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.

Kişinin DersWeb siteleri

• BSB 501 Biyolojide Programlama
• BSB 521 Sistem Biyolojisi Yaklaşımıyla Hücre Kaderi ve Epigenetik
• BSB 525 Biyoinformatikte Yapay Zeka Teknikleri
• BSB 615 Biyoistatistik
• BSB 616 Tıbbi Araştırmalar için İleri İstatistik
• BSB 625 Sistem Biyolojisinde İleri Veri Analizi ve Modelleme
• BSB 680 Sistem Biyolojisinde Güncel Konular
• BYM 215 Biyomühendisler için Python
• BYM 331 Biyoistatistik
• BYM 432 İleri Biyoistatistik
• BYM 434 Biyomühendislikte Veri Madenciliği
• MBG 430 Biyoistatistiğe Giriş
• MBG 524 Biyolojide Bilgisayar Programlama

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

• Doktora: 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
  
• Yüksek lisans: Bogazici University, Department of Chemical Engineering: M.Sc., 1998-2001
  Thesis: Modelling and Simulation of a Wet Scrubber
  
• Lisans: Bogazici University, Department of Chemical Engineering: M.Sc., 1993-1998

Projeler:

ERA-NET TRANSCAN-3 122N905 (Partner) - Metastatik Lezyonların Tümör Mikroçevresindeki Immünosupresif Parakrin Sitokinlerin Terapötik Potansiyelinin Değerlendirilmesi - 01/01/2023 - 01/01/2026

GTÜ - BAP (Araştırmacı) - Transkriptom verilerinden hastalık alt tiplerine özel ilaç hedeflerinin ve yenilikçi ilaç adaylarının tahmini: Alzheimer hastalığı ve karaciğer kanseri uygulamaları - 01/10/2022 - 10/10/2023

Tubitak Bideb 2232 116C062 (Yürütücü) - Eubacterium limosum soylarının metabolik ağlarının ve karbon asimilasyonu yol izlerinin oluşturulması yoluyla biyoyakıt üretimine yeni nesil çözümlerin geliştirilmesi: Sistem biyolojisi yaklaşımı 01/05/2016-01/05/2018

Tubitak Ardeb 1001 116S388 (Yürütücü) - Uyarılmış Kök Hücrelerin Oluşum ve Başkalaşım Süreçlerinin Sistem Biyolojisi ve Biyomühendislik Yaklaşımlarıyla Modellenerek Geliştirilmesi 01/05/2017-01/05/2020

Tubitak Ardeb 1003 216S489 (Arastirmaci) - Küçük Hücreli Dışı Akciğer Kanseri Modelleri Oluşturulması Ve Etiyopatogenezinin Omik Yöntemlerle Araştırılması - 15/12/2017 - 15/06/2021

TÜSEB 2019-TA-01(3936) (Yürütücü) - Tümör örneklerindeki nadir hücre türlerinin belirlenmesi ve prognostik özelliklerinin incelenmesi - 15/05/2020 - 15/05/2022

Tubitak Ardeb 1001 116987 (Yürütücü) - Tümör ve mikroçevrelerinin üç boyutlu matematiksel modellerinin geliştirilmesi - Bütçesi onay aşamasındadır

Projects:

GTÜ - BAP (Araştırmacı) - Transkriptom verilerinden hastalık alt tiplerine özel ilaç hedeflerinin ve yenilikçi ilaç adaylarının tahmini: Alzheimer hastalığı ve karaciğer kanseri uygulamaları - 01/10/2022 - 10/10/2023

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