Dr. Öğr. Üyesi Pınar PİR

Pınar PİR
+90 (262) 3321
, Elektronik/Insaat/Biyomuhendislik Binasi 147
Areas of interest
Systems Biology, Mathematical Modelling, Bioinformatics, Metabolism, Gene Expression, Epigenetics
Detailed CV

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 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.,  Pir, P. (2019) “Next-Generation Genome-Scale Models Incorporating Multilevel ‘Omics Data: From Yeast to Human”, Yeast Systems Biology,; 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”, 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.

Hamza Umut Karakurt, MSc Thesis (2019), Modelling
and Comparative Analysis of Adipose-Derived Stem Cells, Brown and White Adipose
Tissue Cells

Batuhan Çakır, MSc Thesis (2020), Mathematical
Modelling of Molecular Trajectories in Stem Cell Transformation Processes Via Bioınformatic
Analysis of Single Cell Omics Data

Hamza Umut Karakurt, Yüksek Lisans Tezi (2019),
Isıya dayalı adiposit aktivasyonunun biyoinformatik analizi

Batuhan Çakır, Yüksek Lisans Tezi (2020), Kök
Hücre Başkalaşım Süreçlerindeki Moleküler Yörüngelerin Tek Hücre Omik Verisinin
Biyoinformatik Analiziyle Matematiksel Modellenmesi

  • 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
  • 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

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 116987 (Lead PI) - Reconstruction of 3D mathematical models of tumors and their microenvironment - at budget approval stage

ORCID: 0000-0002-0078-4904
Europe PMC open citation report http://europepmc.org/authors/0000-0002-0078-4904