biology, 8, 68. (* equal contribution authors)
King R., J. Rowland, W. Aubrey, M. Liakata, M. Markham, L.N. Soldatova, K.E. Whelan, A. Clare, M. Young, A. Sparkes, S.G. Oliver, P. Pir, 2009, "The Robot Scientist Adam," Computer, 42, 8, 46-54.
King, R.D., J. Jowland, S.G. Oliver, M. Young, W. Aubrey, E. Byrne, M. Liakata, M. Markham, P. Pir, L.N. Soldatova, A. Sparkes, K.E. Whelan, A. Clare, 2009, “The Automation of Science”, Science, 324, 5923, 85-89.
Dikicioğlu, D., P. Pir, Z. I. Önsan, B. Kırdar, K. Ö. Ülgen, A. Hayes, S. G. Oliver, 2008, “Integration of metabolic modeling and phenotypic data in the evaluation and improvement of ethanol production using respiratory deficient mutants of Saccharomyces cerevisiae”, Applied and Environmental Microbiology, 74, 18, 5809-5816.
Pir, P., B. Kırdar, A. Hayes, Z. I. Önsan, K. Ö. Ülgen, S. G. Oliver, 2008, “Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae”, Yeast, 25, 9, 661-672.
Pir, P., B. Kırdar, Z. I. Önsan, K. Ö. Ülgen, A. Hayes, S. G. Oliver, 2006, “Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches”, Yeast, 23, 553-571
Pir, P., B. Kırdar, Z. I. Önsan, K. Ö. Ülgen, A. Hayes, S. G. Oliver, 2006, ”Integrative investigation of metabolic and transcriptomic data”, BMC Bioinformatics, 7, 203
Arga, K.Y.,T. Çakır, P. Pir, N. Özer, M. M. Altıntaş and K.Ö. Ülgen, 2004, “Transfer function approach in structured modeling of recombinant yeast utilizing starch”, Process Biochemistry, 39,10,1237-1248.
Pir, P., and M. Arıkol, 2002, “Modelling and simulation of a wet scrubber”, Appropriate Environmental and Solid Waste Management and Technologies for Developing Countries, Proceedings of ISWA 2002, 2521-2528.
- BSB 501 BioComputing
- BSB 521 Systems Biology of Cell Fate and Epigenetics
- BSB 525 Artificial Intelligence Techniques for Bioinformatics
- BSB 615 Biostatistics
- BSB 616 Advanced Statistics for Medical Research
- BSB 625 Advanced Data Analysis and Modelling in Systems Biology
- BSB 680 Current Topics in Systems Biology
- BENG 215 Python for Bioengineers
- BENG 331 Biostatistics
- BENG 432 Advanced Biostatistics
- BENG 434 Data Mining in Bioengineering
- MBG 430 Introduction to Biostatistics
- MBG 524 Computer Programming in Biology
ENES AK 2022, MSc
Identification of TF-mediated dynamics of signalling pathways in stem cell reprogramming and differentiation using NGS data
Kök hücrelerin farklılaşmasında ve geri programlanmasında sinyal yollarının TF-aracılı dinamiklerinin NGS verileri kullanılarak tanımlanması
TUĞBERK TALAK 2021, MSc
Temporospatial metabolic modelling of Pseudomonas aeruginosa and Staphylococcus aureus on a chronic wound
Kronik bir yarada Pseudomonas aeruginosa ve Staphylococcus aureus'un zaman-mekansal metabolik modellenmesi
BATUHAN ÇAKIR 2021, MSc
Mathematical modelling of molecular trajectories in stem cell transformation processes via bioinformatic analysis of single cell omics data
Kök hücre başkalaşim süreçlerindeki moleküler yörüngelerin tek hücre omik verisinin biyoinformatik analiziyle matematiksel modellenmesi
SİMGE ŞENGÜL BABAL 2021, MSc
Quantitative kinetic modelling of signaling pathways regulating pluripotency
Pluripotensiyi regüle eden sinyal yolaklarının kantitatif kinetik modellenmesi
CEMAL YILDIZ 2020, MSc
Identification and investigation of cell types and cell-to-cell communication in non-small cell lung cancer
Küçük hücre dışı akciğer kanserinde hücre tiplerinin ve hücre-hücre etkileşimlerinin belirlenmesi ve araştırılması
HAMZA UMUT KARAKURT 2018, MSc
Bioinformatic analysis of temperature-based activation of adipocytes
Sıcaklığa bağlı adipoz aktivasyonunun biyoinformatik analizi
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Third Cycle (Doctoral): Bogazici University, Department of Chemical Engineering : Ph.D., 2001- 2005
Thesis: Integrated Analysis of Metabolome Profiles and Gene Expression in Respiratory Deficient Deletion Mutants of Saccharomyces cerevisiae
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Second Cycle (Master's): Bogazici University, Department of Chemical Engineering: M.Sc., 1998-2001
Thesis: Modelling and Simulation of a Wet Scrubber
- First Cycle (Undergraduate): Bogazici University, Department of Chemical Engineering: M.Sc., 1993-1998
Projects:
ERA-NET TRANSCAN-3 122N905 (Partner) - Evaluating the therapeutic potential of immunosuppressive paracrine cytokines in the tumor microenvironment of metastatic lesions - 01/01/2023 - 01/01/2026
Tubitak Bideb 2232 116C062 (Lead PI) - Metabolic modelling of Eubacterium limosum strains 01/05/2016-01/05/2018
Tubitak Ardeb 1001 116S388 (Lead PI) - Mathematical Modelling and Improvement of Reprogramming and Differentiation Processes of Induced Pluripotent Stem Cells 01/05/2017-01/05/2020
Tubitak Ardeb 1003 216S489 (Researcher) - Creation of dormancy models of non-small cell lung carcinoma and investigation of its etiopathogenesis using omics methods - 15/12/2017 - 15/06/2021
TÜSEB 2019-TA-01(3936) (Lead PI) - Identification of rare cell types in tumor samples and investigation of their prognostic properties - 15/05/2020 - 15/05/2022
Tubitak Ardeb 1001 120S987 (Lead PI) - Reconstruction of 3D mathematical models of tumors and their microenvironment - 1/3/2021 - 1/3/2024
ORCID: 0000-0002-0078-4904
Europe PMC open citation report http://europepmc.org/authors/0000-0002-0078-4904