gtu_logoBİYOMÜHENDİSLİK

Dr. Öğr. Üyesi Pınar PİR
Biyomühendislik

Pınar PİR
Telefon
(262) NA
E-Posta
pinarpir@gtu.edu.tr
Web sayfası
https://pirismlab.org/
Ofis
, Biyomuhendislik Binasi Ofis 109
Çalışma alanları
Sistem Biyolojisi, Matematiksel Modelleme, Bioinformatik, Metabolizma, Gen regulasyonu, Epigenetik
Detaylı özgeçmiş
ppir-CV-kasım24.pdf

Cesur, M. F., Çakır, T., & Pir, P. (2022). Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data. </span>Msystems, </span>7(3), e01347-21.</span></span>

Karakurt, H. U., & Pir, P. (2022). In silico analysis of metabolic effects of bipolar disorder on prefrontal cortex identified altered GABA, glutamate-glutamine cycle, energy metabolism and amino acid synthesis pathways. </span>Integrative Biology, </span>14(6), 127-136.</span></span>

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, </span>Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D231–D235, </span>https://doi.org/10.1093/nar/gkab1083</span>

Uzuner, D., Akkoç, Y., Peker, N., Pir, P., Gözüaçık, D., & Çakır, T. (2021). Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. </span>Scientific reports, </span>11(1), 1-10.</span></span>

Destefanis, E., Avşar, G., Groza, P., Romitelli, A., Torrini, S., Pir, P., ... & Dassi, E. (2021). A mark of disease: how mRNA modifications shape genetic and acquired pathologies. </span>RNA, </span>27(4), 367-389.</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 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.